Celeste Sagui

Works (67)

Updated: March 2nd, 2024 17:00

2023 article

Conformationally Restricted Glycopeptide Backbone Inhibits Gas-Phase H/D Scrambling between Glycan and Peptide Moieties

Code, C., Qiu, D., Solov'yov, I. A., Lee, J.-G., Shin, H.-C., Roland, C., … Jorgensen, T. J. D. (2023, October 26). JOURNAL OF THE AMERICAN CHEMICAL SOCIETY.

co-author countries: Germany 🇩🇪 Denmark 🇩🇰 Korea (Republic of) 🇰🇷 United States of America 🇺🇸
Source: Web Of Science
Added: November 20, 2023

2023 journal article

Frustration Between Preferred States of Complementary Trinucleotide Repeat DNA Hairpins Anticorrelates with Expansion Disease Propensity

JOURNAL OF MOLECULAR BIOLOGY, 435(10).

By: P. Xu n, J. Zhang n, F. Pan n, C. Mahn n, C. Roland n, C. Sagui n, K. Weninger n

co-author countries: United States of America 🇺🇸
author keywords: single molecule FRET; hairpin slippage; molecular dynamics; kinetics; trinucleotide interrupts; Huntington's disease
MeSH headings : Humans; DNA / genetics; DNA / chemistry; DNA, Complementary; Nucleic Acid Conformation; Trinucleotide Repeat Expansion / genetics; Trinucleotide Repeats; Neurodegenerative Diseases / genetics
Sources: Web Of Science, ORCID
Added: May 22, 2023

2023 journal article

Pathologic polyglutamine aggregation begins with a self-poisoning polymer crystal

ELIFE, 12.

By: T. Kandola*, S. Venkatesan*, J. Zhang n, B. Lerbakken*, A. Von Schulze*, J. Blanck*, J. Wu*, J. Unruh* ...

co-author countries: United Kingdom of Great Britain and Northern Ireland 🇬🇧 United States of America 🇺🇸
author keywords: amyloid; phase separation; Huntington's disease; polyglutamine; aging; S. cerevisiae
Source: Web Of Science
Added: February 19, 2024

2023 article

Structure and Dynamics of DNA and RNA Double Helices Formed by d(CTG), d(GTC), r(CUG), and r(GUC) Trinucleotide Repeats and Associated DNA-RNA Hybrids

Fakharzadeh, A., Qu, J., Pan, F., Sagui, C., & Roland, C. (2023, September 8). JOURNAL OF PHYSICAL CHEMISTRY B.

By: A. Fakharzadeh n, J. Qu n, F. Pan*, C. Sagui n & C. Roland n

co-author countries: United States of America 🇺🇸
Source: Web Of Science
Added: October 10, 2023

2023 journal article

Unpolarized laser method for infrared spectrum calculation of amide I C=O bonds in proteins using molecular dynamics simulation

COMPUTERS IN BIOLOGY AND MEDICINE, 159.

co-author countries: France 🇫🇷 United States of America 🇺🇸
author keywords: IR spectra; Amide I; Radiation absorption; External electric field; MD simulation
MeSH headings : Molecular Dynamics Simulation; Amides / chemistry; Spectrophotometry, Infrared / methods; Proteins / chemistry; Peptides / chemistry; Hydrogen Bonding
Source: Web Of Science
Added: May 30, 2023

2022 article

Novel eGZ-motif formed by regularly extruded guanine bases in a left-handed Z-DNA helix as a major motif behind CGG trinucleotide repeats

Fakharzadeh, A., Zhang, J., Roland, C., & Sagui, C. (2022, May 10). NUCLEIC ACIDS RESEARCH.

By: A. Fakharzadeh n, J. Zhang n, C. Roland n & C. Sagui n

co-author countries: United States of America 🇺🇸
MeSH headings : Base Pairing; DNA / chemistry; DNA / genetics; DNA, Z-Form; Guanine / chemistry; Nucleic Acid Conformation; Trinucleotide Repeats / genetics
Source: Web Of Science
Added: May 23, 2022

2022 journal article

RNA as a Major-Groove Ligand: RNA-RNA and RNA-DNA Triplexes Formed by GAA and UUC or TTC Sequences

ACS OMEGA, 7(43), 38728–38743.

By: J. Zhang n, A. Fakharzadeh n, C. Roland n & C. Sagui n

co-author countries: United States of America 🇺🇸
Source: Web Of Science
Added: November 21, 2022

2021 journal article

Construction of DNA/RNA Triplex Helices Based on GAA/TTC Trinucleotide Repeats

BIO-PROTOCOL, 11(18).

By: J. Zhang*, A. Fakharzadeh, F. Pan, C. Roland* & C. Sagui*

author keywords: DNA/RNA; Triplex helices; Molecular dynamics; Trinucleotide repeats
Source: Web Of Science
Added: October 26, 2021

2021 review

Molecular conformations and dynamics of nucleotide repeats associated with neurodegenerative diseases: double helices and CAG hairpin loops

[Review of ]. COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL, 19, 2819–2832.

By: F. Pan*, Y. Zhang*, P. Xu n, V. Man n, C. Roland n, K. Weninger n, C. Sagui n

co-author countries: United States of America 🇺🇸
author keywords: Trinucleotide hexanucleotide repeats; CAG; GAC; CTG; CUG; CCG; GGC; GGGGCC; GGCCCC; Hairpin loops; smFRET; Molecular dynamics
Sources: Web Of Science, ORCID
Added: August 30, 2021

2021 journal article

The F19W mutation reduces the binding affinity of the transmembrane A beta(11-40) trimer to the membrane bilayer

RSC ADVANCES, 11(5), 2664–2676.

By: T. Tran*, F. Pan*, L. Tran*, C. Roland n & C. Sagui n

co-author countries: United Kingdom of Great Britain and Northern Ireland 🇬🇧 United States of America 🇺🇸 Viet Nam 🇻🇳
Source: Web Of Science
Added: February 15, 2021

2020 journal article

Atypical structures of GAA/TTC trinucleotide repeats underlying Friedreich's ataxia: DNA triplexes and RNA/DNA hybrids

NUCLEIC ACIDS RESEARCH, 48(17), 9899–9917.

By: J. Zhang n, A. Fakharzadeh n, F. Pan n, C. Roland n & C. Sagui n

co-author countries: United States of America 🇺🇸
MeSH headings : DNA / chemistry; Friedreich Ataxia / genetics; Humans; Nucleic Acid Heteroduplexes / chemistry; R-Loop Structures; Trinucleotide Repeats
Source: Web Of Science
Added: January 4, 2021

2018 journal article

E-motif formed by extrahelical cytosine bases in DNA homoduplexes of trinucleotide and hexanucleotide repeats

NUCLEIC ACIDS RESEARCH, 46(2), 942–955.

By: F. Pan n, Y. Zhang n, V. Man n, C. Roland n & C. Sagui n

co-author countries: United States of America 🇺🇸
MeSH headings : Base Pairing; Base Sequence; Cytosine / chemistry; DNA / chemistry; DNA / genetics; Guanine / chemistry; Hydrogen Bonding; Microsatellite Repeats / genetics; Molecular Dynamics Simulation; Nucleic Acid Conformation; Nucleotide Motifs; Trinucleotide Repeats / genetics
Source: Web Of Science
Added: August 6, 2018

2018 journal article

Structural and Dynamical Characterization of DNA and RNA Quadruplexes Obtained from the GGGGCC and GGGCCT Hexanucleotide Repeats Associated with C9FTD/ALS and SCA36 Diseases

ACS CHEMICAL NEUROSCIENCE, 9(5), 1104–1117.

By: Y. Zhang n, C. Roland n & C. Sagui n

co-author countries: United States of America 🇺🇸
author keywords: Quadruplex; hexanucleotide repeats; DNA; RNA; G-quartets
MeSH headings : Amyotrophic Lateral Sclerosis / genetics; C9orf72 Protein / genetics; Circular Dichroism / methods; DNA / genetics; DNA Repeat Expansion / genetics; G-Quadruplexes / radiation effects; Humans; Models, Molecular; Nerve Tissue Proteins / genetics; Nuclear Proteins; Nucleic Acid Conformation / drug effects; RNA / genetics
Source: Web Of Science
Added: August 6, 2018

2018 journal article

Structure and Dynamics of DNA and RNA Double Helices Obtained from the CCG and GGC Trinucleotide Repeats

JOURNAL OF PHYSICAL CHEMISTRY B, 122(16), 4491–4512.

By: F. Pan n, V. Man n, C. Roland n & C. Sagui n

co-author countries: United States of America 🇺🇸
MeSH headings : DNA / chemistry; Molecular Dynamics Simulation; Nucleic Acid Conformation; RNA / chemistry; Trinucleotide Repeats
Source: Web Of Science
Added: August 6, 2018

2017 journal article

Structure and Dynamics of DNA and RNA Double Helices Obtained from the GGGGCC and CCCCGG Hexanucleotide Repeats That Are the Hallmark of C9FTD/ALS Diseases

ACS CHEMICAL NEUROSCIENCE, 8(3), 578–591.

By: Y. Zhang n, C. Roland n & C. Sagui n

co-author countries: United States of America 🇺🇸
author keywords: Nucleotide repeat disorder; hexanucleotide repeat; C-C and G-G mismatches; C9FTD; ALS; e-motif
MeSH headings : Amyotrophic Lateral Sclerosis / genetics; Base Pair Mismatch; C9orf72 Protein; Chromosomes, Human, Pair 9 / genetics; DNA / chemistry; DNA Repeat Expansion; Frontotemporal Dementia / genetics; Humans; Models, Molecular; Nucleic Acid Conformation; Principal Component Analysis; Proteins / genetics; RNA / chemistry; Repetitive Sequences, Nucleic Acid / genetics
Source: Web Of Science
Added: August 6, 2018

2017 journal article

Structure and Dynamics of DNA and RNA Double Helices of CAG and GAC Trinucleotide Repeats

BIOPHYSICAL JOURNAL, 113(1), 19–36.

By: F. Pan n, V. Man n, C. Roland n & C. Sagui n

co-author countries: United States of America 🇺🇸
MeSH headings : Cations / chemistry; DNA / chemistry; Hydrogen-Ion Concentration; Molecular Dynamics Simulation; Nucleic Acid Conformation; Principal Component Analysis; RNA / chemistry; Sodium / chemistry; Trinucleotide Repeats
Source: Web Of Science
Added: August 6, 2018

2016 journal article

Amyloid Properties of Asparagine and Glutamine in Prion-like Proteins

ACS Chemical Neuroscience, 7(5), 576–587.

By: Y. Zhang n, V. Man n, C. Roland n & C. Sagui n

co-author countries: United States of America 🇺🇸
author keywords: Prion; amyloid; protein aggregation; intrinsically disordered proteins; polyglutamine disease
MeSH headings : Amyloidogenic Proteins / chemistry; Amyloidogenic Proteins / metabolism; Asparagine / chemistry; Asparagine / metabolism; GPI-Linked Proteins / chemistry; GPI-Linked Proteins / metabolism; Glutamine / chemistry; Glutamine / metabolism; Molecular Dynamics Simulation; Prion Proteins / chemistry; Prion Proteins / metabolism; Prions / chemistry; Prions / metabolism
Sources: Web Of Science, Crossref
Added: August 6, 2018

2016 journal article

Comparative melting and healing of B-DNA and Z-DNA by an infrared laser pulse

JOURNAL OF CHEMICAL PHYSICS, 144(14).

By: V. Man n, F. Pan n, C. Sagui n & C. Roland n

co-author countries: United States of America 🇺🇸
MeSH headings : DNA, B-Form / chemistry; DNA, Z-Form / chemistry; Lasers; Molecular Dynamics Simulation; Thermodynamics
Source: Web Of Science
Added: August 6, 2018

2016 journal article

Contrasting Roles of Asparagine and Glutamine in the Aggregation of Prion-Like Proteins

Biophysical Journal, 110(3), 214a–215a.

co-author countries: United States of America 🇺🇸
Source: Crossref
Added: February 24, 2020

2016 journal article

Picosecond infrared laser-induced all-atom nonequilibrium molecular dynamics simulation of dissociation of viruses

PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 18(17), 11951–11958.

co-author countries: France 🇫🇷 Poland 🇵🇱 United States of America 🇺🇸 Viet Nam 🇻🇳
MeSH headings : Biocompatible Materials / chemistry; Humans; Infrared Rays; Lasers; Molecular Dynamics Simulation; Poliomyelitis / virology; Poliovirus / chemistry; Poliovirus / radiation effects; Virion / chemistry; Virion / radiation effects
Source: Web Of Science
Added: August 6, 2018

2016 journal article

Stability and Ion Distributions Around Left- and Right-Handed DNA and RNA Duplexes: A Comparative Study

Biophysical Journal, 110(3), 407a.

By: F. Pan n, V. Man n, C. Roland n & C. Sagui n

co-author countries: United States of America 🇺🇸
Source: Crossref
Added: February 24, 2020

2016 journal article

Structural Determinants of Polyqlutamine Protofibrils and Crystallites

Biophysical Journal, 110(3), 215a.

By: V. Man n, C. Roland n & C. Sagui n

co-author countries: United States of America 🇺🇸
Source: Crossref
Added: February 24, 2020

2015 article

Calculating transition and reaction rates with nonequilibrium work measurements

XXVI IUPAP CONFERENCE ON COMPUTATIONAL PHYSICS (CCP2014), Vol. 640.

By: M. Moradi*, C. Sagui n & C. Roland n

co-author countries: United States of America 🇺🇸
Source: Web Of Science
Added: August 6, 2018

2015 journal article

Picosecond dissociation of amyloid fibrils with infrared laser: A nonequilibrium simulation study

JOURNAL OF CHEMICAL PHYSICS, 143(15).

co-author countries: France 🇫🇷 Poland 🇵🇱 United States of America 🇺🇸 Viet Nam 🇻🇳
MeSH headings : Amyloid / chemistry; Amyloid / radiation effects; Infrared Rays; Lasers; Molecular Dynamics Simulation; Time Factors
Source: Web Of Science
Added: August 6, 2018

2015 journal article

Picosecond melting of peptide nanotubes using an infrared laser: a nonequilibrium simulation study

PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 17(41), 27275–27280.

By: M. Viet n, P. Truong*, P. Derreumaux*, M. Li*, C. Roland n, C. Sagui n, P. Nguyen*

co-author countries: France 🇫🇷 Poland 🇵🇱 United States of America 🇺🇸 Viet Nam 🇻🇳
MeSH headings : Dipeptides; Freezing; Infrared Rays; Lasers; Molecular Dynamics Simulation; Nanotechnology; Nanotubes / chemistry; Peptides / chemistry; Phenylalanine / analogs & derivatives; Phenylalanine / chemistry; Time Factors
Source: Web Of Science
Added: August 6, 2018

2015 journal article

Secondary structure assignment for conformationally irregular peptides: Comparison between DSSP, STRIDE and KAKSI

JOURNAL OF MOLECULAR GRAPHICS & MODELLING, 55, 72–84.

By: Y. Zhang n & C. Sagui n

co-author countries: United States of America 🇺🇸
author keywords: Residual transient secondary structure; Intrinsically disordered proteins; gp41; Asparagine
MeSH headings : Amino Acid Sequence; Amino Acids / chemistry; Computer Simulation; Hydrogen Bonding; Peptides / chemistry; Protein Structure, Secondary; Software
Source: Web Of Science
Added: August 6, 2018

2015 journal article

Structural Determinants of Polyglutamine Protofibrils and Crystallites

ACS CHEMICAL NEUROSCIENCE, 6(4), 632–645.

By: V. Man n, C. Roland n & C. Sagui n

co-author countries: United States of America 🇺🇸
author keywords: Aggregation; amyloid fibrils; parallel sheets; antiparallel sheets; polyglutamine diseases; steric zippers
MeSH headings : Amyloid / chemistry; Amyloid / genetics; Hydrogen Bonding; Models, Chemical; Molecular Dynamics Simulation; Peptides / chemistry; Protein Conformation; Protein Stability; Time Factors
Source: Web Of Science
Added: August 6, 2018

2015 article

The Adaptively Biased Molecular Dynamics method revisited: New capabilities and an application

XXVI IUPAP CONFERENCE ON COMPUTATIONAL PHYSICS (CCP2014), Vol. 640.

By: M. Moradi*, V. Babin n, C. Roland n & C. Sagui n

co-author countries: United States of America 🇺🇸
Source: Web Of Science
Added: August 6, 2018

2014 review

Classical Electrostatics for Biomolecular Simulations

[Review of ]. CHEMICAL REVIEWS, 114(1), 779–814.

co-author countries: Canada 🇨🇦 United States of America 🇺🇸
MeSH headings : Molecular Dynamics Simulation; Monte Carlo Method; Proteins / chemistry; Proteins / metabolism; Quantum Theory; Static Electricity
Source: Web Of Science
Added: August 6, 2018

2014 journal article

Correction to Classical Electrostatics for Biomolecular Simulations

Chemical Reviews, 114(9), 5116–5116.

By: G. Cisneros, M. Karttunen, P. Ren & C. Sagui*

Source: Crossref
Added: February 24, 2020

2014 journal article

Investigating rare events with nonequilibrium work measurements. I. Nonequilibrium transition path probabilities

The Journal of Chemical Physics, 140(3), 034114.

By: M. Moradi n, C. Sagui n & C. Roland n

co-author countries: United States of America 🇺🇸
MeSH headings : Cluster Analysis; Computer Simulation; Dimerization; Models, Chemical; Probability; Proline / chemistry; Thermodynamics
Source: Crossref
Added: February 24, 2020

2014 article

Investigating rare events with nonequilibrium work measurements. I. Nonequilibrium transition path probabilities (vol 140, 034114, 2014)

Moradi, M., Sagui, C., & Roland, C. (2014, February 14). JOURNAL OF CHEMICAL PHYSICS, Vol. 140.

By: M. Moradi n, C. Sagui n & C. Roland n

co-author countries: United States of America 🇺🇸
Source: Web Of Science
Added: August 6, 2018

2014 journal article

Investigating rare events with nonequilibrium work measurements. II. Transition and reaction rates

The Journal of Chemical Physics, 140(3), 034115.

By: M. Moradi n, C. Sagui n & C. Roland n

co-author countries: United States of America 🇺🇸
MeSH headings : Computer Simulation; Dipeptides / chemistry; Models, Chemical; Molecular Dynamics Simulation; Probability; Thermodynamics
Source: Crossref
Added: February 24, 2020

2014 article

Investigating rare events with nonequilibrium work measurements. II. Transition and reaction rates (vol 140, 034115, 2014)

Moradi, M., Sagui, C., & Roland, C. (2014, February 14). JOURNAL OF CHEMICAL PHYSICS, Vol. 140.

By: M. Moradi n, C. Sagui n & C. Roland n

co-author countries: United States of America 🇺🇸
Source: Web Of Science
Added: August 6, 2018

2014 journal article

Ion distributions around left- and right-handed DNA and RNA duplexes: a comparative study

NUCLEIC ACIDS RESEARCH, 42(22), 13981–13996.

By: F. Pan n, C. Roland n & C. Sagui n

co-author countries: United States of America 🇺🇸
MeSH headings : Cations / chemistry; Cations, Divalent / chemistry; Cations, Monovalent / chemistry; Chlorides / chemistry; DNA, A-Form / chemistry; DNA, B-Form / chemistry; DNA, Z-Form / chemistry; Magnesium / chemistry; Molecular Dynamics Simulation; Osmolar Concentration; Potassium / chemistry; RNA, Double-Stranded / chemistry; Sodium / chemistry
Source: Web Of Science
Added: August 6, 2018

2014 journal article

The gp41(659-671) HIV-1 Antibody Epitope: A Structurally Challenging Small Peptide

JOURNAL OF PHYSICAL CHEMISTRY B, 118(1), 69–80.

By: Y. Zhang n & C. Sagui n

co-author countries: United States of America 🇺🇸
MeSH headings : Epitopes / chemistry; Epitopes / immunology; HIV Antibodies / immunology; HIV Antigens / chemistry; HIV Antigens / immunology; HIV Envelope Protein gp41 / chemistry; HIV Envelope Protein gp41 / immunology; HIV-1 / chemistry; HIV-1 / immunology; Molecular Dynamics Simulation; Peptide Fragments / chemistry; Peptide Fragments / immunology; Protein Conformation
Source: Web Of Science
Added: August 6, 2018

2013 journal article

Binding Polymorphism in the DNA Bound State of the Pdx1 Homeodomain

PLOS COMPUTATIONAL BIOLOGY, 9(8).

By: V. Babin n, D. Wang n, R. Rose n & C. Sagui n

co-author countries: United States of America 🇺🇸
Sources: Web Of Science, ORCID
Added: August 6, 2018

2013 journal article

Reaction path ensemble of the B-Z-DNA transition: a comprehensive atomistic study

NUCLEIC ACIDS RESEARCH, 41(1), 33–43.

By: M. Moradi n, V. Babin n, C. Roland n & C. Sagui n

co-author countries: United States of America 🇺🇸
MeSH headings : Base Pairing; DNA, B-Form / chemistry; DNA, Z-Form / chemistry; Models, Molecular; Molecular Dynamics Simulation
Source: Web Of Science
Added: August 6, 2018

2011 journal article

A Statistical Analysis of the PPII Propensity of Amino Acid Guests in Proline-Rich Peptides

Biophysical Journal, 100(4), 1083–1093.

By: M. Moradi n, V. Babin n, C. Sagui n & C. Roland n

co-author countries: United States of America 🇺🇸
MeSH headings : Models, Statistical; Odds Ratio; Peptides / chemistry; Proline / chemistry; Protein Structure, Secondary
Sources: Web Of Science, Crossref
Added: August 6, 2018

2011 journal article

Calculating relative transition rates with driven nonequilibrium simulations

CHEMICAL PHYSICS LETTERS, 518, 109–113.

By: M. Moradi n, C. Sagui n & C. Roland n

co-author countries: United States of America 🇺🇸
Source: Web Of Science
Added: August 6, 2018

2011 journal article

PPII Propensity of Multiple-Guest Amino Acids in a Proline-Rich Environment

The Journal of Physical Chemistry B, 115(26), 8645–8656.

By: M. Moradi n, V. Babin n, C. Sagui n & C. Roland n

co-author countries: United States of America 🇺🇸
MeSH headings : Amino Acid Sequence; Amino Acids / chemistry; Molecular Structure; Peptides / chemistry; Peptides / genetics; Protein Conformation
Sources: Crossref, Web Of Science
Added: August 6, 2018

2011 journal article

The α-sheet: A missing-in-action secondary structure?

Proteins: Structure, Function, and Bioinformatics, 79(3), 937–946.

By: V. Babin n, C. Roland n & C. Sagui n

co-author countries: United States of America 🇺🇸
author keywords: protein structure; molecular mechanics; amyloid; polyglutamine; protein aggregation
MeSH headings : Molecular Dynamics Simulation; Peptides / chemistry; Protein Structure, Secondary
Sources: Web Of Science, Crossref
Added: August 6, 2018

2010 journal article

A classical molecular dynamics investigation of the free energy and structure of short polyproline conformers

JOURNAL OF CHEMICAL PHYSICS, 133(12).

By: M. Moradi n, V. Babin n, C. Roland n & C. Sagui n

co-author countries: United States of America 🇺🇸
MeSH headings : Molecular Dynamics Simulation; Peptides / chemistry; Phase Transition; Protein Conformation; Thermodynamics
Source: Web Of Science
Added: August 6, 2018

2010 journal article

Conformational free energies of methyl-alpha-L-iduronic and methyl-beta-D-glucuronic acids in water

JOURNAL OF CHEMICAL PHYSICS, 132(10).

By: V. Babin n & C. Sagui n

co-author countries: United States of America 🇺🇸
author keywords: free energy; molecular dynamics method; organic compounds; simulation
MeSH headings : Algorithms; Carbohydrate Sequence; Computer Simulation; Glucuronic Acid / chemistry; Iduronic Acid / chemistry; Molecular Conformation; Molecular Sequence Data; Thermodynamics; Water / chemistry
Source: Web Of Science
Added: August 6, 2018

2010 journal article

Dimerization free energy of vancomycin-group antibiotics and the cooperative effect: A density functional approach

International Journal of Quantum Chemistry, 110(15), 2894–2902.

By: J. Lee n, C. Sagui n & C. Roland n

co-author countries: United States of America 🇺🇸
author keywords: vancomycin; chloro-eremomycin; cooperative effect; ab initio QM; divide- and conquer; free energy
Sources: Crossref, NC State University Libraries
Added: August 6, 2018

2010 journal article

Free energy and structure of polyproline peptides: An ab initio and classical molecular dynamics investigation

International Journal of Quantum Chemistry, 110(15), 2865–2879.

By: M. Moradi n, J. Lee n, V. Babin n, C. Roland n & C. Sagui n

co-author countries: United States of America 🇺🇸
author keywords: polyproline; free energy; PPII
Sources: Crossref, NC State University Libraries
Added: August 6, 2018

2009 article

Adaptively Biased Molecular Dynamics: An Umbrella Sampling Method With a Time-Dependent Potential

Babin, V., Karpusenka, V., Moradi, M., Roland, C., & Sagui, C. (2009, December). INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Vol. 109, pp. 3666–3678.

By: V. Babin n, V. Karpusenka n, M. Moradi n, C. Roland n & C. Sagui n

co-author countries: United States of America 🇺🇸
author keywords: free energy; nonequilibrium; simulation
Source: Web Of Science
Added: August 6, 2018

2009 journal article

Conformations and free energy landscapes of polyproline peptides

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 106(49), 20746–20751.

By: M. Moradi n, V. Babin n, C. Roland n, T. Darden & C. Sagui n

co-author countries: United States of America 🇺🇸
author keywords: cis-trans isomerization; left-handed helix; molecular dynamics; PPI; PPII
MeSH headings : Peptides / chemistry; Protein Conformation; Thermodynamics
Source: Web Of Science
Added: August 6, 2018

2008 journal article

Adaptively biased molecular dynamics for free energy calculations

Journal of Chemical Physics, 128(13).

By: V. Babin n, C. Roland n & C. Sagui n

co-author countries: United States of America 🇺🇸
Source: NC State University Libraries
Added: August 6, 2018

2008 journal article

Amino acid adsorption on the Si(100) surface: The case of glycine

JOURNAL OF PHYSICAL CHEMISTRY C, 112(7), 2640–2648.

By: X. Luo n, G. Qian n, C. Sagui n & C. Roland n

co-author countries: United States of America 🇺🇸
Source: Web Of Science
Added: August 6, 2018

2008 article

Electrostatics in biomolecular simulations: Where are we now and where are we heading?

COMPUTATIONAL MODELING OF MEMBRANE BILAYERS, Vol. 60, pp. 49–89.

co-author countries: Canada 🇨🇦 Denmark 🇩🇰 Finland 🇫🇮 United States of America 🇺🇸
Source: Web Of Science
Added: August 6, 2018

2007 journal article

Theoretical investigation of the interaction of glycine with diamond C(100) and C(111) (2x1) surfaces

JOURNAL OF PHYSICAL CHEMISTRY C, 111(34), 12760–12767.

By: K. Odbadrakh n, X. Luo n, J. Lee n, C. Sagui n & C. Roland n

co-author countries: United States of America 🇺🇸
Source: Web Of Science
Added: August 6, 2018

2006 journal article

Deprotonation of solvated formic acid: Car-Parrinello and metadynamics simulations

JOURNAL OF PHYSICAL CHEMISTRY B, 110(5), 2325–2331.

By: J. Lee n, E. Asciutto n, V. Babin n, C. Sagui n, T. Darden n & C. Roland n

co-author countries: United States of America 🇺🇸
MeSH headings : Computational Biology; Computer Simulation; Formates / chemistry; Hydrogen / chemistry; Models, Molecular; Oxygen / chemistry; Protons; Solvents / chemistry; Thermodynamics; Time Factors
Source: Web Of Science
Added: August 6, 2018

2006 journal article

Molecular dynamics simulations of DNA with polarizable force fields: Convergence of an ideal B-DNA structure to the crystallographic structure

JOURNAL OF PHYSICAL CHEMISTRY B, 110(23), 11571–11581.

By: V. Babin n, J. Baucom n, T. Darden n & C. Sagui n

co-author countries: United States of America 🇺🇸
MeSH headings : Base Sequence; Crystallography; DNA / chemistry; Nucleic Acid Conformation
Source: Web Of Science
Added: August 6, 2018

2006 journal article

Molecular dynamics simulations of polarizable DNA in crystal environment

International Journal of Quantum Chemistry, 106(15), 3260–3269.

By: V. Babin n, J. Baucom n, T. Darden* & C. Sagui n

co-author countries: United States of America 🇺🇸
author keywords: DNA; electrostatics; polarizable; crystal
Sources: Crossref, Web Of Science
Added: August 6, 2018

2006 journal article

The free energy landscape of small peptides as obtained from metadynamics with umbrella sampling corrections

JOURNAL OF CHEMICAL PHYSICS, 125(20).

By: V. Babin n, C. Roland n, T. Darden* & C. Sagui n

co-author countries: United States of America 🇺🇸
MeSH headings : Algorithms; Computer Simulation; Energy Transfer; Kinetics; Models, Chemical; Models, Molecular; Peptides / chemistry; Protein Conformation
Source: Web Of Science
Added: August 6, 2018

2005 journal article

Exploring intramolecular reactions in complex systems with metadynamics: The case of the malonate anions

JOURNAL OF PHYSICAL CHEMISTRY A, 109(34), 7682–7687.

By: E. Asciutto n & C. Sagui n

co-author countries: United States of America 🇺🇸
Source: Web Of Science
Added: August 6, 2018

2005 journal article

New and exotic self-organized patterns for modulated nanoscale systems

NANO LETTERS, 5(2), 389–395.

By: C. Sagui n, E. Asciutto n & C. Roland n

co-author countries: United States of America 🇺🇸
MeSH headings : Computer Simulation; Crystallization / methods; Models, Chemical; Models, Molecular; Molecular Conformation; Nanostructures / analysis; Nanostructures / chemistry; Nanostructures / ultrastructure; Nanotechnology / methods; Phase Transition
Source: Web Of Science
Added: August 6, 2018

2005 journal article

Quantum simulations of the structure and binding of glycopeptide antibiotic aglycons to cell wall analogues

JOURNAL OF PHYSICAL CHEMISTRY B, 109(43), 20588–20596.

By: J. Lee n, C. Sagui n & C. Roland n

co-author countries: United States of America 🇺🇸
MeSH headings : Anti-Bacterial Agents / chemistry; Anti-Bacterial Agents / metabolism; Binding Sites; Cell Wall / metabolism; Computer Simulation; Dipeptides; Drug Resistance, Bacterial; Glycopeptides / chemistry; Glycopeptides / metabolism; Models, Molecular; Protein Conformation; Quantum Theory; Staphylococcus aureus / drug effects; Vancomycin / chemistry; Vancomycin / pharmacology
Source: Web Of Science
Added: August 6, 2018

2005 journal article

Self-assembled patterns and strain-induced instabilities for modulated systems

PHYSICAL REVIEW E, 72(2).

By: E. Asciutto n, C. Roland n & C. Sagui n

co-author countries: United States of America 🇺🇸
Source: Web Of Science
Added: August 6, 2018

2005 journal article

Surface solvation for an ion in a water cluster

JOURNAL OF CHEMICAL PHYSICS, 122(2).

By: D. Herce n, L. Perera*, T. Darden* & C. Sagui n

co-author countries: United States of America 🇺🇸
Source: Web Of Science
Added: August 6, 2018

2004 journal article

Ab initio calculation of electrostatic multipoles with Wannier functions for large-scale biomolecular simulations

JOURNAL OF CHEMICAL PHYSICS, 120(9), 4530–4544.

By: C. Sagui n, P. Pomorski n, T. Darden* & C. Roland n

co-author countries: United States of America 🇺🇸
MeSH headings : Algorithms; Biopolymers / chemistry; Computer Simulation; Electrochemistry / methods; Models, Chemical; Models, Molecular; Static Electricity
Source: Web Of Science
Added: August 6, 2018

2004 journal article

First principles investigation of vancomycin and teicoplanin binding to bacterial cell wall termini

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 126(27), 8384–8385.

By: J. Lee n, C. Sagui n & C. Roland n

co-author countries: United States of America 🇺🇸
MeSH headings : Alanine / analogs & derivatives; Alanine / metabolism; Anti-Bacterial Agents / metabolism; Anti-Bacterial Agents / pharmacology; Bacteria / drug effects; Bacteria / metabolism; Cell Wall / drug effects; Cell Wall / metabolism; Dipeptides / metabolism; Kinetics; Lactates / metabolism; Teicoplanin / metabolism; Teicoplanin / pharmacology; Thermodynamics; Vancomycin / metabolism; Vancomycin / pharmacology
Source: Web Of Science
Added: August 6, 2018

2004 journal article

Molecular dynamics simulations of the d(CCAACGTTGG)(2) decamer in crystal environment: Comparison of atomic point-charge, extra-point, and polarizable force fields

JOURNAL OF CHEMICAL PHYSICS, 121(14), 6998–7008.

By: J. Baucom n, T. Transue*, M. Fuentes-Cabrera n, J. Krahn*, T. Darden* & C. Sagui n

co-author countries: United States of America 🇺🇸
MeSH headings : Computer Simulation; Crystallization; Nucleic Acid Conformation; Oligodeoxyribonucleotides / chemistry; Sequence Analysis, DNA; Thermodynamics
Source: Web Of Science
Added: August 6, 2018

2004 journal article

Towards an accurate representation of electrostatics in classical force fields: Efficient implementation of multipolar interactions in biomolecular simulations

JOURNAL OF CHEMICAL PHYSICS, 120(1), 73–87.

By: C. Sagui n, L. Pedersen* & T. Darden*

co-author countries: United States of America 🇺🇸
MeSH headings : Algorithms; Computational Biology; Computer Simulation; Molecular Conformation; Static Electricity; Thermodynamics; Water / chemistry
Source: Web Of Science
Added: August 6, 2018

2003 journal article

Calculation of ionic charging free energies in simulation systems with atomic charges, dipoles, and quadrupoles

Journal of Chemical Physics, 119(15), 7621–7632.

By: H. Herce n, T. Darden* & C. Sagui n

co-author countries: United States of America 🇺🇸
Source: NC State University Libraries
Added: August 6, 2018

2001 journal article

Liquid-crystal phases of capped carbon nanotubes

PHYSICAL REVIEW B, 63(8).

By: A. Somoza*, C. Sagui n & C. Roland n

co-author countries: Spain 🇪🇸 United States of America 🇺🇸
Source: Web Of Science
Added: August 6, 2018

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