Works (86)
Updated: June 4th, 2024 05:01
2024 article
Protein-adaptive differential scanning fluorimetry using conformationally responsive dyes
Wu, T., Yu, J. C., Suresh, A., Gale-Day, Z. J., Alteen, M. G., Woo, A. S., … Gestwicki, J. E. (2024, May 14). NATURE BIOTECHNOLOGY, Vol. 5.
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, NC State University Libraries
Added: June 3, 2024
2021 article
A critical overview of computational approaches employed for COVID-19 drug discovery
Muratov, E. N., Amaro, R., Andrade, C. H., Brown, N., Ekins, S., Fourches, D., … Tropsha, A. (2021, July 2). CHEMICAL SOCIETY REVIEWS.
MeSH headings : Antiviral Agents / therapeutic use; COVID-19 / virology; Clinical Trials as Topic; Computer Simulation; Drug Design; Drug Discovery / methods; Drug Repositioning; Humans; Pandemics; SARS-CoV-2 / drug effects; COVID-19 Drug Treatment
TL;DR:
It is proposed that truly impactful computational tools must deliver actionable, experimentally testable hypotheses enabling the discovery of novel drugs and drug combinations, and that open science and rapid sharing of research results are critical to accelerate the development of novel, much needed therapeutics for COVID-19.
(via Semantic Scholar)
open access via doi.org (publisher)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Source: Web Of Science
Added: July 26, 2021
2021 journal article
CATMoS: Collaborative Acute Toxicity Modeling Suite
ENVIRONMENTAL HEALTH PERSPECTIVES, 129(4).
MeSH headings : Animals; Computer Simulation; Government Agencies; Rats; Toxicity Tests, Acute; United States; United States Environmental Protection Agency
TL;DR:
In silico models built using existing data facilitate rapid acute toxicity predictions without using animals, and CATMoS is being evaluated by regulatory agencies for its utility and applicability as a potential replacement for in vivo rat acute oral toxicity studies.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Source: Web Of Science
Added: June 28, 2021
2021 journal article
SMILES Pair Encoding: A Data-Driven Substructure Tokenization Algorithm for Deep Learning
JOURNAL OF CHEMICAL INFORMATION AND MODELING, 61(4), 1560–1569.
MeSH headings : Algorithms; Cheminformatics; Deep Learning; Humans; Quantitative Structure-Activity Relationship
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
4. Quality Education
(OpenAlex)
Source: Web Of Science
Added: May 24, 2021
2021 journal article
The VKORC1 ER-luminal loop mutation (Leu76Pro) leads to a significant resistance to warfarin in black rats (Rattus rattus)
PESTICIDE BIOCHEMISTRY AND PHYSIOLOGY, 173.
author keywords: Vitamin K epoxide reductase; Warfarin; Rodenticide-resistance; Molecular docking; Molecular dynamics simulations
MeSH headings : Animals; Drug Resistance / genetics; Mutation; Rats; Rodenticides / toxicity; Vitamin K Epoxide Reductases / genetics; Warfarin / pharmacology
TL;DR:
It is concluded that a single mutation of VKOR at position 76 leads to a significant resistance to warfarin by modifying the types and numbers of intermolecular interactions between the two.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Source: Web Of Science
Added: April 26, 2021
2020 journal article
Benchmarking 2D/3D/MD-QSAR Models for Imatinib Derivatives: How Far Can We Predict?
JOURNAL OF CHEMICAL INFORMATION AND MODELING, 60(7), 3342–3360.
MeSH headings : Benchmarking; Imatinib Mesylate / pharmacology; Molecular Docking Simulation; Quantitative Structure-Activity Relationship; Reproducibility of Results
TL;DR:
This work employed molecular docking and molecular dynamics on a large series of Imatinib derivatives and developed an ensemble of QSAR models relying on deep neural nets (DNN) and hybrid sets of 2D/3D/MD descriptors in order to predict the binding affinity and inhibition potencies of those compounds.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science; OpenAlex)
Sources: Web Of Science, NC State University Libraries
Added: August 24, 2020
2020 journal article
Cheminformatics Analysis of Fluoroquinolones and Their Inhibition Potency Against Four Pathogens
MOLECULAR INFORMATICS, 40(5).
MeSH headings : Anti-Bacterial Agents / chemistry; Anti-Bacterial Agents / pharmacology; Bacteria / drug effects; Cheminformatics; Drug Discovery; Escherichia coli / drug effects; Fluoroquinolones / chemistry; Fluoroquinolones / pharmacology; Microbial Sensitivity Tests; Pseudomonas aeruginosa / drug effects; Quantitative Structure-Activity Relationship; Staphylococcus aureus / drug effects; Streptococcus pneumoniae / drug effects
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science; OpenAlex)
Source: Web Of Science
Added: December 21, 2020
2020 journal article
CoMPARA: Collaborative Modeling Project for Androgen Receptor Activity
ENVIRONMENTAL HEALTH PERSPECTIVES, 128(2).
MeSH headings : Androgens; Computer Simulation; Databases, Factual; Endocrine Disruptors; High-Throughput Screening Assays; Humans; Receptors, Androgen; United States; United States Environmental Protection Agency
TL;DR:
The Collaborative Modeling Project for Androgen Receptor Activity (CoMPARA) efforts are described, which follows the steps of the Collaborative Estrogen Recept Activity Prediction Project (CERAPP).
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Source: Web Of Science
Added: March 30, 2020
2020 journal article
Hierarchical Quantitative Structure-Activity Relationship Modeling Approach for Integrating Binary, Multiclass, and Regression Models of Acute Oral Systemic Toxicity
CHEMICAL RESEARCH IN TOXICOLOGY, 33(2), 353–366.
MeSH headings : Administration, Oral; Algorithms; Animals; Models, Molecular; Molecular Structure; Organic Chemicals / administration & dosage; Organic Chemicals / toxicity; Quantitative Structure-Activity Relationship; Rats; Regression Analysis
TL;DR:
A novel, dual-layer hierarchical modeling method to fully integrate regression and classification QSAR models for assessing rat acute oral systemic toxicity, with respect to regulatory classifications of concern is presented.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Source: Web Of Science
Added: March 30, 2020
2020 journal article
INTEGRATIVE STATISTICAL METHODS FOR EXPOSURE MIXTURES AND HEALTH
ANNALS OF APPLIED STATISTICS, 14(4), 1945–1963.
author keywords: Cheminformatics; collinearity; factor analysis; principal components; stochastic search; variable selection
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science; OpenAlex)
11. Sustainable Cities and Communities
(Web of Science)
Sources: Web Of Science, NC State University Libraries
Added: March 1, 2021
2020 journal article
In vitroandin vivoEvaluation ofin silicoPredicted Pneumococcal UDPG:PP Inhibitors
FRONTIERS IN MICROBIOLOGY, 11.
author keywords: Streptococcus pneumoniae; GalU; in silicomodeling; virulence; Galleria mellonella; novel drug target
TL;DR:
UDPG:PP inhibitors proved to have an effect on streptococcal virulence by lowering the amount of polysaccharide and thereby probably boosting recognition of this pathogen by the innate immune system.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science; OpenAlex)
Source: Web Of Science
Added: August 24, 2020
2020 journal article
Inductive transfer learning for molecular activity prediction: Next-Gen QSAR Models with MolPMoFiT
JOURNAL OF CHEMINFORMATICS, 12(1).
author keywords: Transfer learning; Neural networks; Self-supervised learning; QSPR; QSAR
TL;DR:
The Molecular Prediction Model Fine-Tuning approach is proposed, an effective transfer learning method based on self-supervised pre-training + task-specific fine-tuning for QSPR/QSAR modeling for smaller chemical datasets with specific endpoints.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Source: Web Of Science
Added: May 18, 2020
2020 journal article
Novel peptide ligands for antibody purification provide superior clearance of host cell protein impurities
JOURNAL OF CHROMATOGRAPHY A, 1625.
author keywords: Peptide affinity ligands; Protein A; mAb purification; Affinity chromatography; Peptide design
MeSH headings : Amino Acid Sequence; Animals; Antibodies, Monoclonal / isolation & purification; Antibodies, Monoclonal / metabolism; CHO Cells; Chromatography, Affinity / methods; Cricetinae; Cricetulus; Immunoglobulin G / isolation & purification; Immunoglobulin G / metabolism; Ligands; Peptides / chemical synthesis; Peptides / chemistry; Peptides / metabolism; Protein Binding; Staphylococcal Protein A / chemistry; Staphylococcal Protein A / metabolism
TL;DR:
WQRHGI-WorkBeads resin was finally characterized by purification of a monoclonal antibody from a Chinese Hamster Ovary cell culture harvest, affording a remarkable HCP LRV of 2.7, and consistent product yield and purity over 100 chromatographic cycles.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
7. Affordable and Clean Energy
(OpenAlex)
Sources: Web Of Science, NC State University Libraries
Added: August 10, 2020
2020 journal article
Photoinduced reconfiguration to control the protein-binding affinity of azobenzene-cyclized peptides
JOURNAL OF MATERIALS CHEMISTRY B, 8(33), 7413–7427.
MeSH headings : Amino Acid Sequence; Azo Compounds / chemistry; Hydrogen-Ion Concentration; Isomerism; Osmolar Concentration; Peptides, Cyclic / chemistry; Photochemical Processes
TL;DR:
This study demonstrates a general method to develop azobenzene-cyclized peptide ligands with light-controlled affinity for target proteins by designing photo-switchable peptides targeting vascular cell adhesion marker 1 (VCAM1), a cell marker implicated in stem cell function.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
7. Affordable and Clean Energy
(Web of Science)
Sources: Web Of Science, NC State University Libraries
Added: September 14, 2020
2020 review
QSAR without borders
[Review of ]. CHEMICAL SOCIETY REVIEWS, 49(11), 3525–3564.
MeSH headings : Algorithms; Animals; Artificial Intelligence; Chemistry, Pharmaceutical / methods; Databases, Factual; Drug Design; Drug-Related Side Effects and Adverse Reactions / metabolism; History, 20th Century; History, 21st Century; Humans; Models, Molecular; Pharmaceutical Preparations / chemistry; Quantitative Structure-Activity Relationship; Quantum Theory; Reproducibility of Results
TL;DR:
This Perspective summarizes recent technological advances in QSAR modeling but it also highlights the applicability of algorithms, modeling methods, and validation practices developed inQSAR to a wide range of research areas outside of traditional QSar boundaries including synthesis planning, nanotechnology, materials science, biomaterials, and clinical informatics.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Source: Web Of Science
Added: July 6, 2020
2020 article
QSAR without borders (vol 10, pg 531, 2020)
Muratov, E. N., Bajorath, J., Sheridan, R. P., Tetko, I. V., Filimonov, D., Poroikov, V., … Tropsha, A. (2020, June 7). CHEMICAL SOCIETY REVIEWS, Vol. 49, pp. 3716–3716.
TL;DR:
This research presents a novel probabilistic procedure called QSAR without borders, which can be used to assess the severity of the impact of natural disasters on the response of the immune system.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Source: Web Of Science
Added: July 6, 2020
2020 journal article
SIME: synthetic insight-based macrolide enumerator to generate the V1B library of 1 billion macrolides
Journal of Cheminformatics, 12(1).
author keywords: Macrolides; PKS enumerator; In silico chemical library software; Polyketides
TL;DR:
A new cheminformatics enumeration technology—SIME, synthetic insight-based macrolide enumerator—a new and improved software technology that can enumerate fully assembled macrolides with synthetic feasibility by utilizing the constitutional and structural knowledge extracted from biosynthetic aspects of macrolided.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, NC State University Libraries, Crossref
Added: April 27, 2020
2020 journal article
Structural-based connectivity and omic phenotype evaluations (SCOPE): a cheminformatics toolbox for investigating lipidomic changes in complex systems
ANALYST, 145(22), 7197–7209.
MeSH headings : Cheminformatics; Lipidomics; Lipids; Mass Spectrometry; Phenotype
TL;DR:
A Structural-based Connectivity and Omic Phenotype Evaluations (SCOPE) cheminformatics toolbox to aid in these evaluations of lipid species and their respective biological roles is developed.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, NC State University Libraries
Added: November 24, 2020
2020 journal article
Structure-based virtual screening of perfluoroalkyl and polyfluoroalkyl substances (PFASs) as endocrine disruptors of androgen receptor activity using molecular docking and machine learning
ENVIRONMENTAL RESEARCH, 190.
author keywords: Steroid hormones; Modeling; Tox21
MeSH headings : Endocrine Disruptors / analysis; Endocrine Disruptors / toxicity; Fluorocarbons / toxicity; Machine Learning; Mass Screening; Molecular Docking Simulation; Receptors, Androgen
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
6. Clean Water and Sanitation
(Web of Science)
Source: Web Of Science
Added: November 2, 2020
2020 journal article
Unveiling molecular signatures of preeclampsia and gestational diabetes mellitus with multi-omics and innovative cheminformatics visualization tools
MOLECULAR OMICS, 16(6).
MeSH headings : Case-Control Studies; Diabetes, Gestational / genetics; Female; Genomics; Humans; Lipidomics; Metabolic Networks and Pathways; Pre-Eclampsia / genetics; Pregnancy
TL;DR:
The multi-omic evaluations performed here provide new insight into the end-stage molecular profiles of each disease, thereby supplying information potentially crucial for earlier diagnosis and treatments.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science; OpenAlex)
5. Gender Equality
(Web of Science)
Sources: Web Of Science, NC State University Libraries
Added: January 4, 2021
2019 review
4D-quantitative structure-activity relationship modeling: making a comeback
[Review of ]. EXPERT OPINION ON DRUG DISCOVERY, 14(12), 1227–1235.
author keywords: 4D descriptors; cheminformatics; QSAR; molecular dynamics
MeSH headings : Drug Design; Drug Discovery / methods; Humans; Ligands; Models, Molecular; Molecular Dynamics Simulation; Pharmaceutical Preparations / chemistry; Quantitative Structure-Activity Relationship
TL;DR:
There has never been a better time and relevance for molecular modeling teams to engage in hyper-predictive MD-QSAR modeling, which could represent a disruptive technology for analyzing, understanding, and optimizing dynamic protein-ligand interactions with countless applications for drug discovery and chemical toxicity assessment.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science; OpenAlex)
Source: Web Of Science
Added: September 30, 2019
2019 journal article
Adipocytes as Anticancer Drug Delivery Depot
MATTER, 1(5), 1203–1214.
TL;DR:
The lipid metabolism is exploited to engineer adipocytes that serve as a depot to deliver cancer therapeutics at the tumor site, promoting antitumor efficacy and downregulation of PD-L1 expression is observed in tumor cells.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science; OpenAlex)
Source: Web Of Science
Added: April 6, 2020
2019 journal article
Binding of peanut allergen Ara h 2 with Vaccinium fruit polyphenols
FOOD CHEMISTRY, 284, 287–295.
author keywords: Ara h 2; Molecular docking; Polyphenol; IgE binding; Circular dichroism (CD); Food allergy
MeSH headings : 2S Albumins, Plant / chemistry; 2S Albumins, Plant / immunology; 2S Albumins, Plant / metabolism; Antigens, Plant / chemistry; Antigens, Plant / immunology; Antigens, Plant / metabolism; Arachis / metabolism; Biflavonoids / chemistry; Biflavonoids / metabolism; Binding Sites; Catechin / chemistry; Catechin / metabolism; Chlorogenic Acid / chemistry; Chlorogenic Acid / metabolism; Circular Dichroism; Epitopes / chemistry; Epitopes / metabolism; Fruit / chemistry; Fruit / metabolism; Glycoproteins / chemistry; Glycoproteins / immunology; Glycoproteins / metabolism; Humans; Immunoglobulin E / chemistry; Immunoglobulin E / metabolism; Molecular Docking Simulation; Polyphenols / chemistry; Polyphenols / metabolism; Proanthocyanidins / chemistry; Proanthocyanidins / metabolism; Protein Binding; Protein Structure, Secondary; Spectrophotometry; Vaccinium / chemistry; Vaccinium / metabolism
TL;DR:
Results suggest that certain polyphenols can inhibit IgE recognition of Ara h 2 by obstructing linear IgE epitopes.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, NC State University Libraries
Added: February 25, 2019
2019 journal article
Cheminformatics approach to exploring and modeling trait-associated metabolite profiles
JOURNAL OF CHEMINFORMATICS, 11.
author keywords: Metabolomics; Data mining; Cheminformatics; Molecular fragmentation; Statistics; Visualization; Chemical structure
TL;DR:
A novel cheminformatics-based approach capable of identifying predictive, interpretable, and reproducible trait-metabolite relationships that could ultimately facilitate biological understanding and advance research based on metabolomics data, especially with respect to the identification of novel biomarkers.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science; OpenAlex)
Source: Web Of Science
Added: July 15, 2019
2019 journal article
Community assessment to advance computational prediction of cancer drug combinations in a pharmacogenomic screen
NATURE COMMUNICATIONS, 10.
MeSH headings : ADAM17 Protein / antagonists & inhibitors; Antineoplastic Combined Chemotherapy Protocols / pharmacology; Antineoplastic Combined Chemotherapy Protocols / therapeutic use; Benchmarking; Biomarkers, Tumor / genetics; Cell Line, Tumor; Computational Biology / methods; Computational Biology / standards; Datasets as Topic; Drug Antagonism; Drug Resistance, Neoplasm / drug effects; Drug Resistance, Neoplasm / genetics; Drug Synergism; Genomics / methods; Humans; Molecular Targeted Therapy / methods; Mutation; Neoplasms / drug therapy; Neoplasms / genetics; Pharmacogenetics / methods; Pharmacogenetics / standards; Phosphatidylinositol 3-Kinases / genetics; Phosphoinositide-3 Kinase Inhibitors; Treatment Outcome
TL;DR:
A large drug combination screen across cancer cell lines is provided to benchmark crowdsourced methods and to computationally predict drug synergies, and genomic rationale for synergy predictions are identified.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science; OpenAlex)
Source: Web Of Science
Added: July 1, 2019
2019 journal article
Identifying individual risk rare variants using protein structure guided local tests (POINT)
PLOS COMPUTATIONAL BIOLOGY, 15(2).
MeSH headings : Angiopoietin-Like Protein 4 / genetics; Cholesterol Ester Transfer Proteins / genetics; Computational Biology / methods; Computer Simulation; Genetic Association Studies / methods; Genetic Predisposition to Disease / genetics; Genetic Variation / genetics; Humans; Models, Genetic; Proprotein Convertase 9 / genetics; Protein Structure, Tertiary; Risk Factors; Sequence Analysis, DNA / methods
TL;DR:
This work proposes a protein structure guided local test (POINT) to provide variant-specific association information using structure-guided aggregation of signal and assess the selection performance of POINT using simulations and illustrates how it can be used to prioritize individual rare variants in PCSK9, ANGPTL4 and CETP in the Action to Control Cardiovascular Risk in Diabetes (ACCORD) clinical trial data.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Source: Web Of Science
Added: March 25, 2019
2019 review
Ion mobility spectrometry and the omics: Distinguishing isomers, molecular classes and contaminant ions in complex samples
[Review of ]. TRAC-TRENDS IN ANALYTICAL CHEMISTRY, 116, 292–299.
Contributors: K. Burnum-Johnson *, X. Zheng *, J. Dodds n, J. Ash n, n, C. Nicora *, J. Wendler *, T. Metz *
author keywords: Ion mobility spectrometry; Mass spectrometry; Omics; Proteomics; Lipidomics; Metabolomics; Glycomics; Exposomics
TL;DR:
Ion mobility spectrometry has shown great utility in salvaging molecular information for low abundance molecules of interest when high concentration contaminant ions are present in the sample by reducing detector suppression.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, ORCID, NC State University Libraries
Added: July 1, 2019
2018 journal article
Adverse drug reactions triggered by the common HLA-B*57:01 variant: Virtual screening of DrugBank using 3D molecular docking
Journal of Cheminformatics, 10.
Source: NC State University Libraries
Added: August 6, 2018
2018 journal article
Cheminformatics Analysis of Dynamic WNK-Inhibitor Interactions
Molecular Informatics, 37(6-7), 1700138.
author keywords: drug design; kinases; medicinal chemistry; structure-activity relationships; molecular modeling
MeSH headings : Binding Sites; Humans; Molecular Docking Simulation; Protein Binding; Protein Kinase Inhibitors / chemistry; Protein Kinase Inhibitors / pharmacology; WNK Lysine-Deficient Protein Kinase 1 / antagonists & inhibitors; WNK Lysine-Deficient Protein Kinase 1 / chemistry; WNK Lysine-Deficient Protein Kinase 1 / metabolism
TL;DR:
This study reports on the first, cheminformatics‐powered analysis of the entire chemical space of known WNK inhibitors and discusses the conservation of critical WNK‐inhibitor interactions and the existence of isoform‐specific interactions that could enable the rational design of more potent and selective WNK binders.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
15. Life on Land
(OpenAlex)
Sources: Crossref, NC State University Libraries
Added: August 6, 2018
2018 journal article
Cheminformatics-based enumeration and analysis of large libraries of macrolide scaffolds
Journal of Cheminformatics, 10(1).
TL;DR:
A cheminformatics approach and associated software that allows for designing and generating libraries of virtual macrocycle/macrolide scaffolds with user-defined constitutional and structural constraints and the chemical diversity and distribution of structural motifs in V1M library is introduced.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, NC State University Libraries, Crossref
Added: December 3, 2018
2018 journal article
Chemistry-Wide Association Studies (CWAS): A Novel Framework for Identifying and Interpreting Structure-Activity Relationships
JOURNAL OF CHEMICAL INFORMATION AND MODELING, 58(11), 2203–2213.
MeSH headings : Databases, Factual; Drug Discovery / methods; Drug-Related Side Effects and Adverse Reactions / etiology; Humans; Models, Biological; Mutagenicity Tests / methods; Pharmaceutical Preparations / chemistry; Quantitative Structure-Activity Relationship; Stevens-Johnson Syndrome / etiology
TL;DR:
It is demonstrated that CWAS provides a new framework to interpret predictive QSAR models and derive refined structural alerts for more effective design and safety assessment of drugs and drug candidates.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science; OpenAlex)
Source: Web Of Science
Added: December 17, 2018
2018 journal article
Confirmation of high-throughput screening data and novel mechanistic insights into VDR-xenobiotic interactions by orthogonal assays
Scientific Reports, 8(1).
Contributors: D. Mahapatra n, J. Franzosa*, K. Roell n, M. Kuenemann n, K. Houck *, D. Reif n , n, S. Kullman n
MeSH headings : Drug Evaluation, Preclinical; Genes, Reporter; High-Throughput Screening Assays; Humans; Luciferases / analysis; Luciferases / genetics; Protein Binding; Receptors, Calcitriol / agonists; Receptors, Calcitriol / antagonists & inhibitors; Two-Hybrid System Techniques; Xenobiotics / metabolism
TL;DR:
Data emphasizes the molecular complexity of ligand-mediated interactions with VDR and suggest that VDR transactivation may be a target site of action for diverse xenobiotics.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Crossref, ORCID, NC State University Libraries, NC State University Libraries
Added: August 6, 2018
2018 journal article
Corrections to “Toward the Rational Design of Sustainable Hair Dyes Using Cheminformatics Approaches: Step 2. Identification of Hair Dye Substance Database Analogs in the Max Weaver Dye Library”
Corrections to “Toward the Rational Design of Sustainable Hair Dyes Using Cheminformatics Approaches: Step 2. Identification of Hair Dye Substance Database Analogs in the Max Weaver Dye Library.” ACS Sustainable Chemistry & Engineering, 7(1), 1806–1806.
Source: Crossref
Added: December 21, 2020
2018 journal article
Exploring drug space with ChemMaps.com
BIOINFORMATICS, 34(21), 3773–3775.
MeSH headings : Computational Biology; Databases, Pharmaceutical; Molecular Structure; Software; Web Browser
TL;DR:
This work developed the ChemMaps.com webserver to easily browse, navigate and mine chemical space, which features more than 8000 approved, in development, and rejected drugs, as well as over 47 000 environmental chemicals.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Source: Web Of Science
Added: December 3, 2018
2018 journal article
In silico Predicted Glucose-1-phosphate Uridylyltransferase (GalU) Inhibitors Block a Key Pathway Required for Listeria Virulence
Molecular Informatics, 37(6-7), 1800004.
author keywords: drug design; molecular modeling; structure-activity relationships; virtual screening; antibiotics
MeSH headings : Anti-Bacterial Agents / chemistry; Anti-Bacterial Agents / pharmacology; Bacterial Proteins / antagonists & inhibitors; Bacterial Proteins / chemistry; Bacterial Proteins / metabolism; Benzamides / chemistry; Drug Discovery; Enzyme Inhibitors / chemistry; Enzyme Inhibitors / pharmacology; Listeria monocytogenes / drug effects; Listeria monocytogenes / enzymology; Listeria monocytogenes / pathogenicity; Pyrimidines / chemistry; Quantitative Structure-Activity Relationship; UTP-Glucose-1-Phosphate Uridylyltransferase / antagonists & inhibitors; UTP-Glucose-1-Phosphate Uridylyltransferase / chemistry; UTP-Glucose-1-Phosphate Uridylyltransferase / metabolism
TL;DR:
A series of in silico predicted GalU inhibitors identified using structure‐based virtual screening and experimentally validated to be effective in blocking the WTA galactosylation pathway in vitro are reported on.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Crossref, NC State University Libraries
Added: August 6, 2018
2018 journal article
Janus kinase inhibitors differ in their affinity to the TRPV1 receptor - implications for their use in itch and pain
Journal of Veterinary Pharmacology and Therapeutics, 41, 160–160.
Source: NC State University Libraries
Added: August 6, 2018
2018 journal article
Predicting Adverse Drug Effects from Literature- and Database-Mined Assertions
DRUG SAFETY, 41(11), 1059–1072.
MeSH headings : Data Mining / methods; Databases, Factual; Drug-Related Side Effects and Adverse Reactions / epidemiology; Humans; Prescription Drugs / adverse effects; Prescription Drugs / pharmacology; Proteins / drug effects
TL;DR:
The presented workflow, based on free-access databases and an association-based inference scheme, provided novel C–E relationships that have been validated post hoc in case reports and may provide an effective computational method for the early detection of potential drug candidate ADEs that can be followed by targeted experimental investigations.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science; OpenAlex)
Source: Web Of Science
Added: October 29, 2018
2018 journal article
Student-Guided Three-Dimensional Printing Activity in Large Lecture Courses: A Practical Guideline
JOURNAL OF CHEMICAL EDUCATION, 96(2), 291–295.
author keywords: Chemoinformatics; Organic Chemistry; Hands-On Learning/Manipulatives; First-Year Undergraduate/General; Second-Year Undergraduate
TL;DR:
A 3D printing activity in two separate Organic Chemistry lectures of at least 200 students each required students to 3D print a molecule of their choice, relying on services made available through the university libraries.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
4. Quality Education
(Web of Science; OpenAlex)
Sources: Web Of Science, NC State University Libraries
Added: August 12, 2019
2018 journal article
Toward the Rational Design of Sustainable Hair Dyes Using Cheminformatics Approaches: Step 2. Identification of Hair Dye Substance Database Analogs in the Max Weaver Dye Library
ACS SUSTAINABLE CHEMISTRY & ENGINEERING, 6(11), 14248–14256.
author keywords: Cheminformatics; Hair dyes; Hair Dye Substance Database; Max Weaver Dye Library; Skin sensitization; Sustainability
Sources: Web Of Science, ORCID
Added: December 3, 2018
2017 journal article
Adverse drug reactions triggered by the common HLA-B*57:01 variant: A molecular docking study
Journal of Cheminformatics, 9.
Source: NC State University Libraries
Added: August 6, 2018
2017 journal article
Characterizing the Chemical Space of ERK2 Kinase Inhibitors Using Descriptors Computed from Molecular Dynamics Trajectories
JOURNAL OF CHEMICAL INFORMATION AND MODELING, 57(6), 1286–1299.
MeSH headings : Ligands; Mitogen-Activated Protein Kinase 1 / antagonists & inhibitors; Mitogen-Activated Protein Kinase 1 / chemistry; Mitogen-Activated Protein Kinase 1 / metabolism; Molecular Dynamics Simulation; Protein Conformation; Protein Kinase Inhibitors / chemistry; Protein Kinase Inhibitors / metabolism; Protein Kinase Inhibitors / pharmacology; Quantitative Structure-Activity Relationship; Solvents / chemistry; Temperature
TL;DR:
This study represents the largest attempt to utilize MD-extracted chemical descriptors to characterize and model a series of bioactive molecules and showed that MD descriptors had little correlation with conventionally used 2D/3D descriptors, and were able to distinguish the most active ERK2 inhibitors from the moderate/weak actives and inactives.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Source: Web Of Science
Added: August 6, 2018
2017 journal article
Cheminformatics Modeling of Amine Solutions for Assessing their CO2Absorption Properties
Molecular Informatics, 36(7), 1600143.
author keywords: amine scrubbing; molecular modeling; QSPR; CO2 recycling
MeSH headings : Algorithms; Amines / chemistry; Carbon Dioxide / analysis; Carbon Dioxide / chemistry; Cluster Analysis; Databases, Factual; Machine Learning; Models, Chemical; Models, Molecular; Quantitative Structure-Activity Relationship; Reproducibility of Results; Solutions
TL;DR:
The chemical analysis and series of QSPR models presented in this proof‐of‐concept study represent new knowledge and innovative tools that could be very useful for screening and prioritizing hypothetical amines to be synthesized and tested experimentally for their CO2 absorption properties.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Source: Crossref
Added: December 21, 2020
2017 journal article
Cheminformatics modeling of amine solutions for assessing their CO2 absorption properties
Molecular Informatics, 36(7).
Source: NC State University Libraries
Added: August 6, 2018
2017 journal article
Computer-assisted decision support for student admissions based on their predicted academic performance
American Journal of Pharmaceutical Education, 81(3).
Source: NC State University Libraries
Added: August 6, 2018
2017 journal article
Reaction: Molecular Modeling for Novel Antibacterials
Chem, 3(1), 13–14.
TL;DR:
This research focuses on the development and applications of novel predictive cheminformatics methods and their applications in Chemistry and Bioinformatics.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Source: Crossref
Added: December 21, 2020
2017 journal article
RealityConvert: a tool for preparing 3D models of biochemical structures for augmented and virtual reality
BIOINFORMATICS, 33(23), 3816–3818.
MeSH headings : Computational Biology / methods; Models, Molecular; Molecular Conformation; Software; Virtual Reality
TL;DR:
The RealityConvert software tool and associated website are presented, which allow users to easily convert molecular objects to high quality 3D models directly compatible for AR and VR applications.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Source: Web Of Science
Added: August 6, 2018
2017 journal article
Toward the Rational Design of Sustainable Hair Dyes Using Cheminformatics Approaches: Step 1. Database Development and Analysis
ACS SUSTAINABLE CHEMISTRY & ENGINEERING, 6(2), 2344–2352.
author keywords: Cheminformatics; Hair dyes; HDSD; Mutagenicity; Skin sensitization; Sustainability
Sources: Web Of Science, ORCID
Added: August 6, 2018
2017 journal article
Weaver's historic accessible collection of synthetic dyes: a cheminformatics analysis
CHEMICAL SCIENCE, 8(6), 4334–4339.
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, NC State University Libraries
Added: August 6, 2018
2016 journal article
Activity prediction and identification of mis-annotated chemical compounds using extreme descriptors
Journal of Chemometrics, 30(3), 99–108.
author keywords: extreme descriptors; low-variance descriptors; mislabeling; QSAR; Prediction
TL;DR:
It is demonstrated using two case studies (M2 muscarinic receptors and skin sensitization) that extreme descriptors can be used for the identification of possibly mislabeled compounds and should be considered in quantitative structure–activity relationship modeling studies.
(via Semantic Scholar)
Source: Crossref
Added: February 24, 2020
2016 journal article
Alarms about structural alerts
GREEN CHEMISTRY, 18(16), 4348–4360.
TL;DR:
It is demonstrated that contrary to the common perception of QSAR models as "black boxes" they can be used to identify statistically significant chemical substructures (QSAR-based alerts) that influence toxicity.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Source: Web Of Science
Added: August 6, 2018
2016 journal article
Comprehensive characterization of the Published Kinase Inhibitor Set
Nature Biotechnology, 34(1), 95–103.
Source: NC State University Libraries
Added: August 6, 2018
2016 journal article
Genome-wide common and rare variant analysis provides novel insights into clozapine-associated neutropenia
Molecular Psychiatry, 22(10), 1502–1508.
MeSH headings : Carrier Proteins / genetics; Case-Control Studies; Clozapine / adverse effects; Clozapine / therapeutic use; Exome; Female; Genome-Wide Association Study; HLA-DQ beta-Chains / genetics; Humans; Male; Neutropenia / chemically induced; Neutropenia / genetics; Neutropenia / metabolism; Odds Ratio; Schizophrenia / drug therapy; Schizophrenia / genetics; Solute Carrier Organic Anion Transporter Family Member 1B3 / genetics
TL;DR:
The results implicate biological pathways through which clozapine may act to cause this serious adverse effect of schizophrenia, and identify gene-wide associations of uncommon non-synonymous variants within UBAP2 and STARD9.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(OpenAlex)
Source: Crossref
Added: January 28, 2021
2016 journal article
QSAR models of human data can enrich or replace LLNA testing for human skin sensitization
GREEN CHEMISTRY, 18(24), 6501–6515.
TL;DR:
Predictive QSAR models developed here provide more accurate alternative to LLNA testing for human skin sensitization assessment across diverse chemical data and can also be used to guide the structural optimization of toxic compounds to reduce their skin sensitized potential.
(via Semantic Scholar)
Source: Web Of Science
Added: August 6, 2018
2016 journal article
Trust, but Verify II: A Practical Guide to Chemogenomics Data Curation
JOURNAL OF CHEMICAL INFORMATION AND MODELING, 56(7), 1243–1252.
MeSH headings : Consensus; Genomics; Quality Control; Quantitative Structure-Activity Relationship; Reproducibility of Results; Statistics as Topic / standards
TL;DR:
A chemical and biological data curation workflow that relies on existing cheminformatics approaches to flag, and when appropriate, correct possibly erroneous entries in large chemogenomics data sets is proposed.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Source: Web Of Science
Added: August 6, 2018
2015 journal article
Comprehensive characterization of the Published Kinase Inhibitor Set
Nature Biotechnology, 34(1), 95–103.
MeSH headings : Glycosylation; Phosphotransferases / antagonists & inhibitors; Protein Kinase Inhibitors / pharmacology
TL;DR:
A thorough characterization of the Published Kinase Inhibitor Set is provided and chemical starting points for designing new chemical probes of orphan kinases are identified and the utility of these leads are illustrated by developing a selective inhibitor for the previously untargeted kinases LOK and SLK.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Source: Crossref
Added: January 21, 2021
2015 journal article
Computer-aided design of carbon nanotubes with the desired bioactivity and safety profiles
NANOTOXICOLOGY, 10(3), 374–383.
author keywords: Carbon nanotubes; cheminformatics; nanotoxicity; QSAR; virtual screening
MeSH headings : Cell Survival / drug effects; Chemical Safety; Computer Simulation; Computer-Aided Design; Databases, Factual; Nanotubes, Carbon / adverse effects; Nanotubes, Carbon / chemistry; Nanotubes, Carbon / toxicity; Protein Binding; Quantitative Structure-Activity Relationship
TL;DR:
This proof-of-concept study shows that computational models can be employed to guide the design of surface-modified nanomaterials with the desired biological and safety profiles.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Source: Web Of Science
Added: August 6, 2018
2015 personal communication
Curation of chemogenomics data
Fourches, D., Muratov, E., & Tropsha, A. (2015, August).
MeSH headings : Drug Design; Humans; Information Dissemination; Pharmacogenetics / standards; Small Molecule Libraries / chemistry; Small Molecule Libraries / pharmacology; Software
TL;DR:
A general chemical and biological data curation workflow that relies on existing cheminformatics approaches to flag, and in some cases correct, possibly erroneous entries in large chemogenomics datasets is proposed.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Source: Web Of Science
Added: August 6, 2018
2015 journal article
Drug Side Effect Profiles as Molecular Descriptors for Predictive Modeling of Target Bioactivity
Molecular Informatics, 34(2-3), 160–170.
author keywords: Side effects; Machine learning; QSAR; Drug repurposing
MeSH headings : Animals; Data Mining / methods; Dopamine Antagonists / adverse effects; Humans; MEDLINE; Models, Biological; Serotonin Antagonists / adverse effects
TL;DR:
The results demonstrate that side effect profiles can be utilized to predict a drug’s unknown molecular activity, thus representing a valuable opportunity in repositioning the drug for a new indications.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
10. Reduced Inequalities
(OpenAlex)
Source: Crossref
Added: February 24, 2020
2015 journal article
Pred-hERG: A Novel web-Accessible Computational Tool for Predicting Cardiac Toxicity
MOLECULAR INFORMATICS, 34(10), 698–701.
author keywords: hERG; QSAR models; web-Server; Screening
MeSH headings : Animals; Arrhythmias, Cardiac / chemically induced; Arrhythmias, Cardiac / metabolism; Cardiotoxins / chemistry; Cardiotoxins / toxicity; Computer Simulation; Databases, Chemical; ERG1 Potassium Channel / antagonists & inhibitors; ERG1 Potassium Channel / chemistry; ERG1 Potassium Channel / metabolism; Humans
TL;DR:
The development of an innovative and freely accessible web server for early identification of putative hERG blockers and non‐blockers in chemical libraries and develops robust and externally predictive binary and multiclass models.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science; OpenAlex)
Source: Web Of Science
Added: August 6, 2018
2015 journal article
Predicting chemically-induced skin reactions. Part I: QSAR models of skin sensitization and their application to identify potentially hazardous compounds
Toxicology and Applied Pharmacology, 284(2), 262–272.
author keywords: Skin sensitization; QSAR; Virtual screening; Skin toxicants
MeSH headings : Databases, Factual; Dermatitis, Allergic Contact / etiology; Dermatitis, Allergic Contact / immunology; Hazardous Substances / poisoning; Humans; Models, Chemical; Models, Immunological; Quantitative Structure-Activity Relationship; Skin / drug effects; Skin / immunology; Software
TL;DR:
This study aims to compile, curate, and integrate the largest publicly available dataset related to chemically-induced skin sensitization, use this data to generate rigorously validated and QSAR models for skin sensitized individuals, and employ these models as a virtual screening tool for identifying putative sensitizers among environmental chemicals.
(via Semantic Scholar)
Source: Crossref
Added: February 24, 2020
2015 journal article
Predicting chemically-induced skin reactions. Part II: QSAR models of skin permeability and the relationships between skin permeability and skin sensitization
Toxicology and Applied Pharmacology, 284(2), 273–280.
author keywords: Skin sensitization; Skin permeability; QSAR; Virtual screening; Skin toxicants
MeSH headings : Computer Simulation; Databases, Factual; Dermatitis, Allergic Contact / etiology; Dermatitis, Allergic Contact / immunology; Dermatitis, Allergic Contact / metabolism; Hazardous Substances / poisoning; Humans; Models, Theoretical; Permeability; Quantitative Structure-Activity Relationship; Skin / drug effects; Skin / immunology; Skin / metabolism; Skin Absorption / physiology; Software
TL;DR:
The models reported herein as well as those developed in the companion paper on skin sensitization suggest that it may be possible to rationally design compounds with the desired high skin permeability but low sensitization potential.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
15. Life on Land
(OpenAlex)
Source: Crossref
Added: February 24, 2020
2015 journal article
QSAR Modeling and Prediction of Drug-Drug Interactions
MOLECULAR PHARMACEUTICS, 13(2), 545–556.
author keywords: drug-drug interactions; QSAR modeling; simplex descriptors; GUSAR; QNA; DDI; toxicity; adverse drug reactions; mixtures
MeSH headings : Algorithms; Cytochrome P-450 Enzyme System / chemistry; Cytochrome P-450 Enzyme System / metabolism; Databases, Factual; Drug Interactions; Drug-Related Side Effects and Adverse Reactions; Humans; Models, Biological; Models, Molecular; Quantitative Structure-Activity Relationship
TL;DR:
This work generated virtually all possible binary combinations of marketed drugs and employed QSAR models to identify drug pairs predicted to be instances of DDI, and 4500 of these predicted DDIs that were not found in the training sets were confirmed by data from the DrugBank database.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science; OpenAlex)
Source: Web Of Science
Added: August 6, 2018
2014 journal article
Chemical Basis of Interactions Between Engineered Nanoparticles and Biological Systems
Chemical Reviews, 114(15), 7740–7781.
MeSH headings : Biological Transport; Cell Nucleus / drug effects; Cell Nucleus / metabolism; Cytoskeleton / drug effects; Cytoskeleton / metabolism; DNA / chemistry; DNA / metabolism; Humans; Ion Channels / antagonists & inhibitors; Ion Channels / chemistry; Mitochondria / drug effects; Mitochondria / metabolism; Nanoparticles / chemistry; Nanoparticles / metabolism; Nanoparticles / toxicity; Oxidative Stress / drug effects; Phospholipids / chemistry; Phospholipids / metabolism; Proteins / chemistry; Proteins / metabolism; Surface Properties
TL;DR:
As the production and applications of ENMs rapidly expand, their environmental impacts and effects on human health are becoming increasingly significant, and a thorough understanding of how nanomaterials perturb cells and biological molecules is required.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
14. Life Below Water
(OpenAlex)
Source: Crossref
Added: August 28, 2020
2014 journal article
Clozapine-induced agranulocytosis is associated with rare HLA-DQB1 and HLA-B alleles
Nature Communications, 5(1).
MeSH headings : Agranulocytosis / chemically induced; Agranulocytosis / genetics; Agranulocytosis / immunology; Alleles; Amino Acid Substitution; Antipsychotic Agents / adverse effects; Case-Control Studies; Clozapine / adverse effects; Exome; Gene Frequency; Genetic Predisposition to Disease; Genome-Wide Association Study; HLA-B Antigens / genetics; HLA-B Antigens / immunology; HLA-DQ beta-Chains / genetics; HLA-DQ beta-Chains / immunology; Heterozygote; Humans; Odds Ratio; Psychotic Disorders / drug therapy; Psychotic Disorders / genetics; Psychotic Disorders / immunology; Severity of Illness Index
TL;DR:
The largest and most comprehensive genetic study of CIAG to date is performed by interrogating 163 cases using genome-wide genotyping and whole-exome sequencing and finds that two loci in the major histocompatibility complex are independently associated with clozapine-induced agranulocytosis/granulocytopenia.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(OpenAlex)
Source: Crossref
Added: August 28, 2020
2014 journal article
Expanding the scope of drug repurposing in pediatrics: The Children's Pharmacy Collaborative™
Drug Discovery Today, 19(11), 1696–1698.
MeSH headings : Child; Databases, Pharmaceutical; Drug Repositioning; Humans; Pediatrics
TL;DR:
The development of The Children's Pharmacy Collaborative is described, which should grow over time, serve as a resource for professionals and families, and stimulate drug-repurposing efforts for a range of pediatric disorders.
(via Semantic Scholar)
Source: Crossref
Added: August 28, 2020
2014 journal article
Materials Cartography: Representing and Mining Materials Space Using Structural and Electronic Fingerprints
Chemistry of Materials, 27(3), 735–743.
TL;DR:
The issue of scientific discovery in materials databases is addressed by introducing novel analytical approaches based on structural and electronic materials fingerprints, which contribute to the emerging field of materials informati...
(via Semantic Scholar)
Source: Crossref
Added: February 24, 2020
2013 journal article
Data Set Modelability by QSAR
Journal of Chemical Information and Modeling, 54(1), 1–4.
MeSH headings : Computational Biology; Databases, Chemical / statistics & numerical data; Drug Design; Models, Chemical; Quantitative Structure-Activity Relationship
TL;DR:
A simple MODelability Index (MODI) is introduced that estimates the feasibility of obtaining predictive QSAR models (correct classification rate above 0.7) for a binary data set of bioactive compounds.
(via Semantic Scholar)
Source: Crossref
Added: August 28, 2020
2013 journal article
Integrative Chemical–Biological Read-Across Approach for Chemical Hazard Classification
Chemical Research in Toxicology, 26(8), 1199–1208.
MeSH headings : Animals; Anti-Bacterial Agents / chemistry; Anti-Bacterial Agents / toxicity; Anticonvulsants / chemistry; Anticonvulsants / toxicity; Bacteria / metabolism; Benzbromarone / chemistry; Benzbromarone / toxicity; Carbamazepine / chemistry; Carbamazepine / toxicity; Chloramphenicol / chemistry; Chloramphenicol / toxicity; Databases, Chemical; Gout Suppressants / chemistry; Gout Suppressants / toxicity; Hazardous Substances / classification; Hazardous Substances / toxicity; Liver / drug effects; Quantitative Structure-Activity Relationship; Rats; Transcriptome / drug effects
TL;DR:
A hazard classification and visualization method that draws upon both chemical structural similarity and comparisons of biological responses to chemicals measured in multiple short-term assays ("biological" similarity) to predict chemical toxicity.
(via Semantic Scholar)
Source: Crossref
Added: August 28, 2020
2013 journal article
Predicting Binding Affinity of CSAR Ligands Using Both Structure-Based and Ligand-Based Approaches
Journal of Chemical Information and Modeling, 53(8), 1915–1922.
MeSH headings : Databases, Pharmaceutical; Drug Discovery / methods; Ligands; Molecular Docking Simulation; Protein Binding; Quantitative Structure-Activity Relationship; Support Vector Machine
TL;DR:
This study shows that externally validated 2D QSAR models were capable of ranking CSAR ligands at least as accurately as more computationally intensive structure-based approaches used both by us and by other groups and ligand-based QSar models can complement structure- based approaches by boosting the prediction performances when used in consensus.
(via Semantic Scholar)
Source: Crossref
Added: August 28, 2020
2013 journal article
QSAR Modeling: Where Have You Been? Where Are You Going To?
Journal of Medicinal Chemistry, 57(12), 4977–5010.
MeSH headings : Antimicrobial Cationic Peptides / chemistry; Artificial Intelligence; Complex Mixtures / chemistry; Databases, Factual; Drug Design; History, 20th Century; History, 21st Century; Models, Molecular; Nanostructures / chemistry; Pharmacokinetics; Quantitative Structure-Activity Relationship; Quantum Theory; Toxicology / methods
UN Sustainable Development Goal Categories
16. Peace, Justice and Strong Institutions
(OpenAlex)
Source: Crossref
Added: August 28, 2020
2013 journal article
Using Graph Indices for the Analysis and Comparison of Chemical Datasets
Molecular Informatics, 32(9-10), 827–842.
author keywords: Chemical dataset graph; Graph indices; QSAR; ADDAGRA
TL;DR:
It is demonstrated that chemical datasets can be effectively characterized and compared by computing simple graph indices such as the average vertex degree or Randic connectivity index.
(via Semantic Scholar)
Source: Crossref
Added: August 28, 2020
2012 journal article
Discovery of Novel Antimalarial Compounds Enabled by QSAR-Based Virtual Screening
Journal of Chemical Information and Modeling, 53(2), 475–492.
MeSH headings : Antimalarials / chemistry; Antimalarials / pharmacology; Drug Discovery / methods; Humans; Malaria, Falciparum / drug therapy; Models, Biological; Plasmodium falciparum / drug effects; Quantitative Structure-Activity Relationship
TL;DR:
Quantitative structure-activity relationship models developed for a data set of 3133 compounds defined as either active or inactive against P. falciparum revealed novel chemical scaffolds which could be employed as starting points to discover novel antimalarial agents.
(via Semantic Scholar)
Source: Crossref
Added: August 28, 2020
2012 journal article
Human Intestinal Transporter Database: QSAR Modeling and Virtual Profiling of Drug Uptake, Efflux and Interactions
Pharmaceutical Research, 30(4), 996–1007.
author keywords: ADMET; drug transport; efflux; membrane transport proteins; permeability
MeSH headings : Artificial Intelligence; Biological Transport, Active; Computer Simulation; Databases, Pharmaceutical; Databases, Protein; Humans; Intestinal Mucosa / metabolism; Membrane Transport Proteins / chemistry; Membrane Transport Proteins / metabolism; Models, Biological; Pharmaceutical Preparations / chemistry; Pharmaceutical Preparations / metabolism; Pharmacokinetics; Quantitative Structure-Activity Relationship
TL;DR:
The compendium of predictive QSAR models developed in this study can be used for virtual profiling of drug candidates and/or environmental agents with the optimal transporter profiles with high prediction accuracies in the virtual screening of DrugBank compounds.
(via Semantic Scholar)
Source: Crossref
Added: January 21, 2021
2011 journal article
Predicting Drug-Induced Hepatotoxicity Using QSAR and Toxicogenomics Approaches
Chemical Research in Toxicology, 24(8), 1251–1262.
MeSH headings : Animals; Chemical and Drug Induced Liver Injury / metabolism; Chemical and Drug Induced Liver Injury / pathology; Databases, Factual; Hepatocyte Nuclear Factor 4 / metabolism; Male; Models, Statistical; Quantitative Structure-Activity Relationship; Rats; Rats, Sprague-Dawley; Small Molecule Libraries / chemistry; Small Molecule Libraries / toxicity; Toxicogenetics
TL;DR:
Results suggest that concurrent exploration of the chemical features and acute treatment-induced changes in transcript levels will both enrich the mechanistic understanding of subchronic liver injury and afford models capable of accurate prediction of hepatotoxicity from chemical structure and short-term assay results.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
16. Peace, Justice and Strong Institutions
(OpenAlex)
Source: Crossref
Added: August 28, 2020
2010 journal article
Applicability Domains for Classification Problems: Benchmarking of Distance to Models for Ames Mutagenicity Set
Journal of Chemical Information and Modeling, 50(12), 2094–2111.
MeSH headings : Benchmarking / methods; Classification / methods; Mutagenicity Tests / methods; Mutagenicity Tests / standards; Principal Component Analysis; Quantitative Structure-Activity Relationship
TL;DR:
This work demonstrates that the DMs based on an ensemble (consensus) model provide systematically better performance than other DMs and can be used to halve the cost of experimental measurements by providing a similar prediction accuracy.
(via Semantic Scholar)
Source: Crossref
Added: August 28, 2020
2010 journal article
Modeling Liver-Related Adverse Effects of Drugs UsingkNearest Neighbor Quantitative Structure−Activity Relationship Method
Chemical Research in Toxicology, 23(4), 724–732.
MeSH headings : Algorithms; Chemical and Drug Induced Liver Injury / etiology; Databases, Factual; Drug-Related Side Effects and Adverse Reactions; Humans; Models, Biological; Models, Molecular; Quantitative Structure-Activity Relationship
TL;DR:
Validated QSAR models of liver AEDs based on the data from the FDA spontaneous reporting system can be employed as sensitive and specific predictors of Aeds in preclinical screening of drug candidates for potential hepatotoxicity in humans.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(OpenAlex)
Source: Crossref
Added: January 24, 2021
2010 journal article
Quantitative Nanostructure−Activity Relationship Modeling
ACS Nano, 4(10), 5703–5712.
author keywords: nanoparticles; QSAR; cheminformatics; nanotoxicity; modeling
MeSH headings : Animals; Cell Line, Tumor; Humans; Metal Nanoparticles / chemistry; Microscopy, Atomic Force / methods; Models, Statistical; Models, Theoretical; Nanotechnology / methods; Oxides / chemistry; Quantitative Structure-Activity Relationship; Rats; Regression Analysis; Surface Properties; U937 Cells
TL;DR:
The results suggest that QNAR models can be employed for: (i) predicting biological activity profiles of novel nanomaterials, and (ii) prioritizing the design and manufacturing of nanom material toward better and safer products.
(via Semantic Scholar)
Source: Crossref
Added: August 28, 2020
2010 journal article
Trust, But Verify: On the Importance of Chemical Structure Curation in Cheminformatics and QSAR Modeling Research
Journal of Chemical Information and Modeling, 50(7), 1189–1204.
MeSH headings : Animals; Models, Chemical; Molecular Structure; Organometallic Compounds / chemistry; Quantitative Structure-Activity Relationship
TL;DR:
The need for a standardized chemical data curation strategy that should be followed at the onset of any molecular modeling investigation is emphasized and it is demonstrated that in some cases rigorously developed QSAR models could be even used to correct erroneous biological data associated with chemical compounds.
(via Semantic Scholar)
Source: Crossref
Added: August 28, 2020
2009 journal article
Cheminformatics Analysis of Assertions Mined from Literature That Describe Drug-Induced Liver Injury in Different Species
Chemical Research in Toxicology, 23(1), 171–183.
MeSH headings : Animals; Chemical and Drug Induced Liver Injury; Cluster Analysis; Databases, Factual; Humans; MEDLINE; Mice; Models, Chemical; Molecular Conformation; Quantitative Structure-Activity Relationship
TL;DR:
This is the first study for chemical toxicity prediction that applied QSAR modeling and other cheminformatics techniques to observational data generated by the means of automated text mining with limited manual curation, opening up new opportunities for generating and modeling chemical toxicology data.
(via Semantic Scholar)
Source: Crossref
Added: August 28, 2020
2008 journal article
Combinatorial QSAR Modeling of Chemical Toxicants Tested against Tetrahymena pyriformis
Journal of Chemical Information and Modeling, 48(4), 766–784.
MeSH headings : Animals; Combinatorial Chemistry Techniques; Quantitative Structure-Activity Relationship; Tetrahymena pyriformis / drug effects; Toxicity Tests
TL;DR:
An international virtual collaboratory consisting of six independent groups with shared interests in computational chemical toxicology develops 15 different types of QSAR models of aquatic toxicity and finds that consensus models afford higher prediction accuracy for the external validation data sets with the highest space coverage as compared to individual constituent models.
(via Semantic Scholar)
Source: Crossref
Added: August 28, 2020
2008 journal article
Critical Assessment of QSAR Models of Environmental Toxicity against Tetrahymena pyriformis: Focusing on Applicability Domain and Overfitting by Variable Selection
Journal of Chemical Information and Modeling, 48(9), 1733–1746.
MeSH headings : Animals; Computer Simulation; Databases, Factual; Environmental Pollutants / chemistry; Environmental Pollutants / toxicity; Models, Biological; Models, Statistical; Normal Distribution; Predictive Value of Tests; Quantitative Structure-Activity Relationship; Reproducibility of Results; Tetrahymena pyriformis / drug effects; Toxicity Tests / standards
TL;DR:
It is shown that incorrect validation of a model may result in the wrong estimation of its performance and suggested how this problem could be circumvented and the distance to model metric could also be used to augment mechanistic QSAR models by estimating their prediction errors.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
10. Reduced Inequalities
(OpenAlex)
Source: Crossref
Added: August 28, 2020
2007 journal article
QSPR Modeling of the AmIII/EuIIISeparation Factor: How Far Can we Predict ?
Solvent Extraction and Ion Exchange, 25(1), 1–26.
author keywords: solvent extraction; Am/Eu separation factor; substructural molecular fragments; QSPR; polydentate nitrogen ligands; aqueous solubility; neural networks; clustering
Source: Crossref
Added: January 24, 2021
2007 journal article
Successful “In Silico” Design of New Efficient Uranyl Binders
Solvent Extraction and Ion Exchange, 25(4), 433–462.
author keywords: QSPR; ISIDA program; in silico design; solvent extraction; uranyl cation
UN Sustainable Development Goal Categories
6. Clean Water and Sanitation
(OpenAlex)
Source: Crossref
Added: August 28, 2020
2006 journal article
Benchmarking of Linear and Nonlinear Approaches for Quantitative Structure−Property Relationship Studies of Metal Complexation with Ionophores
Journal of Chemical Information and Modeling, 46(2), 808–819.
MeSH headings : Algorithms; Europium / chemistry; Ionophores / chemistry; Linear Models; Models, Theoretical; Nonlinear Dynamics; Organometallic Compounds / chemistry; Quantitative Structure-Activity Relationship; Silver / chemistry; Software Validation
TL;DR:
Individual structure-complexation property models obtained with nonlinear methods demonstrated a significantly better performance than the models built using multilinear regression analysis (MLRA), however, the averaging of several MLRA models based on SMF descriptors provided as good of a prediction as the most efficient nonlinear techniques.
(via Semantic Scholar)
Source: Crossref
Added: August 28, 2020
2005 journal article
Substructural fragments: an universal language to encode reactions, molecular and supramolecular structures
Journal of Computer-Aided Molecular Design, 19(9-10), 693–703.
author keywords: chemical reactions; clustering; condensed graphs of reactions; exchange of information; hydrogen bonds; QSPR; similarity; solubility; substructural fragments
MeSH headings : Computer Simulation; Hydrogen Bonding; Macromolecular Substances; Models, Chemical; Molecular Structure; Quantitative Structure-Activity Relationship; Solubility; Thermodynamics; Water
TL;DR:
Substructural fragments are proposed as a simple and safe way to encode molecular structures in a matrix containing the occurrence of fragments of a given type and the knowledge retrieved from QSPR modelling can also be stored in that matrix in addition to the information about fragments.
(via Semantic Scholar)
Source: Crossref
Added: August 28, 2020
2004 journal article
“In Silico” Design of New Uranyl Extractants Based on Phosphoryl-Containing Podands: QSPR Studies, Generation and Screening of Virtual Combinatorial Library, and Experimental Tests
Journal of Chemical Information and Computer Sciences, 44(4), 1365–1382.
TL;DR:
Computer-aided design of new extractants of the uranyl cation involving three main steps: a QSPR study, generation and screening of a virtual combinatorial library, and synthesis of several predicted compounds and their experimental extraction studies.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
6. Clean Water and Sanitation
(OpenAlex)
Source: Crossref
Added: January 21, 2021
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