Published in J Chem Phys on January 08, 2004
The Amber biomolecular simulation programs. J Comput Chem (2005) 28.84
DOCK 6: combining techniques to model RNA-small molecule complexes. RNA (2009) 2.75
Balancing solvation and intramolecular interactions: toward a consistent generalized Born force field. J Am Chem Soc (2006) 2.59
Prediction of water and metal binding sites and their affinities by using the Fold-X force field. Proc Natl Acad Sci U S A (2005) 2.31
Recent advances in implicit solvent-based methods for biomolecular simulations. Curr Opin Struct Biol (2008) 2.20
MIBPB: a software package for electrostatic analysis. J Comput Chem (2010) 1.77
Progress in the prediction of pKa values in proteins. Proteins (2011) 1.36
APBSmem: a graphical interface for electrostatic calculations at the membrane. PLoS One (2010) 1.12
Computational protein design is a challenge for implicit solvation models. Biophys J (2004) 1.08
Thermodynamics of beta-sheet formation in polyglutamine. Biophys J (2009) 1.07
Conformational sampling of peptides in cellular environments. Biophys J (2007) 1.04
Conformational sampling of peptides in the presence of protein crowders from AA/CG-multiscale simulations. J Phys Chem B (2012) 1.01
Polarizable Atomic Multipole Solutes in a Generalized Kirkwood Continuum. J Chem Theory Comput (2007) 0.98
Coarse-grained model for simulation of RNA three-dimensional structures. J Phys Chem B (2010) 0.98
Continuum polarizable force field within the Poisson-Boltzmann framework. J Phys Chem B (2008) 0.97
Discovery of ligands for a novel target, the human telomerase RNA, based on flexible-target virtual screening and NMR. J Med Chem (2008) 0.92
Flexible gates generate occluded intermediates in the transport cycle of LacY. J Mol Biol (2014) 0.92
Dynamic Heterogeneous Dielectric Generalized Born (DHDGB): An implicit membrane model with a dynamically varying bilayer thickness. J Chem Theory Comput (2013) 0.90
A revised density function for molecular surface definition in continuum solvent models. J Chem Theory Comput (2010) 0.89
Effect of membrane thickness on conformational sampling of phospholamban from computer simulations. Biophys J (2010) 0.89
An N log N approximation based on the natural organization of biomolecules for speeding up the computation of long range interactions. J Comput Chem (2010) 0.87
A strategy for reducing gross errors in the generalized Born models of implicit solvation. J Chem Phys (2011) 0.87
Ab initio simulation of a 57-residue protein in explicit solvent reproduces the native conformation in the lowest free-energy cluster. Protein Sci (2011) 0.85
Distinct phenotype of a Wilson disease mutation reveals a novel trafficking determinant in the copper transporter ATP7B. Proc Natl Acad Sci U S A (2014) 0.85
Cooperative nature of gating transitions in K(+) channels as seen from dynamic importance sampling calculations. Proteins (2010) 0.85
An induced pocket for the binding of potent fusion inhibitor CL-385319 with H5N1 influenza virus hemagglutinin. PLoS One (2012) 0.84
Speed of conformational change: comparing explicit and implicit solvent molecular dynamics simulations. Biophys J (2015) 0.83
Double bilayers and transmembrane gradients: a molecular dynamics study of a highly charged peptide. Biophys J (2008) 0.83
Fast Analytical Methods for Macroscopic Electrostatic Models in Biomolecular Simulations. SIAM Rev Soc Ind Appl Math (2011) 0.81
From the gating charge response to pore domain movement: initial motions of Kv1.2 dynamics under physiological voltage changes. Mol Membr Biol (2009) 0.80
Perspectives on the simulation of protein-surface interactions using empirical force field methods. Colloids Surf B Biointerfaces (2014) 0.80
Molecular dynamics and docking simulations as a proof of high flexibility in E. coli FabH and its relevance for accurate inhibitor modeling. J Comput Aided Mol Des (2011) 0.80
Effect of flanking residues on the conformational sampling of the internal fusion peptide from Ebola virus. Proteins (2011) 0.79
The role of domain: domain interactions versus domain: water interactions in the coarse-grained simulations of the E1P to E2P transitions in Ca-ATPase (SERCA). Proteins (2012) 0.77
Conformational preferences of DNA in reduced dielectric environments. J Phys Chem B (2014) 0.77
Wrapping effects within a proposed function-rescue strategy for the Y220C oncogenic mutation of protein p53. PLoS One (2013) 0.76
A protocol for the refinement of NMR structures using simultaneously pseudocontact shift restraints from multiple lanthanide ions. J Biomol NMR (2016) 0.75
Prediction of consensus binding mode geometries for related chemical series of positive allosteric modulators of adenosine and muscarinic acetylcholine receptors. J Comput Chem (2017) 0.75
Molecular dynamics exploration of the binding mechanism and properties of single-walled carbon nanotube to WT and mutant VP35 FBP region of Ebola virus. J Biol Phys (2017) 0.75
Implicit Solvent Model for Million-Atom Atomistic Simulations: Insights into the Organization of 30-nm Chromatin Fiber. J Chem Theory Comput (2016) 0.75
Incorporating excluded solvent volume and physical dipoles for computing solvation free energy. J Mol Model (2015) 0.75
Extending the treatment of backbone energetics in protein force fields: limitations of gas-phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations. J Comput Chem (2004) 17.97
Improved treatment of the protein backbone in empirical force fields. J Am Chem Soc (2004) 5.96
CHARMM-GUI: a web-based graphical user interface for CHARMM. J Comput Chem (2008) 5.81
MMTSB Tool Set: enhanced sampling and multiscale modeling methods for applications in structural biology. J Mol Graph Model (2004) 5.50
Recent advances in the development and application of implicit solvent models in biomolecule simulations. Curr Opin Struct Biol (2004) 4.46
Generalized born model with a simple smoothing function. J Comput Chem (2003) 4.36
Performance comparison of generalized born and Poisson methods in the calculation of electrostatic solvation energies for protein structures. J Comput Chem (2004) 3.83
New analytic approximation to the standard molecular volume definition and its application to generalized Born calculations. J Comput Chem (2003) 3.81
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
Comparative study of several algorithms for flexible ligand docking. J Comput Aided Mol Des (2003) 3.29
CHARMM-GUI Membrane Builder for mixed bilayers and its application to yeast membranes. Biophys J (2009) 3.27
Detailed analysis of grid-based molecular docking: A case study of CDOCKER-A CHARMm-based MD docking algorithm. J Comput Chem (2003) 3.27
Structure of the E. coli protein-conducting channel bound to a translating ribosome. Nature (2005) 3.10
An implicit membrane generalized born theory for the study of structure, stability, and interactions of membrane proteins. Biophys J (2003) 2.91
The origins of asymmetry in the folding transition states of protein L and protein G. Protein Sci (2002) 2.81
CHARMM fluctuating charge force field for proteins: I parameterization and application to bulk organic liquid simulations. J Comput Chem (2004) 2.80
CHARMM fluctuating charge force field for proteins: II protein/solvent properties from molecular dynamics simulations using a nonadditive electrostatic model. J Comput Chem (2004) 2.79
Normal mode based flexible fitting of high-resolution structure into low-resolution experimental data from cryo-EM. J Struct Biol (2004) 2.78
Automated builder and database of protein/membrane complexes for molecular dynamics simulations. PLoS One (2007) 2.65
Balancing solvation and intramolecular interactions: toward a consistent generalized Born force field. J Am Chem Soc (2006) 2.59
Constant-pH molecular dynamics using continuous titration coordinates. Proteins (2004) 2.52
Correlated motion and the effect of distal mutations in dihydrofolate reductase. Proc Natl Acad Sci U S A (2003) 2.50
VIPERdb: a relational database for structural virology. Nucleic Acids Res (2006) 2.46
Constant pH molecular dynamics with proton tautomerism. Biophys J (2005) 2.44
Assessing scoring functions for protein-ligand interactions. J Med Chem (2004) 2.41
Theoretical and computational models of biological ion channels. Q Rev Biophys (2004) 2.41
VIPERdb2: an enhanced and web API enabled relational database for structural virology. Nucleic Acids Res (2008) 2.38
Symmetry, form, and shape: guiding principles for robustness in macromolecular machines. Annu Rev Biophys Biomol Struct (2006) 2.24
The mechanism and pathway of pH induced swelling in cowpea chlorotic mottle virus. J Mol Biol (2002) 2.24
Large-scale allosteric conformational transitions of adenylate kinase appear to involve a population-shift mechanism. Proc Natl Acad Sci U S A (2007) 2.24
Community-wide assessment of GPCR structure modelling and ligand docking: GPCR Dock 2008. Nat Rev Drug Discov (2009) 2.23
Recent advances in implicit solvent-based methods for biomolecular simulations. Curr Opin Struct Biol (2008) 2.20
Flexible multi-scale fitting of atomic structures into low-resolution electron density maps with elastic network normal mode analysis. J Mol Biol (2004) 2.19
The structural basis for biphasic kinetics in the folding of the WW domain from a formin-binding protein: lessons for protein design? Proc Natl Acad Sci U S A (2003) 2.05
Ribosome assembly factors prevent premature translation initiation by 40S assembly intermediates. Science (2011) 2.01
Exploring global distortions of biological macromolecules and assemblies from low-resolution structural information and elastic network theory. J Mol Biol (2002) 1.98
Ion permeation through the alpha-hemolysin channel: theoretical studies based on Brownian dynamics and Poisson-Nernst-Plank electrodiffusion theory. Biophys J (2004) 1.91
CHARMM-GUI Membrane Builder toward realistic biological membrane simulations. J Comput Chem (2014) 1.89
Toward the accurate first-principles prediction of ionization equilibria in proteins. Biochemistry (2006) 1.88
A modified TIP3P water potential for simulation with Ewald summation. J Chem Phys (2004) 1.86
Can molecular dynamics simulations provide high-resolution refinement of protein structure? Proteins (2007) 1.83
Selectivity in K+ channels is due to topological control of the permeant ion's coordinated state. Proc Natl Acad Sci U S A (2007) 1.82
Diversity and identity of mechanical properties of icosahedral viral capsids studied with elastic network normal mode analysis. J Mol Biol (2005) 1.81
Improved Gō-like models demonstrate the robustness of protein folding mechanisms towards non-native interactions. J Mol Biol (2003) 1.76
Probing the folding free energy landscape of the Src-SH3 protein domain. Proc Natl Acad Sci U S A (2002) 1.68
Interfacial folding and membrane insertion of designed peptides studied by molecular dynamics simulations. Proc Natl Acad Sci U S A (2005) 1.66
PBEQ-Solver for online visualization of electrostatic potential of biomolecules. Nucleic Acids Res (2008) 1.61
Albumin binding to FcRn: distinct from the FcRn-IgG interaction. Biochemistry (2006) 1.57
Deciphering the kinetic mechanism of spontaneous self-assembly of icosahedral capsids. Nano Lett (2007) 1.56
Differences in the electrostatic surfaces of the type III secretion needle proteins PrgI, BsaL, and MxiH. J Mol Biol (2007) 1.53
Insights from coarse-grained Gō models for protein folding and dynamics. Int J Mol Sci (2009) 1.52
Identifying native-like protein structures using physics-based potentials. J Comput Chem (2002) 1.51
Application of torsion angle molecular dynamics for efficient sampling of protein conformations. J Comput Chem (2005) 1.48
Linking folding with aggregation in Alzheimer's beta-amyloid peptides. Proc Natl Acad Sci U S A (2007) 1.42
The coupling of structural fluctuations to hydride transfer in dihydrofolate reductase. Proteins (2004) 1.37
Transmembrane helix tilting: insights from calculating the potential of mean force. Phys Rev Lett (2008) 1.35
The effects of ionic strength on protein stability: the cold shock protein family. J Mol Biol (2002) 1.34
Model-free analysis of protein dynamics: assessment of accuracy and model selection protocols based on molecular dynamics simulation. J Biomol NMR (2004) 1.32
Revisiting hydrophobic mismatch with free energy simulation studies of transmembrane helix tilt and rotation. Biophys J (2010) 1.31
Evolution and physics in comparative protein structure modeling. Acc Chem Res (2002) 1.29
Novel pyrrolopyrimidine-based α-helix mimetics: cell-permeable inhibitors of protein−protein interactions. J Am Chem Soc (2011) 1.29
Ribosome motions modulate electrostatic properties. Biopolymers (2004) 1.27
Structure, thermodynamics, and liquid-vapor equilibrium of ethanol from molecular-dynamics simulations using nonadditive interactions. J Chem Phys (2005) 1.27
Molecular evolution of affinity and flexibility in the immune system. Proc Natl Acad Sci U S A (2007) 1.26
Antibody evolution constrains conformational heterogeneity by tailoring protein dynamics. Proc Natl Acad Sci U S A (2006) 1.26
Lambda-dynamics free energy simulation methods. J Comput Chem (2009) 1.25
Implicit modeling of nonpolar solvation for simulating protein folding and conformational transitions. Phys Chem Chem Phys (2007) 1.25
Membrane assembly of simple helix homo-oligomers studied via molecular dynamics simulations. Biophys J (2006) 1.23
MATCH: an atom-typing toolset for molecular mechanics force fields. J Comput Chem (2011) 1.22
Exploring Flory's isolated-pair hypothesis: statistical mechanics of helix-coil transitions in polyalanine and the C-peptide from RNase A. Proc Natl Acad Sci U S A (2003) 1.21
Coiled coils at the edge of configurational heterogeneity. Structural analyses of parallel and antiparallel homotetrameric coiled coils reveal configurational sensitivity to a single solvent-exposed amino acid substitution. Biochemistry (2006) 1.21
De novo folding of membrane proteins: an exploration of the structure and NMR properties of the fd coat protein. J Mol Biol (2004) 1.21
Integrating folding kinetics and protein function: biphasic kinetics and dual binding specificity in a WW domain. Proc Natl Acad Sci U S A (2004) 1.21
A nonadditive methanol force field: bulk liquid and liquid-vapor interfacial properties via molecular dynamics simulations using a fluctuating charge model. J Chem Phys (2005) 1.21
Invariant polymorphism in virus capsid assembly. J Am Chem Soc (2009) 1.20
Peptide and protein folding and conformational equilibria: theoretical treatment of electrostatics and hydrogen bonding with implicit solvent models. Adv Protein Chem (2005) 1.20
An electrostatic basis for the stability of thermophilic proteins. Proteins (2004) 1.19
The 13 angstroms structure of a chaperonin GroEL-protein substrate complex by cryo-electron microscopy. J Mol Biol (2005) 1.19
Exploring atomistic details of pH-dependent peptide folding. Proc Natl Acad Sci U S A (2006) 1.17
Constant pH Molecular Dynamics Simulations of Nucleic Acids in Explicit Solvent. J Chem Theory Comput (2012) 1.17
The requirement for mechanical coupling between head and S2 domains in smooth muscle myosin ATPase regulation and its implications for dimeric motor function. J Mol Biol (2005) 1.17
A general method to quantify quasi-equivalence in icosahedral viruses. J Mol Biol (2002) 1.16
Influence of hydrophobic mismatch on structures and dynamics of gramicidin a and lipid bilayers. Biophys J (2012) 1.15
Evaluating CASP4 predictions with physical energy functions. Proteins (2002) 1.14
Refinement of NMR structures using implicit solvent and advanced sampling techniques. J Am Chem Soc (2004) 1.14
Critical importance of length-scale dependence in implicit modeling of hydrophobic interactions. J Am Chem Soc (2007) 1.14
Removal of divalent cations induces structural transitions in red clover necrotic mosaic virus, revealing a potential mechanism for RNA release. J Virol (2006) 1.14
An essential sensor histidine kinase controlled by transmembrane helix interactions with its auxiliary proteins. Proc Natl Acad Sci U S A (2008) 1.13
Conformational substates modulate hydride transfer in dihydrofolate reductase. J Am Chem Soc (2005) 1.13
Generation of native-like protein structures from limited NMR data, modern force fields and advanced conformational sampling. J Biomol NMR (2005) 1.12
How dihydrofolate reductase facilitates protonation of dihydrofolate. J Am Chem Soc (2003) 1.11
Tryptophan side chain electrostatic interactions determine edge-to-face vs parallel-displaced tryptophan side chain geometries in the designed beta-hairpin "trpzip2". J Am Chem Soc (2005) 1.11
Modern protein force fields behave comparably in molecular dynamics simulations. J Comput Chem (2002) 1.11