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Generalized Born Implicit Solvent Models for Biomolecules

Annual review of biophysics, 2019-05, Vol.48 (1), p.275-296

2019

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NGLview-interactive molecular graphics for Jupyter notebooks

Bioinformatics, 2018-04, Vol.34 (7), p.1241-1242

2018

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Parmbsc1: a refined force field for DNA simulations

Nature methods, 2016-01, Vol.13 (1), p.55-58

2016

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Diffuse X-ray scattering from correlated motions in a protein crystal

Nature communications, 2020-03, Vol.11 (1), p.1271-1271, Article 1271

2020

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Robust total X-ray scattering workflow to study correlated motion of proteins in crystals

Nature communications, 2023-03, Vol.14 (1), p.1228-1228, Article 1228

2023

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Automatic atom type and bond type perception in molecular mechanical calculations

Journal of molecular graphics & modelling, 2006-10, Vol.25 (2), p.247-260

2006

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Twenty-five years of nucleic acid simulations

Biopolymers, 2013-12, Vol.99 (12), p.969-977

2013

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Structure of the HIV-1 RNA packaging signal

Science (American Association for the Advancement of Science), 2015-05, Vol.348 (6237), p.917-921

2015

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An RNA excited conformational state at atomic resolution

Nature communications, 2023-12, Vol.14 (1), p.8432-8432, Article 8432

2023

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Structural basis for transcriptional start site control of HIV-1 RNA fate

Science (American Association for the Advancement of Science), 2020-04, Vol.368 (6489), p.413-417

2020

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DOCK 6: combining techniques to model RNA-small molecule complexes

RNA (Cambridge), 2009-06, Vol.15 (6), p.1219-1230

2009

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Molecular dynamics simulation of triclinic lysozyme in a crystal lattice

Protein science, 2016-01, Vol.25 (1), p.87-102

2016

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A molecular reconstruction approach to site-based 3D-RISM and comparison to GIST hydration thermodynamic maps in an enzyme active site

PloS one, 2019-07, Vol.14 (7), p.e0219473-e0219473

2019

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Propagated Perturbations from a Peripheral Mutation Show Interactions Supporting WW Domain Thermostability

Structure (London), 2018-11, Vol.26 (11), p.1474-1485.e5

2018

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A systematic molecular dynamics study of nearest-neighbor effects on base pair and base pair step conformations and fluctuations in B-DNA

Nucleic acids research, 2010-01, Vol.38 (1), p.299-313

2010

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Structure of the 30 kDa HIV-1 RNA Dimerization Signal by a Hybrid Cryo-EM, NMR, and Molecular Dynamics Approach

Structure (London), 2018-03, Vol.26 (3), p.490-498.e3

2018

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A quantitative model predicts how m6A reshapes the kinetic landscape of nucleic acid hybridization and conformational transitions

Nature communications, 2021-08, Vol.12 (1), p.5201-5201, Article 5201

2021

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Rescoring Docking Hit Lists for Model Cavity Sites: Predictions and Experimental Testing

Journal of molecular biology, 2008-03, Vol.377 (3), p.914-934

2008

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Structural fidelity and NMR relaxation analysis in a prototype RNA hairpin

RNA (Cambridge), 2015-05, Vol.21 (5), p.963-974

2015

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Colicin E1 opens its hinge to plug TolC

eLife, 2022-02, Vol.11

2022

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NMR Exchange Format: a unified and open standard for representation of NMR restraint data

Nature structural & molecular biology, 2015-06, Vol.22 (6), p.433-434

2015

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Influence of the coupling of interdomain and overall motions on NMR relaxation

Proceedings of the National Academy of Sciences - PNAS, 2009-07, Vol.106 (27), p.11016-11021

2009

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Refinement of RNA Structures Using Amber Force Fields

Crystals (Basel), 2021-07, Vol.11 (7), p.771

2021

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Toward a Chemical Mechanism of Proton Pumping by the B-Type Cytochrome c Oxidases: Application of Density Functional Theory to Cytochrome ba3 of Thermus thermophilus

Journal of the American Chemical Society, 2008-11, Vol.130 (45), p.15002-15021

2008

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Evaluating β-turn mimics as β-sheet folding nucleators

Proceedings of the National Academy of Sciences - PNAS, 2009-07, Vol.106 (27), p.11067-11072

2009

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Generalized Born Implicit Solvent Models for Biomolecules

NGLview-interactive molecular graphics for Jupyter notebooks

Parmbsc1: a refined force field for DNA simulations

Diffuse X-ray scattering from correlated motions in a protein crystal

Robust total X-ray scattering workflow to study correlated motion of proteins in crystals

Automatic atom type and bond type perception in molecular mechanical calculations

Twenty-five years of nucleic acid simulations

Structure of the HIV-1 RNA packaging signal

An RNA excited conformational state at atomic resolution

Structural basis for transcriptional start site control of HIV-1 RNA fate

DOCK 6: combining techniques to model RNA-small molecule complexes

Molecular dynamics simulation of triclinic lysozyme in a crystal lattice

A molecular reconstruction approach to site-based 3D-RISM and comparison to GIST hydration thermodynamic maps in an enzyme active site

Propagated Perturbations from a Peripheral Mutation Show Interactions Supporting WW Domain Thermostability

A systematic molecular dynamics study of nearest-neighbor effects on base pair and base pair step conformations and fluctuations in B-DNA

Structure of the 30 kDa HIV-1 RNA Dimerization Signal by a Hybrid Cryo-EM, NMR, and Molecular Dynamics Approach

A quantitative model predicts how m6A reshapes the kinetic landscape of nucleic acid hybridization and conformational transitions

Rescoring Docking Hit Lists for Model Cavity Sites: Predictions and Experimental Testing

Structural fidelity and NMR relaxation analysis in a prototype RNA hairpin

Colicin E1 opens its hinge to plug TolC

NMR Exchange Format: a unified and open standard for representation of NMR restraint data

Influence of the coupling of interdomain and overall motions on NMR relaxation

Refinement of RNA Structures Using Amber Force Fields

Toward a Chemical Mechanism of Proton Pumping by the B-Type Cytochrome c Oxidases: Application of Density Functional Theory to Cytochrome ba3 of Thermus thermophilus

Evaluating β-turn mimics as β-sheet folding nucleators

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