Published in J Comput Chem on November 30, 2005
Balancing solvation and intramolecular interactions: toward a consistent generalized Born force field. J Am Chem Soc (2006) 2.59
Principles of flexible protein-protein docking. Proteins (2008) 1.71
Computational techniques for efficient conformational sampling of proteins. Curr Opin Struct Biol (2008) 1.54
Prediction of protein-ligand binding affinity by free energy simulations: assumptions, pitfalls and expectations. J Comput Aided Mol Des (2010) 1.41
Development of a new physics-based internal coordinate mechanics force field and its application to protein loop modeling. Proteins (2011) 1.13
Folding of small proteins using constrained molecular dynamics. J Phys Chem B (2011) 1.11
Structure refinement of protein low resolution models using the GNEIMO constrained dynamics method. J Phys Chem B (2012) 1.08
Application of solid-state NMR restraint potentials in membrane protein modeling. J Magn Reson (2008) 1.03
Transmembrane helix orientation and dynamics: insights from ensemble dynamics with solid-state NMR observables. Biophys J (2011) 1.00
An Evaluation of Explicit Receptor Flexibility in Molecular Docking Using Molecular Dynamics and Torsion Angle Molecular Dynamics. J Chem Theory Comput (2009) 0.98
Solid-state NMR ensemble dynamics as a mediator between experiment and simulation. Biophys J (2011) 0.98
Advanced techniques for constrained internal coordinate molecular dynamics. J Comput Chem (2013) 0.98
On the characterization of protein native state ensembles. Biophys J (2006) 0.97
Molecular dynamics-based approaches for enhanced sampling of long-time, large-scale conformational changes in biomolecules. F1000 Biol Rep (2009) 0.96
Equipartition Principle for Internal Coordinate Molecular Dynamics. J Chem Theory Comput (2012) 0.95
Mapping conformational dynamics of proteins using torsional dynamics simulations. Biophys J (2013) 0.92
Fixman compensating potential for general branched molecules. J Chem Phys (2013) 0.87
Protein structure refinement of CASP target proteins using GNEIMO torsional dynamics method. J Chem Inf Model (2014) 0.86
Computational models of protein kinematics and dynamics: beyond simulation. Annu Rev Anal Chem (Palo Alto Calif) (2012) 0.84
GneimoSim: a modular internal coordinates molecular dynamics simulation package. J Comput Chem (2014) 0.83
Monte Carlo, harmonic approximation, and coarse-graining approaches for enhanced sampling of biomolecular structure. F1000 Biol Rep (2009) 0.81
Bioactive conformational generation of small molecules: a comparative analysis between force-field and multiple empirical criteria based methods. BMC Bioinformatics (2010) 0.80
A simple molecular mechanics integrator in mixed rigid body and dihedral angle space. J Chem Phys (2014) 0.80
Deuterium Labeling Together with Contrast Variation Small-Angle Neutron Scattering Suggests How Skp Captures and Releases Unfolded Outer Membrane Proteins. Methods Enzymol (2015) 0.77
Atomistic modelling of scattering data in the Collaborative Computational Project for Small Angle Scattering (CCP-SAS). J Appl Crystallogr (2016) 0.77
Internal coordinate molecular dynamics: a foundation for multiscale dynamics. J Phys Chem B (2015) 0.75
Overcoming potential energy distortions in constrained internal coordinate molecular dynamics simulations. J Chem Phys (2016) 0.75
Adaptive conformational sampling based on replicas. J Math Biol (2011) 0.75
Hamiltonian Monte Carlo with Constrained Molecular Dynamics as Gibbs Sampling. J Chem Theory Comput (2017) 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
The mechanism and pathway of pH induced swelling in cowpea chlorotic mottle virus. J Mol Biol (2002) 2.24
Symmetry, form, and shape: guiding principles for robustness in macromolecular machines. Annu Rev Biophys Biomol Struct (2006) 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
Implicit solvation based on generalized Born theory in different dielectric environments. J Chem Phys (2004) 2.00
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
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
Structure, thermodynamics, and liquid-vapor equilibrium of ethanol from molecular-dynamics simulations using nonadditive interactions. J Chem Phys (2005) 1.27
Ribosome motions modulate electrostatic properties. Biopolymers (2004) 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
Implicit modeling of nonpolar solvation for simulating protein folding and conformational transitions. Phys Chem Chem Phys (2007) 1.25
Lambda-dynamics free energy simulation methods. J Comput Chem (2009) 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
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
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
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
The 13 angstroms structure of a chaperonin GroEL-protein substrate complex by cryo-electron microscopy. J Mol Biol (2005) 1.19
An electrostatic basis for the stability of thermophilic proteins. Proteins (2004) 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
Subdomain competition, cooperativity, and topological frustration in the folding of CheY. J Mol Biol (2008) 1.10