Significance of Molecular Dynamics Simulations for Life Sciences

Atomistic molecular simulations of protein folding

(2012) Robert B Best   CURRENT OPINION IN STRUCTURAL BIOLOGY

Tension induces a base-paired overstretched DNA conformation

(2012) N. Bosaeus et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Convergence and error estimation in free energy calculations using the weighted histogram analysis method

(2011) Fangqiang Zhu et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Unsuspected pathway of the allosteric transition in hemoglobin

(2011) S. Fischer et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Mechanism of folding chamber closure in a group II chaperonin

(2010) Junjie Zhang et al.   NATURE

Two distinct overstretched DNA states

(2010) Hongxia Fu et al.   NUCLEIC ACIDS RESEARCH

Modeling the early stage of DNA sequence recognition within RecA nucleoprotein filaments

(2010) Adrien Saladin et al.   NUCLEIC ACIDS RESEARCH

PR65, the HEAT-repeat scaffold of phosphatase PP2A, is an elastic connector that links force and catalysis

(2010) A. Grinthal et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Ketosteroid isomerase provides further support for the idea that enzymes work by electrostatic preorganization

(2010) S. C. L. Kamerlin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Dynamics of the Hck-SH3 domain: Comparison of experiment with multiple molecular dynamics simulations

(2010) David A. Horita et al.   PROTEIN SCIENCE

Application of normal-mode refinement to X-ray crystal structures at the lower resolution limit

(2009) Fengyun Ni et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

Structural improvement of unliganded simian immunodeficiency virus gp120 core by normal-mode-based X-ray crystallographic refinement

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

Hydrogen Bond Coupling in the Ketosteroid Isomerase Active Site

(2009) Paul A. Sigala et al.   BIOCHEMISTRY

Hybrid Quantum/Classical Molecular Dynamics Simulations of the Proton Transfer Reactions Catalyzed by Ketosteroid Isomerase: Analysis of Hydrogen Bonding, Conformational Motions, and Electrostatics

(2009) Dhruva K. Chakravorty et al.   BIOCHEMISTRY

Mechanism of the Orotidine 5′-Monophosphate Decarboxylase-Catalyzed Reaction: Evidence for Substrate Destabilization,

(2009) Kui K. Chan et al.   BIOCHEMISTRY

Deforming DNA: From Physics to Biology

(2009) Chantal Prévost et al.   CHEMPHYSCHEM

Single DNA/protein studies with magnetic traps

(2009) Adrien Meglio et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Force and function: probing proteins with AFM-based force spectroscopy

(2009) Elias M Puchner et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Long-timescale molecular dynamics simulations of protein structure and function

(2009) John L Klepeis et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Scaling of Multimillion-Atom Biological Molecular Dynamics Simulation on a Petascale Supercomputer

(2009) Roland Schulz et al.   Journal of Chemical Theory and Computation

Torque generation and elastic power transmission in the rotary FOF1-ATPase

(2009) Wolfgang Junge et al.   NATURE

Encounter and extrusion of an intrahelical lesion by a DNA repair enzyme

(2009) Yan Qi et al.   NATURE

The nature of the globular- to fibrous-actin transition

(2009) Toshiro Oda et al.   NATURE

Helix movement is coupled to displacement of the second extracellular loop in rhodopsin activation

(2009) Shivani Ahuja et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

The structure of DNA overstretched from the 5'5' ends differs from the structure of DNA overstretched from the 3'3' ends

(2009) C. Danilowicz et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Determining the catalytic role of remote substrate binding interactions in ketosteroid isomerase

(2009) J. P. Schwans et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Peeling back the mystery of DNA overstretching

(2009) M. C. Williams et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Relative CO2/NH3 selectivities of AQP1, AQP4, AQP5, AmtB, and RhAG

(2009) R. Musa-Aziz et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Unraveling the structure of DNA during overstretching by using multicolor, single-molecule fluorescence imaging

(2009) J. van Mameren et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Force Signaling in Biology

(2009) J. Christof et al.   SCIENCE

Structural Insight into Nascent Polypeptide Chain-Mediated Translational Stalling

(2009) B. Seidelt et al.   SCIENCE

Quantitative Determination of the Conformational Properties of Partially Folded and Intrinsically Disordered Proteins Using NMR Dipolar Couplings

(2009) Malene Ringkjøbing Jensen et al.   STRUCTURE

Discovery Through the Computational Microscope

(2009) Eric H. Lee et al.   STRUCTURE

Integrating Diverse Data for Structure Determination of Macromolecular Assemblies

(2008) Frank Alber et al.   Annual Review of Biochemistry

Recent Advances in Optical Tweezers

(2008) Jeffrey R. Moffitt et al.   Annual Review of Biochemistry

Molecular Force Balance Measurements Reveal that Double-Stranded DNA Unbinds Under Force in Rate-Dependent Pathways

(2008) Christian H. Albrecht et al.   BIOPHYSICAL JOURNAL

Packaging Double-Helical DNA into Viral Capsids: Structures, Forces, and Energetics

(2008) Anton S. Petrov et al.   BIOPHYSICAL JOURNAL

Anton, a special-purpose machine for molecular dynamics simulation

(2008) David E. Shaw et al.   COMMUNICATIONS OF THE ACM

Recent advances in the study of nucleic acid flexibility by molecular dynamics

(2008) Modesto Orozco et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Molecular dynamics simulations of nucleic acid–protein complexes

(2008) Alexander D MacKerell et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Combining experiment and simulation in protein folding: closing the gap for small model systems

(2008) R Dustin Schaeffer et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Experimental Investigation of the Seesaw Mechanism of the Relay Region That Moves the Myosin Lever Arm

(2008) Bálint Kintses et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

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

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

Backbone Dynamics in the DNAHhaI Protein Binding Site

(2008) Kari Pederson et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Biomolecular simulation and modelling: status, progress and prospects

(2008) M. W van der Kamp et al.   Journal of the Royal Society Interface

Kinesin's cover-neck bundle folds forward to generate force

(2008) A. S. Khalil et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Comparison of successive transition states for folding reveals alternative early folding pathways of two homologous proteins

(2008) N. Calosci et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Force Generation in Kinesin Hinges on Cover-Neck Bundle Formation

(2008) Wonmuk Hwang et al.   STRUCTURE

Of torques, forces, and protein machines

(2004) Carlos Bustamante   PROTEIN SCIENCE