Works (40)
Updated: June 24th, 2024 08:26
2024 article
Explicit Ion Modeling Predicts Physicochemical Interactions for Chromatin Organization
Lin, X., & Zhang, B. (2024, January 10).
doi.org (publisher)
UN Sustainable Development Goal Categories
7. Affordable and Clean Energy
(OpenAlex)
Source: ORCID
Added: February 1, 2024
2024 journal article
Explicit ion modeling predicts physicochemical interactions for chromatin organization
ELife.
UN Sustainable Development Goal Categories
7. Affordable and Clean Energy
(OpenAlex)
Source: ORCID
Added: February 1, 2024
2024 journal article
Explicit ion modeling predicts physicochemical interactions for chromatin organization
ELIFE, 12.
author keywords: chromatin folding; coarse-grained modeling; explicit ions; 30 nm fiber; None
TL;DR:
The model reproduces the energetics of protein-DNA binding and unwinding of single nucleosomal DNA, and resolves the differential impact of mono- and divalent ions on chromatin conformations.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
7. Affordable and Clean Energy
(OpenAlex)
Sources: ORCID, Web Of Science, NC State University Libraries
Added: February 1, 2024
2024 article
Interpretable Protein-DNA Interactions Captured by Structure-based Optimization
Zhang, Y., Silvernail, I., Lin, Z., & Lin, X. (2024, May 27).
Source: ORCID
Added: June 1, 2024
2024 journal article
RACER-m leverages structural features for sparse T cell specificity prediction
SCIENCE ADVANCES, 10(20).
Sources: ORCID, Web Of Science, NC State University Libraries
Added: May 22, 2024
2024 journal article
Residue coevolution and mutational landscape for OmpR and NarL response regulator subfamilies
BIOPHYSICAL JOURNAL, 123(6), 681–692.
Sources: Web Of Science, NC State University Libraries
Added: May 13, 2024
2023 article
Explicit Ion Modeling Predicts Physicochemical Interactions for Chromatin Organization
Lin, X., & Zhang, B. (2023, May 18).
TL;DR:
The model reproduces the energetics of protein-DNA binding and unwinding of single nucleosomal DNA, and resolves the differential impact of mono and divalent ions on chromatin conformations.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
7. Affordable and Clean Energy
(OpenAlex)
Source: ORCID
Added: February 1, 2024
2023 article
Explicit Ion Modeling Predicts Physicochemical Interactions for Chromatin Organization
Lin, X., & Zhang, B. (2023, August 21).
UN Sustainable Development Goal Categories
7. Affordable and Clean Energy
(OpenAlex)
Source: ORCID
Added: February 1, 2024
2023 article
RACER-m Leverages Structural Features for Sparse T Cell Specificity Prediction
Wang, A., Lin, X., Chau, K. N., Onuchic, J. N., Levine, H., & George, J. T. (2023, August 7). (Vol. 8). Vol. 8.
TL;DR:
RACER-m is presented, a coarse-grained structural template model leveraging key biophysical information from the diversity of publicly available TCR-antigen crystal structures and capably identifies biophysically meaningful point-mutants that affect overall binding affinity, distinguishing its ability in predicting TCR specificity of point mutants peptides from alternative sequence-based methods.
(via Semantic Scholar)
Source: ORCID
Added: February 1, 2024
2023 article
Single-molecule acceptor rise time (smART) FRET for nanoscale distance sensitivity
Guo, J., Chen, X., Manna, P., Lin, X., Scott, M. N., Chen, W. J., … Schlau-Cohen, G. S. (2023, March 16).
TL;DR:
Using the nanoscale sensitivity, the architectures of DNA bound to the single-stranded binding protein from E. coli are resolved, demonstrating the ability of smART FRET to elucidate the complex behaviors of biomolecules.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
7. Affordable and Clean Energy
(OpenAlex)
Source: ORCID
Added: April 5, 2023
2022 journal article
Chromatin fiber breaks into clutches under tension and crowding
Nucleic Acids Research, 50(17), 9738–9747.
MeSH headings : Cell Nucleus; Chromatin; Molecular Conformation; Nucleosomes
TL;DR:
It is revealed that chromatin segments with fibril or clutch structures engaged in distinct binding modes and the implications of these inter-chain interactions for a potential sol-gel phase transition are discussed.
(via Semantic Scholar)
Sources: ORCID, Crossref, NC State University Libraries
Added: April 5, 2023
2022 journal article
Contact map dependence of a T-cell receptor binding repertoire
Physical Review E.
TL;DR:
It is found that the TCR-pMHC binding energy distribution strongly depends both on the number of contacts and the repeat structure allowed by the topology of the contact map of choice; this in turn influences T-cell recognition probability during negative selection, with higher variances leading to higher survival probabilities.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
10. Reduced Inequalities
(OpenAlex)
Source: ORCID
Added: April 5, 2023
2022 journal article
Ligand-induced transmembrane conformational coupling in monomeric EGFR
Nature Communications, 13(1).
MeSH headings : Cell Membrane / metabolism; ErbB Receptors / metabolism; Ligands; Protein Binding; Protein Conformation
TL;DR:
It is shown that transmembrane conformational coupling is the first step in EGFR signaling, providing evidence for the existence of trans Membrane intramolecular conformational changes in a single pass membrane protein.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
7. Affordable and Clean Energy
(OpenAlex)
Sources: ORCID, Crossref, NC State University Libraries
Added: April 5, 2023
2021 article
Chromatin fiber breaks into clutches under tension and crowding
Liu, S., Lin, X., & Zhang, B. (2021, November 18). (Vol. 11). Vol. 11.
Source: ORCID
Added: February 1, 2024
2021 journal article
Cooperative DNA looping by PRC2 complexes
Nucleic Acids Research, 49(11), 6238–6248.
TL;DR:
The study suggests that accessory proteins may regulate the genomic location of PRC2 by interfering with its DNA interactions, and single-molecule experiments supportPRC2-mediated DNA looping and the role of AEBP2 in regulating such loop formation.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
7. Affordable and Clean Energy
(OpenAlex)
Sources: ORCID, Crossref, NC State University Libraries
Added: April 5, 2023
2021 journal article
Exploring Energy Landscapes of Intrinsically Disordered Proteins: Insights into Functional Mechanisms
Journal of Chemical Theory and Computation, 17(5), 3178–3187.
MeSH headings : Amino Acid Sequence; Intrinsically Disordered Proteins / chemistry; Intrinsically Disordered Proteins / metabolism; Phosphorylation; Protein Conformation; Protein Isoforms / chemistry; Protein Isoforms / metabolism; Reproducibility of Results; Sequence Homology, Amino Acid
UN Sustainable Development Goal Categories
7. Affordable and Clean Energy
(OpenAlex)
Sources: ORCID, Crossref, NC State University Libraries
Added: April 5, 2023
2021 article
Ligand-induced transmembrane conformational coupling in monomeric EGFR
Srinivasan, S., Regmi, R., Lin, X., Dreyer, C. A., Chen, X., Quinn, S. D., … Schlau-Cohen, G. S. (2021, October 28). (Vol. 10). Vol. 10.
UN Sustainable Development Goal Categories
7. Affordable and Clean Energy
(OpenAlex)
Source: ORCID
Added: February 1, 2024
2021 journal article
Multiscale modeling of genome organization with maximum entropy optimization
The Journal of Chemical Physics, 155(1), 010901.
MeSH headings : Algorithms; DNA / genetics; Entropy; Humans; Models, Genetic; Molecular Dynamics Simulation
TL;DR:
Applications ofarse-grained models parameterized to reproduce experimental data via the maximum entropy optimization algorithm serve as effective means to study genome organization at various length scales and revealed physicochemical interactions that drive the phase separation of disordered proteins and dictate chromatin stability in situ.
(via Semantic Scholar)
Sources: ORCID, Crossref, NC State University Libraries
Added: April 5, 2023
2021 journal article
Rapid assessment of T-cell receptor specificity of the immune repertoire
Nature Computational Science, 1(5), 362–373.
TL;DR:
RACER applies supervised machine learning to efficiently and accurately resolve strong TCR–peptide binding pairs from weak ones and accurately estimates recognition rates for tumor-associated neoantigens and foreign peptides, thus demonstrating its utility in helping address the computational challenge of reliably identifying properties of tumor antigen-specific T-cells at the level of an individual patient’s immune repertoire.
(via Semantic Scholar)
Sources: Crossref, NC State University Libraries
Added: April 7, 2023
2021 journal article
Rapid assessment of T-cell receptor specificity of the immune repertoire
Nature Computational Science.
Source: ORCID
Added: February 1, 2024
2021 journal article
Stability and folding pathways of tetra-nucleosome from six-dimensional free energy surface
Nature Communications, 12(1).
MeSH headings : Acetylation; Algorithms; Animals; Chromatin / chemistry; Chromatin / genetics; Chromatin / metabolism; DNA / chemistry; DNA / genetics; DNA / metabolism; Histones / chemistry; Histones / metabolism; Humans; Models, Molecular; Nucleic Acid Conformation; Nucleosomes / chemistry; Nucleosomes / genetics; Nucleosomes / metabolism; Protein Conformation; Thermodynamics
TL;DR:
A near atomistic model is applied to study the structure and dynamics of the chromatin folding unit - the tetra-nucleosome to provide insight into how chromatin folds and has implications on the in situ relevance of the 30 nm fiber.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
7. Affordable and Clean Energy
(OpenAlex)
Sources: ORCID, Crossref, NC State University Libraries
Added: April 5, 2023
2020 journal article
Enhancing intracellular accumulation and target engagement of PROTACs with reversible covalent chemistry
Nature Communications, 11(1).
MeSH headings : Acrylamides / chemistry; Adaptor Proteins, Signal Transducing / metabolism; Agammaglobulinaemia Tyrosine Kinase / genetics; Agammaglobulinaemia Tyrosine Kinase / metabolism; Cell Line; Cell Survival; Fluorescent Dyes; Half-Life; Humans; Intracellular Space / metabolism; Ligands; Molecular Dynamics Simulation; Mutation; Organic Chemistry Phenomena; Protein Binding; Protein Interaction Domains and Motifs; Proteolysis; Ubiquitin-Protein Ligases / metabolism
TL;DR:
It is shown that reversible covalent warhead chemistry improves PROTAC intracellular accumulation and target engagement, and develops a dual inhibitor/degrader of Bruton’s tyrosine kinase, opening a path to enhance PROTAC efficacy.
(via Semantic Scholar)
Sources: ORCID, Crossref, NC State University Libraries
Added: April 5, 2023
2020 journal article
Molecular-replacement phasing using predicted protein structures from <i>AWSEM-Suite
IUCrJ, 7(6), 1168–1178.
TL;DR:
This paper describes and evaluates the performance of AWSEM-Suite, an algorithm that includes template-guided refinement and coevolutionary information within the framework of the energy-landscape theory, in using molecular replacement to solve the phase problem by the de novo prediction of structures.
(via Semantic Scholar)
Sources: ORCID, Crossref, NC State University Libraries
Added: April 5, 2023
2020 journal article
Protein Structure Prediction in CASP13 Using AWSEM-Suite
Journal of Chemical Theory and Computation, 16(6), 3977–3988.
MeSH headings : Algorithms; Humans; Molecular Dynamics Simulation / standards; Protein Conformation; Protein Folding; Proteins / chemistry
Sources: ORCID, Crossref, NC State University Libraries
Added: April 5, 2023
2020 journal article
Protein Structure Refinement Guided by Atomic Packing Frustration Analysis
The Journal of Physical Chemistry B, 124(48), 10889–10898.
MeSH headings : Computational Biology; Machine Learning; Molecular Dynamics Simulation; Protein Conformation; Protein Folding; Proteins
UN Sustainable Development Goal Categories
7. Affordable and Clean Energy
(OpenAlex)
Sources: Crossref, NC State University Libraries
Added: April 6, 2023
2020 journal article
Single-molecule and in silico dissection of the interaction between Polycomb repressive complex 2 and chromatin
Proceedings of the National Academy of Sciences, 117(48), 30465–30475.
MeSH headings : Chromatin / chemistry; Chromatin / genetics; Chromatin / metabolism; Epigenesis, Genetic; Heterochromatin / genetics; Histones / metabolism; Humans; Methylation; Models, Biological; Models, Molecular; Molecular Dynamics Simulation; Mutation; Nucleosomes; Polycomb Repressive Complex 2 / chemistry; Polycomb Repressive Complex 2 / metabolism; Protein Binding; Protein Conformation; Single Molecule Imaging / methods; Spectrum Analysis; Structure-Activity Relationship
TL;DR:
The experimental and computational platforms developed here provide a framework for understanding the molecular basis of epigenetic maintenance mediated by Polycomb-group proteins and reveal an unexpectedly diverse repertoire of PRC2 binding configurations on chromatin.
(via Semantic Scholar)
Sources: ORCID, Crossref, NC State University Libraries
Added: April 5, 2023
2019 journal article
Forging tools for refining predicted protein structures
Proceedings of the National Academy of Sciences, 116(19), 9400–9409.
MeSH headings : Crystallography, X-Ray; Models, Molecular; Protein Conformation; Proteins / chemistry; Software
TL;DR:
Inspiration from blacksmithing is drawn to help devise methods that can refine intermediate resolution models to within experimental accuracy using only modest computational resources, and a two-step refinement procedure that involves identifying collective variables for mechanical deformations using a coarse-grained model and then sampling along these deformation modes in all-atom simulations.
(via Semantic Scholar)
Sources: ORCID, Crossref, NC State University Libraries
Added: April 5, 2023
2019 journal article
Recent Advances in Computational Protocols Addressing Intrinsically Disordered Proteins
Biomolecules, 9(4), 146.
MeSH headings : Animals; Drug Discovery / methods; Humans; Intrinsically Disordered Proteins / antagonists & inhibitors; Intrinsically Disordered Proteins / chemistry; Intrinsically Disordered Proteins / metabolism; Molecular Docking Simulation / methods; Molecular Dynamics Simulation; Small Molecule Libraries / chemistry; Small Molecule Libraries / pharmacology
TL;DR:
An overview of the current state of computational methods for studying IDP structure and dynamics is provided and the major challenges faced are discussed.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
7. Affordable and Clean Energy
(OpenAlex)
Sources: ORCID, Crossref, NC State University Libraries
Added: April 5, 2023
2019 journal article
Structural and Dynamical Order of a Disordered Protein: Molecular Insights into Conformational Switching of PAGE4 at the Systems Level
Biomolecules, 9(2), 77.
author keywords: PAGE4; intrinsically disordered proteins; conformational plasticity; order-disorder transition; phosphorylation
MeSH headings : Antigens, Neoplasm / chemistry; Antigens, Neoplasm / metabolism; Humans; Intrinsically Disordered Proteins / chemistry; Intrinsically Disordered Proteins / metabolism; Molecular Dynamics Simulation; Protein Conformation
TL;DR:
It is argued that, although the structural plasticity of an IDP is important in promoting promiscuous interactions, the modulation of the structural ordering is important for sculpting its interactions so as to rewire with agility biomolecular interaction networks with significant functional consequences.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: ORCID, Crossref, NC State University Libraries, Web Of Science
Added: March 25, 2019
2018 journal article
Atomistic simulations indicate the functional loop-to-coiled-coil transition in influenza hemagglutinin is not downhill
Proceedings of the National Academy of Sciences, 115(34).
MeSH headings : Hemagglutinin Glycoproteins, Influenza Virus / chemistry; Hemagglutinin Glycoproteins, Influenza Virus / metabolism; Influenza A virus / chemistry; Influenza A virus / metabolism; Molecular Dynamics Simulation; Protein Structure, Quaternary; Protein Structure, Secondary
TL;DR:
The results do not support a description of the B loop in group 2 HAs as a stiff spring, but, rather, it allows for more structural heterogeneity in the placement of the fusion peptides during the fusion process.
(via Semantic Scholar)
Sources: ORCID, Crossref, NC State University Libraries
Added: April 5, 2023
2018 journal article
PAGE4 and Conformational Switching: Insights from Molecular Dynamics Simulations and Implications for Prostate Cancer
Journal of Molecular Biology, 430(16), 2422–2438.
Contributors: * , S. Roy *, M. Jolly*, F. Bocci *, N. Schafer *, M. Tsai *, Y. Chen *, Y. He *
author keywords: intrinsically disordered protein; PAGE4; AWSEM; order-disorder transition; non-genetic heterogeneity
MeSH headings : Antigens, Neoplasm / chemistry; Antigens, Neoplasm / metabolism; Fluorescence Resonance Energy Transfer; Humans; Male; Models, Molecular; Models, Theoretical; Molecular Dynamics Simulation; Phosphorylation; Prostatic Neoplasms / metabolism; Protein Conformation; Protein Serine-Threonine Kinases / metabolism; Protein-Tyrosine Kinases / metabolism; Receptors, Androgen / metabolism; Scattering, Small Angle; Signal Transduction; Single Molecule Imaging; Transcription Factor AP-1 / metabolism; X-Ray Diffraction
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
7. Affordable and Clean Energy
(OpenAlex)
Sources: ORCID, Crossref, NC State University Libraries
Added: February 5, 2020
2018 article
PAGE4 and Conformational Switching: Insights from Molecular Dynamics Simulations and Implications for Prostate Cancer
Lin, X., Roy, S., Jolly, M. K., Bocci, F., Schafer, N., Tsai, M.-Y., … Onuchic, J. N. (2018, February 14). (Vol. 2). Vol. 2.
TL;DR:
A mechanism-based mathematical model is constructed that allows for the interactions of different forms of PAGE4 with AP-1 and AR, a key therapeutic target in prostate cancer, to be captured and predicts intracellular oscillatory dynamics of HIPK1-PAGE4, CLK2- PAGE4 and AR activity.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(OpenAlex)
Source: ORCID
Added: February 1, 2024
2018 journal article
Template-Guided Protein Structure Prediction and Refinement Using Optimized Folding Landscape Force Fields
Journal of Chemical Theory and Computation, 14(11), 6102–6116.
MeSH headings : Models, Molecular; Protein Conformation; Protein Folding; Proteins / chemistry
TL;DR:
This study combines template-based modeling with a realistic coarse-grained force field, AWSEM, that has been optimized using the principles of energy landscape theory to form a model that is able to achieve high-resolution structure prediction and confirms that using a combination of AWSEM and a template-guided potential leads to more accurate prediction of protein structures than simply using a template
(via Semantic Scholar)
Sources: ORCID, Crossref, NC State University Libraries
Added: April 5, 2023
2017 journal article
Quantum Image Processing and Its Application to Edge Detection: Theory and Experiment
Physical Review X, 7(3).
TL;DR:
The framework of quantum image processing is demonstrated, where a pure quantum state encodes the image information: the authors encode the pixel values in the probability amplitudes and the pixel positions in the computational basis states, and the required number of qubits are reduced.
(via Semantic Scholar)
Sources: ORCID, Crossref, NC State University Libraries
Added: April 5, 2023
2016 journal article
Lowered pH Leads to Fusion Peptide Release and a Highly Dynamic Intermediate of Influenza Hemagglutinin
The Journal of Physical Chemistry B, 120(36), 9654–9660.
Contributors: * , J. Noel *, Q. Wang *, J. Ma * & J. Onuchic *
MeSH headings : Hemagglutinin Glycoproteins, Influenza Virus / chemistry; Humans; Hydrogen-Ion Concentration; Influenza, Human; Molecular Dynamics Simulation; Peptides / chemistry; Protons
TL;DR:
It is found that, after the dissociation of FPs, a structural order-disorder transition in a loop connecting the central coiled-coil to the C-terminal domains produces a highly mobile HA, suggesting the existence of a long-lived asymmetric or "symmetry-broken" intermediate during the HA conformational change.
(via Semantic Scholar)
Sources: ORCID, Crossref, NC State University Libraries
Added: April 5, 2023
2016 journal article
Protein Folding and Structure Prediction from the Ground Up II: AAWSEM for α/β Proteins
The Journal of Physical Chemistry B, 121(15), 3473–3482.
Contributors: M. Chen *, * , W. Lu *, J. Onuchic * & P. Wolynes*
MeSH headings : Molecular Dynamics Simulation; Protein Conformation; Protein Folding; Proteins / chemistry; Thermodynamics
TL;DR:
The capability of AAWSEM to predict the structure of α/β proteins is examined and the use of clustering analyses as a way of evaluating the confidence in various structure prediction models is explored.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
7. Affordable and Clean Energy
(OpenAlex)
Sources: ORCID, Crossref, NC State University Libraries
Added: April 5, 2023
2016 journal article
Protein Folding and Structure Prediction from the Ground Up: The Atomistic Associative Memory, Water Mediated, Structure and Energy Model
The Journal of Physical Chemistry B, 120(33), 8557–8565.
Contributors: M. Chen *, * , W. Zheng *, J. Onuchic * & P. Wolynes*
MeSH headings : Algorithms; Cluster Analysis; Computer Simulation; Models, Molecular; Myoglobin / chemistry; Myoglobin / metabolism; Protein Folding; Protein Structure, Secondary; Solvents / chemistry; Water / chemistry
TL;DR:
Study of the structure prediction capabilities of the atomistic associative memory, water mediated, structure and energy model for six α-helical proteins suggests that a hybrid use of atomistic fragment memory and database memory in structural predictions may well be optimal for many practical applications.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
7. Affordable and Clean Energy
(OpenAlex)
Sources: ORCID, Crossref, NC State University Libraries
Added: April 5, 2023
2014 journal article
Order and disorder control the functional rearrangement of influenza hemagglutinin
Proceedings of the National Academy of Sciences, 111(33), 12049–12054.
Contributors: * , N. Eddy*, J. Noel *, P. Whitford *, Q. Wang *, J. Ma *, J. Onuchic *
MeSH headings : Hemagglutinin Glycoproteins, Influenza Virus / chemistry; Molecular Dynamics Simulation
TL;DR:
This study reiterates the roles that cracking and disorder can play in functional molecular motions, in contrast to the downhill mechanical interpretations of the “spring-loaded” model proposed for the HA2 conformational transition.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(OpenAlex)
Sources: ORCID, Crossref, NC State University Libraries
Added: April 5, 2023
2010 journal article
Measurement method of logical gate in bulk spin quantum computer
Wuhan Ligong Daxue Xuebao/Journal of Wuhan University of Technology, 32(15), 142–145.
Source: ORCID
Added: April 5, 2023
2010 journal article
Subspace quantum process tomography via nuclear magnetic resonance
Acta Physica Sinica, 59(10), 6837.
Sources: Crossref, NC State University Libraries
Added: April 7, 2023
Employment
Updated: July 20th, 2023 10:51
2023 - present
North Carolina State University Raleigh, North Carolina, US
Assistant Professor
Physics
2018 - 2023
Massachusetts Institute of Technology Cambridge, MA, US
Postdoctoral Associate
Chemistry
2018 - 2018
Rice University Houston, TX, US
Postdoctoral Researcher
Center for Theoretical Biological Physics
Education
Updated: February 11th, 2018 23:45
2011 - present
Rice University Houston, TX, US
Doctor
Physics and Astronomy
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