VMD: visual molecular dynamics.

Scalable molecular dynamics with NAMD. J Comput Chem (2005) 59.49

The Amber biomolecular simulation programs. J Comput Chem (2005) 28.84

CHARMM: the biomolecular simulation program. J Comput Chem (2009) 27.71

Molecular basis of bacterial outer membrane permeability revisited. Microbiol Mol Biol Rev (2003) 13.49

GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit. Bioinformatics (2013) 11.01

PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res (2007) 7.07

Anatomy of protein pockets and cavities: measurement of binding site geometry and implications for ligand design. Protein Sci (1998) 7.03

Molecular dynamics study of unbinding of the avidin-biotin complex. Biophys J (1997) 6.93

Presenting your structures: the CCP4mg molecular-graphics software. Acta Crystallogr D Biol Crystallogr (2011) 6.27

Architecture and secondary structure of an entire HIV-1 RNA genome. Nature (2009) 6.12

Flexible fitting of atomic structures into electron microscopy maps using molecular dynamics. Structure (2008) 5.97

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

Phytochrome structure and signaling mechanisms. Annu Rev Plant Biol (2006) 5.31

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Unfolding of titin immunoglobulin domains by steered molecular dynamics simulation. Biophys J (1998) 5.01

Structural basis for the histone chaperone activity of Asf1. Cell (2006) 4.95

Mutation of key residues of RPE65 abolishes its enzymatic role as isomerohydrolase in the visual cycle. Proc Natl Acad Sci U S A (2005) 4.67

Imaging alpha-hemolysin with molecular dynamics: ionic conductance, osmotic permeability, and the electrostatic potential map. Biophys J (2005) 4.45

Nonlinear elasticity, proteinquakes, and the energy landscapes of functional transitions in proteins. Proc Natl Acad Sci U S A (2003) 4.36

Biomechanics and biophysics of cancer cells. Acta Biomater (2007) 4.35

The mechanism of a neurotransmitter:sodium symporter--inward release of Na+ and substrate is triggered by substrate in a second binding site. Mol Cell (2008) 4.29

Avogadro: an advanced semantic chemical editor, visualization, and analysis platform. J Cheminform (2012) 4.10

Neurexin-neuroligin signaling in synapse development. Curr Opin Neurobiol (2007) 3.94

The Cfr rRNA methyltransferase confers resistance to Phenicols, Lincosamides, Oxazolidinones, Pleuromutilins, and Streptogramin A antibiotics. Antimicrob Agents Chemother (2006) 3.94

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

Microscopic Kinetics of DNA Translocation through synthetic nanopores. Biophys J (2004) 3.83

The molecular basis for the chemical denaturation of proteins by urea. Proc Natl Acad Sci U S A (2003) 3.82

Ten-microsecond molecular dynamics simulation of a fast-folding WW domain. Biophys J (2008) 3.81

Conformational analysis of nucleic acids revisited: Curves+. Nucleic Acids Res (2009) 3.76

STRIDE: a web server for secondary structure assignment from known atomic coordinates of proteins. Nucleic Acids Res (2004) 3.71

Diffusion, crowding & protein stability in a dynamic molecular model of the bacterial cytoplasm. PLoS Comput Biol (2010) 3.65

Dynamic reorganization of the functionally active ribosome explored by normal mode analysis and cryo-electron microscopy. Proc Natl Acad Sci U S A (2003) 3.64

Energetics of glycerol conduction through aquaglyceroporin GlpF. Proc Natl Acad Sci U S A (2002) 3.60

Peptide conformation and supramolecular organization in amylin fibrils: constraints from solid-state NMR. Biochemistry (2007) 3.57

The key event in force-induced unfolding of Titin's immunoglobulin domains. Biophys J (2000) 3.40

Molecular dynamics: survey of methods for simulating the activity of proteins. Chem Rev (2006) 3.18

Using Situs for the integration of multi-resolution structures. Biophys Rev (2010) 3.07

Orientation discrimination of single-stranded DNA inside the alpha-hemolysin membrane channel. Proc Natl Acad Sci U S A (2005) 3.06

X-ray structures of general anaesthetics bound to a pentameric ligand-gated ion channel. Nature (2011) 3.00

Defining the sequence-recognition profile of DNA-binding molecules. Proc Natl Acad Sci U S A (2006) 2.97

Interface connections of a transmembrane voltage sensor. Proc Natl Acad Sci U S A (2005) 2.92

Gating of MscL studied by steered molecular dynamics. Biophys J (2003) 2.91

Simulating movement of tRNA into the ribosome during decoding. Proc Natl Acad Sci U S A (2005) 2.91

Head swivel on the ribosome facilitates translocation by means of intra-subunit tRNA hybrid sites. Nature (2010) 2.85

Cyanine fluorophore derivatives with enhanced photostability. Nat Methods (2011) 2.85

MultiSeq: unifying sequence and structure data for evolutionary analysis. BMC Bioinformatics (2006) 2.81

Pressure-induced water transport in membrane channels studied by molecular dynamics. Biophys J (2002) 2.78

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

An avian influenza H5N1 virus that binds to a human-type receptor. J Virol (2007) 2.77

Heterogeneity even at the speed limit of folding: large-scale molecular dynamics study of a fast-folding variant of the villin headpiece. J Mol Biol (2007) 2.77

MDAnalysis: a toolkit for the analysis of molecular dynamics simulations. J Comput Chem (2011) 2.76

Ribosome-induced changes in elongation factor Tu conformation control GTP hydrolysis. Proc Natl Acad Sci U S A (2009) 2.69

Progress and challenges in the automated construction of Markov state models for full protein systems. J Chem Phys (2009) 2.64

CAVER 3.0: a tool for the analysis of transport pathways in dynamic protein structures. PLoS Comput Biol (2012) 2.64

Actin depolymerizing factor stabilizes an existing state of F-actin and can change the tilt of F-actin subunits. J Cell Biol (2001) 2.63

Theory and simulation of water permeation in aquaporin-1. Biophys J (2004) 2.63

Structural dynamics of the lac repressor-DNA complex revealed by a multiscale simulation. Proc Natl Acad Sci U S A (2005) 2.61

CHARMM Additive All-Atom Force Field for Glycosidic Linkages between Hexopyranoses. J Chem Theory Comput (2009) 2.61

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

ProDy: protein dynamics inferred from theory and experiments. Bioinformatics (2011) 2.55

Water dynamics and dewetting transitions in the small mechanosensitive channel MscS. Biophys J (2004) 2.54

Unbinding of retinoic acid from its receptor studied by steered molecular dynamics. Biophys J (1999) 2.54

Nature designs tough collagen: explaining the nanostructure of collagen fibrils. Proc Natl Acad Sci U S A (2006) 2.53

Dynameomics: a comprehensive database of protein dynamics. Structure (2010) 2.50

Conformational transitions of adenylate kinase: switching by cracking. J Mol Biol (2006) 2.49

Structure of the photolyase-like domain of cryptochrome 1 from Arabidopsis thaliana. Proc Natl Acad Sci U S A (2004) 2.48

The free energy landscapes governing conformational changes in a glutamate receptor ligand-binding domain. Structure (2007) 2.45

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

An all-atom structure-based potential for proteins: bridging minimal models with all-atom empirical forcefields. Proteins (2009) 2.44

Structure and mechanism of proton transport through the transmembrane tetrameric M2 protein bundle of the influenza A virus. Proc Natl Acad Sci U S A (2010) 2.43

Definition and testing of the GROMOS force-field versions 54A7 and 54B7. Eur Biophys J (2011) 2.43

Platelet glycoprotein Ibalpha forms catch bonds with human WT vWF but not with type 2B von Willebrand disease vWF. J Clin Invest (2008) 2.43

Thermal fluctuations of grafted microtubules provide evidence of a length-dependent persistence length. Proc Natl Acad Sci U S A (2006) 2.41

Molecular dynamics flexible fitting: a practical guide to combine cryo-electron microscopy and X-ray crystallography. Methods (2009) 2.39

Probing ion-channel pores one proton at a time. Nature (2005) 2.39

Tools for integrated sequence-structure analysis with UCSF Chimera. BMC Bioinformatics (2006) 2.38

Direct observation of Bin/amphiphysin/Rvs (BAR) domain-induced membrane curvature by means of molecular dynamics simulations. Proc Natl Acad Sci U S A (2006) 2.37

Structures of the human and Drosophila 80S ribosome. Nature (2013) 2.36

Crosstalk in G protein-coupled receptors: changes at the transmembrane homodimer interface determine activation. Proc Natl Acad Sci U S A (2005) 2.33

Dynamical networks in tRNA:protein complexes. Proc Natl Acad Sci U S A (2009) 2.31

Electrostatic tuning of permeation and selectivity in aquaporin water channels. Biophys J (2003) 2.31

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

Lipid bilayer pressure profiles and mechanosensitive channel gating. Biophys J (2004) 2.30

Phosphorylation regulates SIRT1 function. PLoS One (2008) 2.30

Integrins as therapeutic targets: lessons and opportunities. Nat Rev Drug Discov (2010) 2.27

A coarse-grained normal mode approach for macromolecules: an efficient implementation and application to Ca(2+)-ATPase. Biophys J (2002) 2.26

Cloud-based simulations on Google Exacycle reveal ligand modulation of GPCR activation pathways. Nat Chem (2013) 2.26

Cryo-EM structure of the ribosome-SecYE complex in the membrane environment. Nat Struct Mol Biol (2011) 2.25

Mechanisms of selectivity in channels and enzymes studied with interactive molecular dynamics. Biophys J (2003) 2.24

Dynamic pathways for viral capsid assembly. Biophys J (2006) 2.23

On the evolution of structure in aminoacyl-tRNA synthetases. Microbiol Mol Biol Rev (2003) 2.22

Crowding and hydrodynamic interactions likely dominate in vivo macromolecular motion. Proc Natl Acad Sci U S A (2010) 2.22

3D complex: a structural classification of protein complexes. PLoS Comput Biol (2006) 2.21

An improved relaxed complex scheme for receptor flexibility in computer-aided drug design. J Comput Aided Mol Des (2008) 2.16

Cell-cycle dynamics of chromosomal organization at single-cell resolution. Nature (2017) 2.16

Ensemble refinement of protein crystal structures: validation and application. Structure (2007) 2.16

Role of a novel PH-kinase domain interface in PKB/Akt regulation: structural mechanism for allosteric inhibition. PLoS Biol (2009) 2.15

Structure and hydration of membranes embedded with voltage-sensing domains. Nature (2009) 2.15

Ensemble-based virtual screening reveals potential novel antiviral compounds for avian influenza neuraminidase. J Med Chem (2008) 2.14

Models of macromolecular crowding effects and the need for quantitative comparisons with experiment. Curr Opin Struct Biol (2010) 2.14

Molecular dynamics study of unbinding of the avidin-biotin complex. Biophys J (1997) 6.93

Mechanical unfolding intermediates in titin modules. Nature (1999) 6.12

Steered molecular dynamics and mechanical functions of proteins. Curr Opin Struct Biol (2001) 5.97

Unfolding of titin immunoglobulin domains by steered molecular dynamics simulation. Biophys J (1998) 5.01

A model for photoreceptor-based magnetoreception in birds. Biophys J (2000) 4.96

The crystal structure of the light-harvesting complex II (B800-850) from Rhodospirillum molischianum. Structure (1996) 4.34

The key event in force-induced unfolding of Titin's immunoglobulin domains. Biophys J (2000) 3.40

Steered molecular dynamics investigations of protein function. J Mol Graph Model (2001) 3.04

Steered molecular dynamics simulations of force-induced protein domain unfolding. Proteins (1999) 3.02

Binding pathway of retinal to bacterio-opsin: a prediction by molecular dynamics simulations. Biophys J (1997) 2.99

The mechanism of glycerol conduction in aquaglyceroporins. Structure (2001) 2.75

Unbinding of retinoic acid from its receptor studied by steered molecular dynamics. Biophys J (1999) 2.54

Molecular dynamics study of aquaporin-1 water channel in a lipid bilayer. FEBS Lett (2001) 2.53

The electromechanics of DNA in a synthetic nanopore. Biophys J (2005) 2.43

Protein domain movements: detection of rigid domains and visualization of hinges in comparisons of atomic coordinates. Proteins (1997) 2.42

Forced unfolding of the fibronectin type III module reveals a tensile molecular recognition switch. Proc Natl Acad Sci U S A (1999) 2.36

Reconstructing potential energy functions from simulated force-induced unbinding processes. Biophys J (1997) 2.12

Steered molecular dynamics simulation of the Rieske subunit motion in the cytochrome bc(1) complex. Biophys J (1999) 2.10

Efficient light harvesting through carotenoids. Photosynth Res (2000) 2.06

Modelling DNA loops using continuum and statistical mechanics. Philos Trans A Math Phys Eng Sci (2004) 2.02

Binding of the estrogen receptor to DNA. The role of waters. Biophys J (1997) 2.02

Structural determinants of MscL gating studied by molecular dynamics simulations. Biophys J (2001) 1.96

Forced detachment of the CD2-CD58 complex. Biophys J (2003) 1.92

A mechanism for the light-driven proton pump of Halobacterium halobium. Nature (1978) 1.88

Electron transfer and spin exchange contributing to the magnetic field dependence of the primary photochemical reaction of bacterial photosynthesis. Biochim Biophys Acta (1978) 1.82

Oxygen and proton pathways in cytochrome c oxidase. Proteins (1998) 1.80

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Molecular dynamics study of bacteriorhodopsin and artificial pigments. Biochemistry (1994) 1.60

Beyond the Gene Chip. Bell Labs Tech J (2005) 1.57

Phylogenetic analysis of metabolic pathways. J Mol Evol (2001) 1.56

Architecture and mechanism of the light-harvesting apparatus of purple bacteria. Proc Natl Acad Sci U S A (1998) 1.53

Insulin-like growth factor system components in hyperparathyroidism and renal osteodystrophy. Kidney Int (2000) 1.52

Investigating a back door mechanism of actin phosphate release by steered molecular dynamics. Proteins (1999) 1.47

Self-organizing neural networks bridge the biomolecular resolution gap. J Mol Biol (1998) 1.45

Chromophore-protein interactions and the function of the photosynthetic reaction center: a molecular dynamics study. Proc Natl Acad Sci U S A (1992) 1.40

Comparison of the early stages of forced unfolding for fibronectin type III modules. Proc Natl Acad Sci U S A (2001) 1.33

Predicting the structure of apolipoprotein A-I in reconstituted high-density lipoprotein disks. Biophys J (1997) 1.33

The effect of protonation and electrical interactions on the stereochemistry of retinal schiff bases. Biophys J (1985) 1.33

Molecular dynamics study of the proton pump cycle of bacteriorhodopsin. Biochemistry (1993) 1.30

Structure and dynamics of calmodulin in solution. Biophys J (1998) 1.27

Molecular dynamics study of early picosecond events in the bacteriorhodopsin photocycle: dielectric response, vibrational cooling and the J, K intermediates. Biophys J (1996) 1.25

Molecular dynamics study of the nature and origin of retinal's twisted structure in bacteriorhodopsin. Biophys J (2000) 1.23

Proton conduction through proteins: an overview of theoretical principles and applications. Methods Enzymol (1986) 1.22

Nanoelectromechanics of methylated DNA in a synthetic nanopore. Biophys J (2009) 1.20

Excitation transfer in the peridinin-chlorophyll-protein of Amphidinium carterae. Biophys J (2000) 1.19

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A model for the resistance of the proton channel formed by the proteolipid of ATPase. Eur Biophys J (1985) 1.13

Models of orientation and ocular dominance columns in the visual cortex: a critical comparison. Neural Comput (1995) 1.12

Molecular dynamics study of the M412 intermediate of bacteriorhodopsin. Biophys J (1995) 1.11

Exploring fast electron transfer processes by magnetic fields. Biophys J (1978) 1.08

Multiple probes reveal a native-like intermediate during low-temperature refolding of ubiquitin. J Mol Biol (2004) 1.07

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Nucleotide-dependent movements of the kinesin motor domain predicted by simulated annealing. Biophys J (1998) 1.05

Squeezing protein shells: how continuum elastic models, molecular dynamics simulations, and experiments coalesce at the nanoscale. Biophys J (2010) 1.05

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Simulated refolding of stretched titin immunoglobulin domains. Biophys J (2001) 1.03

Model for the light-harvesting complex I (B875) of Rhodobacter sphaeroides. Biophys J (1998) 1.02

Possible pathway for ubiquinone shuttling in Rhodospirillum rubrum revealed by molecular dynamics simulation. Biophys J (2006) 1.00

How Quantum Coherence Assists Photosynthetic Light Harvesting. J Phys Chem Lett (2012) 0.99

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Predicting the structure of the light-harvesting complex II of Rhodospirillum molischianum. Protein Sci (1995) 0.96

Molecular dynamics study of glucocorticoid receptor-DNA binding. Proteins (1996) 0.96

Stability and dynamics of G-actin: back-door water diffusion and behavior of a subdomain 3/4 loop. Biophys J (1997) 0.96

How hormone receptor-DNA binding affects nucleosomal DNA: the role of symmetry. Biophys J (1997) 0.96

Quantum dynamics of the femtosecond photoisomerization of retinal in bacteriorhodopsin. Faraday Discuss (1998) 0.95

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Molecular dynamics and experimental investigation of H(2) and O(2) diffusion in [Fe]-hydrogenase. Biochem Soc Trans (2005) 0.94

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Single-cell flux measurement by continuous fluorescence microphotolysis. Eur Biophys J (1985) 0.76

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Neuronal oscillations and stochastic limit cycles. Int J Neural Syst (1996) 0.75

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