Published in Proteins on June 01, 2007
Progress and challenges in protein structure prediction. Curr Opin Struct Biol (2008) 3.48
Atomic-level protein structure refinement using fragment-guided molecular dynamics conformation sampling. Structure (2011) 2.97
Protein structure prediction: when is it useful? Curr Opin Struct Biol (2009) 2.52
Recent advances in implicit solvent-based methods for biomolecular simulations. Curr Opin Struct Biol (2008) 2.20
Toward better refinement of comparative models: predicting loops in inexact environments. Proteins (2008) 2.06
Assessment of protein structure refinement in CASP9. Proteins (2011) 2.06
A novel side-chain orientation dependent potential derived from random-walk reference state for protein fold selection and structure prediction. PLoS One (2010) 1.56
Assessment of the protein-structure refinement category in CASP8. Proteins (2009) 1.53
Identification of a 3rd Na+ Binding Site of the Glycine Transporter, GlyT2. PLoS One (2016) 1.40
Solvent dramatically affects protein structure refinement. Proc Natl Acad Sci U S A (2008) 1.29
Refining homology models by combining replica-exchange molecular dynamics and statistical potentials. Proteins (2008) 1.25
Molecular simulations of protein dynamics: new windows on mechanisms in biology. EMBO Rep (2008) 1.25
Physics-based protein structure refinement through multiple molecular dynamics trajectories and structure averaging. Proteins (2013) 1.20
Protein model refinement using an optimized physics-based all-atom force field. Proc Natl Acad Sci U S A (2008) 1.18
Construction and validation of a homology model of the human voltage-gated proton channel hHV1. J Gen Physiol (2013) 1.17
Development of a physics-based force field for the scoring and refinement of protein models. Biophys J (2008) 1.17
3Drefine: consistent protein structure refinement by optimizing hydrogen bonding network and atomic-level energy minimization. Proteins (2012) 1.12
HAAD: A quick algorithm for accurate prediction of hydrogen atoms in protein structures. PLoS One (2009) 1.02
Protein Structure Refinement through Structure Selection and Averaging from Molecular Dynamics Ensembles. J Chem Theory Comput (2012) 1.00
Intrinsically disordered proteins in a physics-based world. Int J Mol Sci (2010) 0.97
FoldGPCR: structure prediction protocol for the transmembrane domain of G protein-coupled receptors from class A. Proteins (2010) 0.95
Identifying native-like protein structures with scoring functions based on all-atom ECEPP force fields, implicit solvent models and structure relaxation. Proteins (2009) 0.90
Symmetry-restrained molecular dynamics simulations improve homology models of potassium channels. Proteins (2010) 0.87
Can molecular dynamics simulations help in discriminating correct from erroneous protein 3D models? BMC Bioinformatics (2008) 0.86
Protein flexibility: coordinate uncertainties and interpretation of structural differences. Acta Crystallogr D Biol Crystallogr (2009) 0.85
i3Drefine software for protein 3D structure refinement and its assessment in CASP10. PLoS One (2013) 0.82
Structural models of TREK channels and their gating mechanism. Channels (Austin) (2011) 0.82
Ensemble MD simulations restrained via crystallographic data: accurate structure leads to accurate dynamics. Protein Sci (2014) 0.82
Use of decoys to optimize an all-atom force field including hydration. Biophys J (2008) 0.80
Re-evaluation of the reported experimental values of the heat of vaporization of N-methylacetamide. J Chem Theory Comput (2008) 0.79
Predicting structurally conserved contacts for homologous proteins using sequence conservation filters. Proteins (2009) 0.79
Refining near-native protein-protein docking decoys by local resampling and energy minimization. Proteins (2009) 0.79
Molecular dynamics simulations: advances and applications. Adv Appl Bioinform Chem (2015) 0.78
Parallelization and improvements of the generalized born model with a simple sWitching function for modern graphics processors. J Comput Chem (2016) 0.78
The electrostatic profile of consecutive Cβ atoms applied to protein structure quality assessment. F1000Res (2013) 0.77
A versatile method for systematic conformational searches: application to CheY. J Comput Chem (2011) 0.77
Assessment of the utility of contact-based restraints in accelerating the prediction of protein structure using molecular dynamics simulations. Protein Sci (2015) 0.77
Protein NMR structures refined without NOE data. PLoS One (2014) 0.77
Protein Folding and Structure Prediction from the Ground Up II: AAWSEM for α/β Proteins. J Phys Chem B (2016) 0.76
Evaluation of unrestrained replica-exchange simulations using dynamic walkers in temperature space for protein structure refinement. PLoS One (2014) 0.76
FF12MC: A revised AMBER forcefield and new protein simulation protocol. Proteins (2016) 0.76
Modeling of Escherichia coli Endonuclease V structure in complex with DNA. J Mol Model (2008) 0.76
Knowledge-based entropies improve the identification of native protein structures. Proc Natl Acad Sci U S A (2017) 0.76
Computational Approaches for Revealing the Structure of Membrane Transporters: Case Study on Bilitranslocase. Comput Struct Biotechnol J (2017) 0.75
Smoothing protein energy landscapes by integrating folding models with structure prediction. Biophys J (2011) 0.75
Average and extreme multi-atom Van der Waals interactions: strong coupling of multi-atom Van der Waals interactions with covalent bonding. Chem Cent J (2007) 0.75
Computational functional group mapping for drug discovery. Drug Discov Today (2016) 0.75
Use of multiple picosecond high-mass molecular dynamics simulations to predict crystallographic B-factors of folded globular proteins. Heliyon (2016) 0.75
Partial unfolding and refolding for structure refinement: A unified approach of geometric simulations and molecular dynamics. Proteins (2015) 0.75
Examination of the quality of various force fields and solvation models for the equilibrium simulations of GA88 and GB88. J Mol Model (2016) 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
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
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
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
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
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
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
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
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
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
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
Evolution and physics in comparative protein structure modeling. Acc Chem Res (2002) 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
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
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
Modern protein force fields behave comparably in molecular dynamics simulations. J Comput Chem (2002) 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
Subdomain competition, cooperativity, and topological frustration in the folding of CheY. J Mol Biol (2008) 1.10
3D maps of RNA interhelical junctions. Nat Protoc (2011) 1.10
Electrostatic properties of cowpea chlorotic mottle virus and cucumber mosaic virus capsids. Biopolymers (2006) 1.08
Conformational dynamics in human purine nucleoside phosphorylase with reactants and transition-state analogues. J Phys Chem B (2010) 1.07
Exploring icosahedral virus structures with VIPER. Nat Rev Microbiol (2005) 1.07
Chaperone activation by unfolding. Proc Natl Acad Sci U S A (2013) 1.07
Folding intermediate in the villin headpiece domain arises from disruption of a N-terminal hydrogen-bonded network. J Am Chem Soc (2007) 1.07
Deprotonation by dehydration: the origin of ammonium sensing in the AmtB channel. PLoS Comput Biol (2006) 1.06
Unraveling the structural complexity in a single-stranded RNA tail: implications for efficient ligand binding in the prequeuosine riboswitch. Nucleic Acids Res (2011) 1.06
Statistical determinants of selective ionic complexation: ions in solvent, transport proteins, and other "hosts". Biophys J (2009) 1.05
Detailed considerations for a balanced and broadly applicable force field: a study of substituted benzenes modeled with OPLS-AA. J Comput Chem (2005) 1.05
Conformational change of the methionine 20 loop of Escherichia coli dihydrofolate reductase modulates pKa of the bound dihydrofolate. Protein Sci (2007) 1.05
pH-dependent dynamics of complex RNA macromolecules. J Chem Theory Comput (2013) 1.05
Cooperative and directional folding of the preQ1 riboswitch aptamer domain. J Am Chem Soc (2011) 1.05
Hydrophobic cooperativity as a mechanism for amyloid nucleation. J Mol Biol (2007) 1.04
Hierarchy of RNA functional dynamics. Annu Rev Biochem (2014) 1.04
Topological constraints: using RNA secondary structure to model 3D conformation, folding pathways, and dynamic adaptation. Curr Opin Struct Biol (2011) 1.04
Revisiting the hexane-water interface via molecular dynamics simulations using nonadditive alkane-water potentials. J Chem Phys (2006) 1.04
Application of solid-state NMR restraint potentials in membrane protein modeling. J Magn Reson (2008) 1.03