Biomolecular modeling and simulation: a field coming of age

CONCENTRATES

(2011)   CHEMICAL & ENGINEERING NEWS

Tackling Force-Field Bias in Protein Folding Simulations: Folding of Villin HP35 and Pin WW Domains in Explicit Water

(2010) Jeetain Mittal et al.   BIOPHYSICAL JOURNAL

Large conformational changes in proteins: signaling and other functions

(2010) Barry J Grant et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Molecular Dynamics with Multiple Time Scales: How to Avoid Pitfalls

(2010) Joseph A. Morrone et al.   Journal of Chemical Theory and Computation

A Dynamic Model of HIV Integrase Inhibition and Drug Resistance

(2010) Alex L. Perryman et al.   JOURNAL OF MOLECULAR BIOLOGY

Investigation of Protein Folding by Coarse-Grained Molecular Dynamics with the UNRES Force Field

(2010) Gia G. Maisuradze et al.   JOURNAL OF PHYSICAL CHEMISTRY A

Current Status of the AMOEBA Polarizable Force Field

(2010) Jay W. Ponder et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Enhanced Conformational Space Sampling Improves the Prediction of Chemical Shifts in Proteins

(2010) Phineus R. L. Markwick et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Molecular Simulation ofab InitioProtein Folding for a Millisecond Folder NTL9(1−39)

(2010) Vincent A. Voelz et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Protein folding: The dark side of proteins

(2010) Jim Schnabel   NATURE

Human genome at ten: Life is complicated

(2010) Erika Check Hayden   NATURE

Super-resolution biomolecular crystallography with low-resolution data

(2010) Gunnar F. Schröder et al.   NATURE

Experimental evidence for a frustrated energy landscape in a three-helix-bundle protein family

(2010) Beth G. Wensley et al.   NATURE

Predicting protein structures with a multiplayer online game

(2010) Seth Cooper et al.   NATURE

Retroviral intasome assembly and inhibition of DNA strand transfer

(2010) Stephen Hare et al.   NATURE

Large-scale conformational sampling of proteins using temperature-accelerated molecular dynamics

(2010) C. F. Abrams et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Identifying the amylome, proteins capable of forming amyloid-like fibrils

(2010) Lukasz Goldschmidt et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Opportunities for Research and NIH

(2010) F. S. Collins   SCIENCE

Atomic-Level Characterization of the Structural Dynamics of Proteins

(2010) D. E. Shaw et al.   SCIENCE

The Mechanism of the Translocation Step in DNA Replication by DNA Polymerase I: A Computer Simulation Analysis

(2010) Andrei A. Golosov et al.   STRUCTURE

Small Molecule Microarrays of RNA-Focused Peptoids Help Identify Inhibitors of a Pathogenic Group I Intron

(2009) Lucas P. Labuda et al.   ACS Chemical Biology

A molecular model for drug binding to tandem repeats of telomeric G-quadruplexes

(2009) Shozeb M. Haider et al.   BIOCHEMICAL SOCIETY TRANSACTIONS

Functional Dynamics of the Folded Ankyrin Repeats of IκBα Revealed by Nuclear Magnetic Resonance

(2009) Carla F. Cervantes et al.   BIOCHEMISTRY

The Fip35 WW Domain Folds with Structural and Mechanistic Heterogeneity in Molecular Dynamics Simulations

(2009) Daniel L. Ensign et al.   BIOPHYSICAL JOURNAL

Force Field Bias in Protein Folding Simulations

(2009) Peter L. Freddolino et al.   BIOPHYSICAL JOURNAL

Common Structural Transitions in Explicit-Solvent Simulations of Villin Headpiece Folding

(2009) Peter L. Freddolino et al.   BIOPHYSICAL JOURNAL

Reactive flux and folding pathways in network models of coarse-grained protein dynamics

(2009) Alexander Berezhkovskii et al.   JOURNAL OF CHEMICAL PHYSICS

Progress and challenges in the automated construction of Markov state models for full protein systems

(2009) Gregory R. Bowman et al.   JOURNAL OF CHEMICAL PHYSICS

The Predicted Structure of the Headpiece of the Huntingtin Protein and Its Implications on Huntingtin Aggregation

(2009) Nicholas W. Kelley et al.   JOURNAL OF MOLECULAR BIOLOGY

A Tale of Tails: How Histone Tails Mediate Chromatin Compaction in Different Salt and Linker Histone Environments†

(2009) Gaurav Arya et al.   JOURNAL OF PHYSICAL CHEMISTRY A

Relationship Between Conformational Changes in Pol λ’s Active Site Upon Binding Incorrect Nucleotides and Mismatch Incorporation Rates

(2009) Meredith C. Foley et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Toward a Unified Representation of Protein Structural Dynamics in Solution

(2009) Phineus R. L. Markwick et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Fraud rocks protein community

(2009) Brendan Borrell   NATURE

Lessons from 60 years of pharmaceutical innovation

(2009) Bernard Munos   NATURE REVIEWS DRUG DISCOVERY

Single-molecule force spectroscopy reveals a highly compliant helical folding for the 30-nm chromatin fiber

(2009) Maarten Kruithof et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Mesoscale simulations of two nucleosome-repeat length oligonucleosomes

(2009) Tamar Schlick et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Evidence for heteromorphic chromatin fibers from analysis of nucleosome interactions

(2009) S. A. Grigoryev et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Design of therapeutic proteins with enhanced stability

(2009) N. Chennamsetty et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Constructing the equilibrium ensemble of folding pathways from short off-equilibrium simulations

(2009) Frank Noé et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Identification of two distinct inactive conformations of the  2-adrenergic receptor reconciles structural and biochemical observations

(2009) R. O. Dror et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

CASP8 results in context of previous experiments

(2009) Andriy Kryshtafovych et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Assessment of the protein-structure refinement category in CASP8

(2009) Justin L. MacCallum et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Structure prediction for CASP8 with all-atom refinement using Rosetta

(2009) Srivatsan Raman et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Assessment of CASP8 structure predictions for template free targets

(2009) Moshe Ben-David et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Improving Structure-Based Function Prediction Using Molecular Dynamics

(2009) Dariya S. Glazer et al.   STRUCTURE

Discovery Through the Computational Microscope

(2009) Eric H. Lee et al.   STRUCTURE

Outcome of a Workshop on Applications of Protein Models in Biomedical Research

(2009) Torsten Schwede et al.   STRUCTURE

The Protein Folding Problem

(2008) Ken A. Dill et al.   Annual Review of Biophysics

The Effect of Internucleosomal Interaction on Folding of the Chromatin Fiber

(2008) René Stehr et al.   BIOPHYSICAL JOURNAL

Observation of Noncooperative Folding Thermodynamics in Simulations of 1BBL

(2008) Jed W. Pitera et al.   BIOPHYSICAL JOURNAL

Ten-Microsecond Molecular Dynamics Simulation of a Fast-Folding WW Domain

(2008) Peter L. Freddolino et al.   BIOPHYSICAL JOURNAL

Molecular Dynamics and Principal Components Analysis of Human Telomeric Quadruplex Multimers

(2008) Shozeb Haider et al.   BIOPHYSICAL JOURNAL

Are Current Molecular Dynamics Force Fields too Helical?

(2008) Robert B. Best et al.   BIOPHYSICAL JOURNAL

Structure-directed combinatorial library design

(2008) Joe Zhongxiang Zhou   CURRENT OPINION IN CHEMICAL BIOLOGY

Computational techniques for efficient conformational sampling of proteins

(2008) Adam Liwo et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Progress and challenges in protein structure prediction

(2008) Yang Zhang   CURRENT OPINION IN STRUCTURAL BIOLOGY

Transition networks for modeling the kinetics of conformational change in macromolecules

(2008) Frank Noé et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Substrate-induced DNA strand misalignment during catalytic cycling by DNA polymerase λ

(2008) Katarzyna Bebenek et al.   EMBO REPORTS

Building Markov state models along pathways to determine free energies and rates of transitions

(2008) Albert C. Pan et al.   JOURNAL OF CHEMICAL PHYSICS

Normal mode partitioning of Langevin dynamics for biomolecules

(2008) Christopher R. Sweet et al.   JOURNAL OF CHEMICAL PHYSICS

Optimizing the sampling and staging for simulations of rare events via forward flux sampling schemes

(2008) Ernesto E. Borrero et al.   JOURNAL OF CHEMICAL PHYSICS

GROMACS 4:  Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation

(2008) Berk Hess et al.   Journal of Chemical Theory and Computation

Internal Hydration Increases during Activation of the G-Protein-Coupled Receptor Rhodopsin

(2008) Alan Grossfield et al.   JOURNAL OF MOLECULAR BIOLOGY

Microsecond Molecular Dynamics Simulation Shows Effect of Slow Loop Dynamics on Backbone Amide Order Parameters of Proteins†

(2008) Paul Maragakis et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Progress inAb InitioQM/MM Free-Energy Simulations of Electrostatic Energies in Proteins: Accelerated QM/MM Studies of pKa, Redox Reactions and Solvation Free Energies†

(2008) Shina C. L. Kamerlin et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Structural Basis of DNA Quadruplex Recognition by an Acridine Drug

(2008) Nancy H. Campbell et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Structural and dynamic effects of cholesterol at preferred sites of interaction with rhodopsin identified from microsecond length molecular dynamics simulations

(2008) George Khelashvili et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

A Structural Mechanism for MscS Gating in Lipid Bilayers

(2008) V. Vasquez et al.   SCIENCE

De Novo Computational Design of Retro-Aldol Enzymes

(2008) L. Jiang et al.   SCIENCE

Large-Scale Molecular Dynamics Simulations of Self-Assembling Systems

(2008) M. L. Klein et al.   SCIENCE

Conformational Sampling of Peptides in Cellular Environments

(2007) Seiichiro Tanizaki et al.   BIOPHYSICAL JOURNAL

Simulation of the Pressure and Temperature Folding/Unfolding Equilibrium of a Small RNA Hairpin

(2007) Angel E. Garcia et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Implicit modeling of nonpolar solvation for simulating protein folding and conformational transitions

(2007) Jianhan Chen et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS