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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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Lessons learned from comparing molecular dynamics engines on the SAMPL5 dataset

Journal of computer-aided molecular design, 2017-01, Vol.31 (1), p.147-161

2017

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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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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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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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Calculation of chemical shift anisotropy in proteins

Journal of biomolecular NMR, 2011-11, Vol.51 (3), p.303-312

2011

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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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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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Energetic selection of topology in ferredoxins

PLoS computational biology, 2012-04, Vol.8 (4), p.e1002463-e1002463

2012

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Using quantum chemistry to estimate chemical shifts in biomolecules

Biophysical chemistry, 2020-12, Vol.267, p.106476-106476, Article 106476

Case, David A.

2020

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Revealing Accessibility of Cryptic Protein Binding Sites within the Functional Collagen Fibril

Biomolecules (Basel, Switzerland), 2017-11, Vol.7 (4), p.76

2017

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Molecular dynamics analysis of a flexible loop at the binding interface of the SARS‐CoV‐2 spike protein receptor‐binding domain

Proteins, structure, function, and bioinformatics, 2022-05, Vol.90 (5), p.1044-1053

2022

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Chemical shifts in biomolecules

Current opinion in structural biology, 2013-04, Vol.23 (2), p.172-176

Case, David A

2013

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Change in protein flexibility upon complex formation: Analysis of Ras-Raf using molecular dynamics and a molecular framework approach

Proteins, structure, function, and bioinformatics, 2004-08, Vol.56 (2), p.322-337

2004

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Exploring protein native states and large-scale conformational changes with a modified generalized born model

Proteins, structure, function, and bioinformatics, 2004-05, Vol.55 (2), p.383-394

2004

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Dynamic Water-Mediated Hydrogen Bonding in a Collagen Model Peptide

Biochemistry (Easton), 2015-10, Vol.54 (39), p.6029-6037

2015

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Atomistic Simulations of Heme Dissociation Pathways in Human Methemoglobins Reveal Hidden Intermediates

Biochemistry (Easton), 2020-10, Vol.59 (42), p.4093-4107

2020

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Dynamics of the [4Fe-4S] Cluster in Pyrococcus furiosus D14C Ferredoxin via Nuclear Resonance Vibrational and Resonance Raman Spectroscopies, Force Field Simulations, and Density Functional Theory Calculations

Biochemistry (Easton), 2011-06, Vol.50 (23), p.5220-5235

2011

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μABC: a systematic microsecond molecular dynamics study of tetranucleotide sequence effects in B-DNA

Nucleic acids research, 2014-10, Vol.42 (19), p.12272-12283

2014

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NGLview-interactive molecular graphics for Jupyter notebooks

Parmbsc1: a refined force field for DNA simulations

Lessons learned from comparing molecular dynamics engines on the SAMPL5 dataset

Automatic atom type and bond type perception in molecular mechanical calculations

Twenty-five years of nucleic acid simulations

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

Molecular dynamics simulation of triclinic lysozyme in a crystal lattice

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

Calculation of chemical shift anisotropy in proteins

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

Structural fidelity and NMR relaxation analysis in a prototype RNA hairpin

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

Energetic selection of topology in ferredoxins

Using quantum chemistry to estimate chemical shifts in biomolecules

Revealing Accessibility of Cryptic Protein Binding Sites within the Functional Collagen Fibril

Molecular dynamics analysis of a flexible loop at the binding interface of the SARS‐CoV‐2 spike protein receptor‐binding domain

Chemical shifts in biomolecules

Change in protein flexibility upon complex formation: Analysis of Ras-Raf using molecular dynamics and a molecular framework approach

Exploring protein native states and large-scale conformational changes with a modified generalized born model

Dynamic Water-Mediated Hydrogen Bonding in a Collagen Model Peptide

Atomistic Simulations of Heme Dissociation Pathways in Human Methemoglobins Reveal Hidden Intermediates

Dynamics of the [4Fe-4S] Cluster in Pyrococcus furiosus D14C Ferredoxin via Nuclear Resonance Vibrational and Resonance Raman Spectroscopies, Force Field Simulations, and Density Functional Theory Calculations

μABC: a systematic microsecond molecular dynamics study of tetranucleotide sequence effects in B-DNA

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