Ensembler: Enabling High-Throughput Molecular Simulations at the Superfamily Scale

The I-TASSER Suite: protein structure and function prediction

(2015) Jianyi Yang et al.   NATURE METHODS

A dynamically coupled allosteric network underlies binding cooperativity in Src kinase

(2015) Zachariah H. Foda et al.   Nature Communications

Markov state models of biomolecular conformational dynamics

(2014) John D Chodera et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

UniProt: a hub for protein information

(2014)   NUCLEIC ACIDS RESEARCH

Activation pathway of Src kinase reveals intermediate states as targets for drug design

(2014) Diwakar Shukla et al.   Nature Communications

Effects of Temperature Control Algorithms on Transport Properties and Kinetics in Molecular Dynamics Simulations

(2013) Joseph E. Basconi et al.   Journal of Chemical Theory and Computation

Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 2. Explicit Solvent Particle Mesh Ewald

(2013) Romelia Salomon-Ferrer et al.   Journal of Chemical Theory and Computation

Explaining why Gleevec is a specific and potent inhibitor of Abl kinase

(2013) Y.-L. Lin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Critical assessment of methods of protein structure prediction (CASP) - round x

(2013) John Moult et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

High-Resolution Comparative Modeling with RosettaCM

(2013) Yifan Song et al.   STRUCTURE

OpenMM 4: A Reusable, Extensible, Hardware Independent Library for High Performance Molecular Simulation

(2012) Peter Eastman et al.   Journal of Chemical Theory and Computation

SIFTS: Structure Integration with Function, Taxonomy and Sequences resource

(2012) Sameer Velankar et al.   NUCLEIC ACIDS RESEARCH

Structure-based model of allostery predicts coupling between distant sites

(2012) P. Weinkam et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Markov models of molecular kinetics: Generation and validation

(2011) Jan-Hendrik Prinz et al.   JOURNAL OF CHEMICAL PHYSICS

Polarizable Atomic Multipole X-Ray Refinement: Particle Mesh Ewald Electrostatics for Macromolecular Crystals

(2011) Michael J. Schnieders et al.   Journal of Chemical Theory and Computation

MSMBuilder2: Modeling Conformational Dynamics on the Picosecond to Millisecond Scale

(2011) Kyle A. Beauchamp et al.   Journal of Chemical Theory and Computation

Equilibrium Distribution from Distributed Computing (Simulations of Protein Folding)

(2011) Riccardo Scalco et al.   JOURNAL OF PHYSICAL CHEMISTRY B

A Comprehensive Benchmark Study of Multiple Sequence Alignment Methods: Current Challenges and Future Perspectives

(2011) Julie D. Thompson et al.   PLoS One

Assessment of protein structure refinement in CASP9

(2011) Justin L. MacCallum et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Polarizable Atomic Multipole X-Ray Refinement: Hydration Geometry and Application to Macromolecules

(2010) Timothy D. Fenn et al.   BIOPHYSICAL JOURNAL

High-Throughput All-Atom Molecular Dynamics Simulations Using Distributed Computing

(2010) I. Buch et al.   Journal of Chemical Information and Modeling

Rapid communication reply to comment on: “Fast determination of the optimal rotational matrix for macromolecular superpositions”

(2010) Pu Liu et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Everything you wanted to know about Markov State Models but were afraid to ask

(2010) Vijay S. Pande et al.   METHODS

Dynameomics: A Comprehensive Database of Protein Dynamics

(2010) Marc W. van der Kamp et al.   STRUCTURE

MolProbity: all-atom structure validation for macromolecular crystallography

(2009) Vincent B. Chen et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

Biopython: freely available Python tools for computational molecular biology and bioinformatics

(2009) P. J. A. Cock et al.   BIOINFORMATICS

Protein structure prediction: when is it useful?

(2009) Yang Zhang   CURRENT OPINION IN STRUCTURAL BIOLOGY

Src kinases as therapeutic targets for cancer

(2009) Lori C. Kim et al.   Nature Reviews Clinical Oncology

Trapping Moving Targets with Small Molecules

(2009) G. M. Lee et al.   SCIENCE

A Correspondence Between Solution-State Dynamics of an Individual Protein and the Sequence and Conformational Diversity of its Family

(2009) Gregory D. Friedland et al.   PLoS Computational Biology

PROMALS3D: a tool for multiple protein sequence and structure alignments

(2008) Jimin Pei et al.   NUCLEIC ACIDS RESEARCH

A conserved protonation-dependent switch controls drug binding in the Abl kinase

(2008) Y. Shan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

An electrostatic network and long-range regulation of Src kinases

(2008) Elif Ozkirimli et al.   PROTEIN SCIENCE