Long-timescale molecular dynamics simulations of protein structure and function.

Improved side-chain torsion potentials for the Amber ff99SB protein force field. Proteins (2010) 9.43

Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 1. Generalized Born. J Chem Theory Comput (2012) 3.40

How robust are protein folding simulations with respect to force field parameterization? Biophys J (2011) 3.00

ACPYPE - AnteChamber PYthon Parser interfacE. BMC Res Notes (2012) 2.30

Systematic validation of protein force fields against experimental data. PLoS One (2012) 2.29

Virtual screening: an endless staircase? Nat Rev Drug Discov (2010) 2.26

Integrated nanopore sensing platform with sub-microsecond temporal resolution. Nat Methods (2012) 2.19

Systems biology in immunology: a computational modeling perspective. Annu Rev Immunol (2011) 2.15

Accommodation of aminoacyl-tRNA into the ribosome involves reversible excursions along multiple pathways. RNA (2010) 1.91

Scrutinizing molecular mechanics force fields on the submicrosecond timescale with NMR data. Biophys J (2010) 1.75

Discovery through the computational microscope. Structure (2009) 1.67

NMR paves the way for atomic level descriptions of sparsely populated, transiently formed biomolecular conformers. Proc Natl Acad Sci U S A (2013) 1.48

Exploring atomic resolution physiology on a femtosecond to millisecond timescale using molecular dynamics simulations. J Gen Physiol (2010) 1.44

Large conformational changes in proteins: signaling and other functions. Curr Opin Struct Biol (2010) 1.38

Enhanced modeling via network theory: Adaptive sampling of Markov state models. J Chem Theory Comput (2010) 1.37

MATCH: an atom-typing toolset for molecular mechanics force fields. J Comput Chem (2011) 1.22

MDTraj: A Modern Open Library for the Analysis of Molecular Dynamics Trajectories. Biophys J (2015) 1.19

A role for a specific cholesterol interaction in stabilizing the Apo configuration of the human A(2A) adenosine receptor. Structure (2009) 1.19

Benchmarking AMBER force fields for RNA: comparisons to NMR spectra for single-stranded r(GACC) are improved by revised χ torsions. J Phys Chem B (2011) 1.15

The Two Dimensional Vibrational Echo of a Nitrile Probe of the Villin HP35 Protein. J Phys Chem Lett (2010) 1.15

Biomolecular dynamics: order-disorder transitions and energy landscapes. Rep Prog Phys (2012) 1.12

Reliable oligonucleotide conformational ensemble generation in explicit solvent for force field assessment using reservoir replica exchange molecular dynamics simulations. J Phys Chem B (2013) 1.08

Dynamics: the missing link between structure and function of the viral RNA-dependent RNA polymerase? Curr Opin Struct Biol (2009) 1.07

Connecting the kinetics and energy landscape of tRNA translocation on the ribosome. PLoS Comput Biol (2013) 1.07

Network models for molecular kinetics and their initial applications to human health. Cell Res (2010) 1.06

Use of long term molecular dynamics simulation in predicting cancer associated SNPs. PLoS Comput Biol (2014) 1.05

Strategies for protein synthetic biology. Nucleic Acids Res (2010) 1.04

A mechanism for S-adenosyl methionine assisted formation of a riboswitch conformation: a small molecule with a strong arm. Nucleic Acids Res (2009) 1.02

In silico elucidation of the recognition dynamics of ubiquitin. PLoS Comput Biol (2011) 1.02

Multi-scale modeling in biology: how to bridge the gaps between scales? Prog Biophys Mol Biol (2011) 1.00

Harnessing Big Data for Systems Pharmacology. Annu Rev Pharmacol Toxicol (2016) 0.99

Nonadditivity in conformational entropy upon molecular rigidification reveals a universal mechanism affecting folding cooperativity. Biophys J (2011) 0.98

Protein dynamics investigated by inherent structure analysis. Proc Natl Acad Sci U S A (2010) 0.98

Structure-based energetics of protein interfaces guides foot-and-mouth disease virus vaccine design. Nat Struct Mol Biol (2015) 0.97

Visualizing functional motions of membrane transporters with molecular dynamics simulations. Biochemistry (2013) 0.96

Constant pH Replica Exchange Molecular Dynamics in Explicit Solvent Using Discrete Protonation States: Implementation, Testing, and Validation. J Chem Theory Comput (2014) 0.96

Bioinformatics and molecular modeling in glycobiology. Cell Mol Life Sci (2010) 0.95

Predicting interaction sites from the energetics of isolated proteins: a new approach to epitope mapping. Biophys J (2010) 0.95

Evidence of functional protein dynamics from X-ray crystallographic ensembles. PLoS Comput Biol (2010) 0.95

Multibody coarse-grained potentials for native structure recognition and quality assessment of protein models. Proteins (2011) 0.95

PPM: a side-chain and backbone chemical shift predictor for the assessment of protein conformational ensembles. J Biomol NMR (2012) 0.94

Decrypting the sequence of structural events during the gating transition of pentameric ligand-gated ion channels based on an interpolated elastic network model. PLoS Comput Biol (2011) 0.94

Exploring the role of receptor flexibility in structure-based drug discovery. Biophys Chem (2013) 0.93

Global motions exhibited by proteins in micro- to milliseconds simulations concur with anisotropic network model predictions. J Chem Phys (2013) 0.93

Combining experiments and simulations using the maximum entropy principle. PLoS Comput Biol (2014) 0.92

Disruption of Bcr-Abl coiled coil oligomerization by design. J Biol Chem (2011) 0.92

Evaluating the effects of cutoffs and treatment of long-range electrostatics in protein folding simulations. PLoS One (2012) 0.92

Key intermolecular interactions in the E. coli 70S ribosome revealed by coarse-grained analysis. J Am Chem Soc (2011) 0.91

Is N-acetyl-D-glucosamine a rigid 4C1 chair? Glycobiology (2011) 0.91

4D prediction of protein (1)H chemical shifts. J Biomol NMR (2009) 0.90

Multi-scale electrophysiology modeling: from atom to organ. J Gen Physiol (2010) 0.90

Identification of specific lipid-binding sites in integral membrane proteins. J Biol Chem (2010) 0.89

Implementation of molecular dynamics and its extensions with the coarse-grained UNRES force field on massively parallel systems; towards millisecond-scale simulations of protein structure, dynamics, and thermodynamics. J Chem Theory Comput (2010) 0.89

Lipid simulations: a perspective on lipids in action. Cold Spring Harb Perspect Biol (2011) 0.89

Cholesterol modulates the dimer interface of the β₂-adrenergic receptor via cholesterol occupancy sites. Biophys J (2014) 0.89

Atomic level characterization of the nonproton ligand-sensing domain of ASIC3 channels. J Biol Chem (2011) 0.89

Water-exclusion and liquid-structure forces in implicit solvation. J Phys Chem B (2011) 0.89

Protein folding on the ribosome studied using NMR spectroscopy. Prog Nucl Magn Reson Spectrosc (2013) 0.87

Ensemble-based methods for describing protein dynamics. Curr Opin Pharmacol (2010) 0.86

Large scale rigidity-based flexibility analysis of biomolecules. Struct Dyn (2016) 0.86

Fast protein folding kinetics. Q Rev Biophys (2014) 0.86

Molecular recognition in the case of flexible targets. Curr Pharm Des (2011) 0.85

A dynamic structural model of expanded RNA CAG repeats: a refined X-ray structure and computational investigations using molecular dynamics and umbrella sampling simulations. J Am Chem Soc (2013) 0.84

Single ion channel recordings with CMOS-anchored lipid membranes. Nano Lett (2013) 0.84

Multi-timescale conformational dynamics of the SH3 domain of CD2-associated protein using NMR spectroscopy and accelerated molecular dynamics. Angew Chem Int Ed Engl (2012) 0.84

Software and resources for computational medicinal chemistry. Future Med Chem (2011) 0.84

T-cell epitope prediction and immune complex simulation using molecular dynamics: state of the art and persisting challenges. Immunome Res (2010) 0.84

Computational Recipe for Efficient Description of Large-Scale Conformational Changes in Biomolecular Systems. J Chem Theory Comput (2014) 0.84

Anharmonic normal mode analysis of elastic network model improves the modeling of atomic fluctuations in protein crystal structures. Biophys J (2010) 0.83

Millisecond timescale dynamics of human liver fatty acid binding protein: testing of its relevance to the ligand entry process. Biophys J (2010) 0.83

Quantitatively characterizing the ligand binding mechanisms of choline binding protein using Markov state model analysis. PLoS Comput Biol (2014) 0.83

Intrinsic flexibility of NLRP pyrin domains is a key factor in their conformational dynamics, fold stability, and dimerization. Protein Sci (2014) 0.82

Evidence of trem2 variant associated with triple risk of Alzheimer's disease. PLoS One (2014) 0.81

Space warping order parameters and symmetry: application to multiscale simulation of macromolecular assemblies. J Phys Chem B (2012) 0.81

Dynamics simulations for engineering macromolecular interactions. Chaos (2013) 0.81

In-silico assessment of protein-protein electron transfer. a case study: cytochrome c peroxidase--cytochrome c. PLoS Comput Biol (2013) 0.81

Molecular dynamics study of the opening mechanism for DNA polymerase I. PLoS Comput Biol (2014) 0.81

Allosteric activation transitions in enzymes and biomolecular motors: insights from atomistic and coarse-grained simulations. Top Curr Chem (2013) 0.81

Free energies for coarse-grained proteins by integrating multibody statistical contact potentials with entropies from elastic network models. J Struct Funct Genomics (2011) 0.81

A simple molecular mechanics integrator in mixed rigid body and dihedral angle space. J Chem Phys (2014) 0.80

Motional timescale predictions by molecular dynamics simulations: case study using proline and hydroxyproline sidechain dynamics. Proteins (2013) 0.80

How to mark off paths on the protein energy landscape. Proc Natl Acad Sci U S A (2009) 0.80

Coarse-Grained Models for Protein-Cell Membrane Interactions. Polymers (Basel) (2015) 0.80

Analysis of local molecular motions of aromatic sidechains in proteins by 2D and 3D fast MAS NMR spectroscopy and quantum mechanical calculations. Phys Chem Chem Phys (2015) 0.80

Accelerating electrostatic surface potential calculation with multi-scale approximation on graphics processing units. J Mol Graph Model (2010) 0.80

All-atom and coarse-grained molecular dynamics simulations of a membrane protein stabilizing polymer. Langmuir (2011) 0.80

Combining NMR and molecular dynamics studies for insights into the allostery of small GTPase-protein interactions. Methods Mol Biol (2012) 0.80

Active-site residues move independently from the rest of the protein in a 200 ns molecular dynamics simulation of cytochrome P450 CYP119. Arch Biochem Biophys (2011) 0.79

Multiple routes and milestones in the folding of HIV-1 protease monomer. PLoS One (2010) 0.79

Disorder guides protein function. Proc Natl Acad Sci U S A (2013) 0.79

Multiscale macromolecular simulation: role of evolving ensembles. J Chem Inf Model (2012) 0.79

Substrate binding process and mechanistic functioning of type 1 11β-hydroxysteroid dehydrogenase from enhanced sampling methods. PLoS One (2011) 0.79

Slide-and-exchange mechanism for rapid and selective transport through the nuclear pore complex. Proc Natl Acad Sci U S A (2016) 0.79

Dynamics of lipids, cholesterol, and transmembrane α-helices from microsecond molecular dynamics simulations. J Phys Chem B (2014) 0.78

Protein dynamics: whispering within. Nat Chem (2011) 0.78

The two-pathway model of the biological catch-bond as a limit of the allosteric model. Biophys J (2011) 0.78

Conformation analysis of a surface loop that controls active site access in the GH11 xylanase A from Bacillus subtilis. J Mol Model (2011) 0.78

Thermodynamic and structural determinants of differential Pdx1 binding to elements from the insulin and IAPP promoters. J Mol Biol (2013) 0.78

Catch bond interaction between cell-surface sulfatase Sulf1 and glycosaminoglycans. Biophys J (2015) 0.78

Comparing molecular dynamics force fields in the essential subspace. PLoS One (2015) 0.78

Glide: a new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy. J Med Chem (2004) 15.51

Improved side-chain torsion potentials for the Amber ff99SB protein force field. Proteins (2010) 9.43

Atomic-level characterization of the structural dynamics of proteins. Science (2010) 8.36

How fast-folding proteins fold. Science (2011) 6.24

Structure and function of an irreversible agonist-β(2) adrenoceptor complex. Nature (2011) 5.35

A hierarchical approach to all-atom protein loop prediction. Proteins (2004) 5.18

The dynamic process of β(2)-adrenergic receptor activation. Cell (2013) 4.09

Structure and dynamics of the M3 muscarinic acetylcholine receptor. Nature (2012) 3.83

Mechanism of voltage gating in potassium channels. Science (2012) 3.24

Mapping long-range interactions in alpha-synuclein using spin-label NMR and ensemble molecular dynamics simulations. J Am Chem Soc (2005) 3.13

How robust are protein folding simulations with respect to force field parameterization? Biophys J (2011) 3.00

Biomolecular simulation: a computational microscope for molecular biology. Annu Rev Biophys (2012) 2.85

Identification of two distinct inactive conformations of the beta2-adrenergic receptor reconciles structural and biochemical observations. Proc Natl Acad Sci U S A (2009) 2.77

Oncogenic mutations counteract intrinsic disorder in the EGFR kinase and promote receptor dimerization. Cell (2012) 2.67

Structural analysis of the catalytically inactive kinase domain of the human EGF receptor 3. Proc Natl Acad Sci U S A (2009) 2.55

Activation mechanism of the β2-adrenergic receptor. Proc Natl Acad Sci U S A (2011) 2.53

PHASE: a new engine for pharmacophore perception, 3D QSAR model development, and 3D database screening: 1. Methodology and preliminary results. J Comput Aided Mol Des (2006) 2.53

Conformational coupling across the plasma membrane in activation of the EGF receptor. Cell (2013) 2.49

Principles of conduction and hydrophobic gating in K+ channels. Proc Natl Acad Sci U S A (2010) 2.47

Pathway and mechanism of drug binding to G-protein-coupled receptors. Proc Natl Acad Sci U S A (2011) 2.44

High-resolution crystal structure of human protease-activated receptor 1. Nature (2012) 2.44

Gaussian split Ewald: A fast Ewald mesh method for molecular simulation. J Chem Phys (2005) 2.32

Architecture and membrane interactions of the EGF receptor. Cell (2013) 2.29

Systematic validation of protein force fields against experimental data. PLoS One (2012) 2.29

A conserved protonation-dependent switch controls drug binding in the Abl kinase. Proc Natl Acad Sci U S A (2008) 2.18

Real-world illumination and the perception of surface reflectance properties. J Vis (2003) 2.17

How does a drug molecule find its target binding site? J Am Chem Soc (2011) 2.13

Relation between native ensembles and experimental structures of proteins. Proc Natl Acad Sci U S A (2006) 2.10

Microsecond molecular dynamics simulation shows effect of slow loop dynamics on backbone amide order parameters of proteins. J Phys Chem B (2008) 1.90

Structure of human urokinase plasminogen activator in complex with its receptor. Science (2006) 1.84

Mechanism of Na+/H+ antiporting. Science (2007) 1.79

Preconfiguration of the antigen-binding site during affinity maturation of a broadly neutralizing influenza virus antibody. Proc Natl Acad Sci U S A (2012) 1.70

Parallel protein-unfolding pathways revealed and mapped. Nat Struct Biol (2003) 1.67

Atomic-level description of ubiquitin folding. Proc Natl Acad Sci U S A (2013) 1.65

Equally potent inhibition of c-Src and Abl by compounds that recognize inactive kinase conformations. Cancer Res (2009) 1.64

Structural basis for modulation of a G-protein-coupled receptor by allosteric drugs. Nature (2013) 1.59

Superoxide dismutase 1 (SOD1) is essential for H2O2-mediated oxidation and inactivation of phosphatases in growth factor signaling. Proc Natl Acad Sci U S A (2008) 1.58

Copper binding by tetrathiomolybdate attenuates angiogenesis and tumor cell proliferation through the inhibition of superoxide dismutase 1. Clin Cancer Res (2006) 1.58

Refinement of protein structure homology models via long, all-atom molecular dynamics simulations. Proteins (2012) 1.52

The role of ligands on the equilibria between functional states of a G protein-coupled receptor. J Am Chem Soc (2013) 1.48

Computational design and experimental testing of the fastest-folding β-sheet protein. J Mol Biol (2010) 1.46

Structure and dynamics of an unfolded protein examined by molecular dynamics simulation. J Am Chem Soc (2012) 1.46

Protein folding kinetics and thermodynamics from atomistic simulation. Proc Natl Acad Sci U S A (2012) 1.46

Exploring atomic resolution physiology on a femtosecond to millisecond timescale using molecular dynamics simulations. J Gen Physiol (2010) 1.44

A common, avoidable source of error in molecular dynamics integrators. J Chem Phys (2007) 1.34

Transitions to catalytically inactive conformations in EGFR kinase. Proc Natl Acad Sci U S A (2013) 1.34

Dynamic control of slow water transport by aquaporin 0: implications for hydration and junction stability in the eye lens. Proc Natl Acad Sci U S A (2008) 1.30

A non-RGD-based integrin binding peptide (ATN-161) blocks breast cancer growth and metastasis in vivo. Mol Cancer Ther (2006) 1.29

Formation of native and non-native interactions in ensembles of denatured ACBP molecules from paramagnetic relaxation enhancement studies. J Mol Biol (2005) 1.27

The midpoint method for parallelization of particle simulations. J Chem Phys (2006) 1.27

Angiogenesis blockade as a new therapeutic approach to experimental colitis. Gut (2006) 1.26

Assessing the accuracy of physical models used in protein-folding simulations: quantitative evidence from long molecular dynamics simulations. Curr Opin Struct Biol (2014) 1.26

Crystal structures of the JAK2 pseudokinase domain and the pathogenic mutant V617F. Nat Struct Mol Biol (2012) 1.25

Structural basis of interaction between urokinase-type plasminogen activator and its receptor. J Mol Biol (2006) 1.25

Crystal structures of two human vitronectin, urokinase and urokinase receptor complexes. Nat Struct Mol Biol (2008) 1.23

Molecular determinants of drug-receptor binding kinetics. Drug Discov Today (2013) 1.17

BPPred: a Web-based computational tool for predicting biophysical parameters of proteins. Protein Sci (2006) 1.14

In support of the BMRB. Nat Struct Mol Biol (2012) 1.09

Atomic-level simulation of current-voltage relationships in single-file ion channels. J Gen Physiol (2013) 1.06

The future of molecular dynamics simulations in drug discovery. J Comput Aided Mol Des (2011) 1.06

Targeting the urokinase plasminogen activator receptor inhibits ovarian cancer metastasis. Clin Cancer Res (2010) 1.04

An anti-urokinase plasminogen activator receptor antibody (ATN-658) blocks prostate cancer invasion, migration, growth, and experimental skeletal metastasis in vitro and in vivo. Neoplasia (2010) 1.03

Regulation of RAS oncogenicity by acetylation. Proc Natl Acad Sci U S A (2012) 1.02

Structure of the regulatory apparatus of a calcium-dependent protein kinase (CDPK): a novel mode of calmodulin-target recognition. J Mol Biol (2005) 1.01

Transition state contact orders correlate with protein folding rates. J Mol Biol (2005) 1.01

PHAISTOS: a framework for Markov chain Monte Carlo simulation and inference of protein structure. J Comput Chem (2013) 0.95

Experimental parameterization of an energy function for the simulation of unfolded proteins. Biophys J (2007) 0.95

Structure of a functional amyloid protein subunit computed using sequence variation. J Am Chem Soc (2014) 0.94

Accurate and efficient integration for molecular dynamics simulations at constant temperature and pressure. J Chem Phys (2013) 0.94

Pharmacology of the novel antiangiogenic peptide ATN-161 (Ac-PHSCN-NH2): observation of a U-shaped dose-response curve in several preclinical models of angiogenesis and tumor growth. Clin Cancer Res (2008) 0.93

Evaluating the effects of cutoffs and treatment of long-range electrostatics in protein folding simulations. PLoS One (2012) 0.92