Published in Protein Sci on February 01, 2002
Improved side-chain modeling for protein-protein docking. Protein Sci (2005) 2.72
Protein-protein docking with a reduced protein model accounting for side-chain flexibility. Protein Sci (2003) 1.73
Principles of flexible protein-protein docking. Proteins (2008) 1.71
Insights into protein flexibility: The relationship between normal modes and conformational change upon protein-protein docking. Proc Natl Acad Sci U S A (2008) 1.51
Soft docking and multiple receptor conformations in virtual screening. J Med Chem (2004) 1.47
Discrimination of near-native structures in protein-protein docking by testing the stability of local minima. Proteins (2008) 1.27
Pushing structural information into the yeast interactome by high-throughput protein docking experiments. PLoS Comput Biol (2009) 1.22
Rigid Body Energy Minimization on Manifolds for Molecular Docking. J Chem Theory Comput (2012) 1.13
Modeling the structure of bound peptide ligands to major histocompatibility complex. Protein Sci (2004) 1.11
Structural analysis of human and macaque mAbs 2909 and 2.5B: implications for the configuration of the quaternary neutralizing epitope of HIV-1 gp120. Structure (2011) 1.10
FRODOCK: a new approach for fast rotational protein-protein docking. Bioinformatics (2009) 1.09
A simple reference state makes a significant improvement in near-native selections from structurally refined docking decoys. Proteins (2007) 1.05
New benchmark metrics for protein-protein docking methods. Proteins (2011) 0.97
Mapping monomeric threading to protein-protein structure prediction. J Chem Inf Model (2013) 0.94
Configurational-bias sampling technique for predicting side-chain conformations in proteins. Protein Sci (2006) 0.93
Monte Carlo refinement of rigid-body protein docking structures with backbone displacement and side-chain optimization. Protein Sci (2007) 0.91
ASPDock: protein-protein docking algorithm using atomic solvation parameters model. BMC Bioinformatics (2011) 0.90
Stoichiometry and geometry of the CXC chemokine receptor 4 complex with CXC ligand 12: molecular modeling and experimental validation. Proc Natl Acad Sci U S A (2014) 0.88
Modeling Escherichia coli signal peptidase complex with bound substrate: determinants in the mature peptide influencing signal peptide cleavage. BMC Bioinformatics (2008) 0.87
Exploring the interaction between the protein kinase A catalytic subunit and caveolin-1 scaffolding domain with shotgun scanning, oligomer complementation, NMR, and docking. Protein Sci (2006) 0.85
Towards universal structure-based prediction of class II MHC epitopes for diverse allotypes. PLoS One (2010) 0.85
Functional implications of the binding mode of a human conformation-dependent V2 monoclonal antibody against HIV. J Virol (2014) 0.84
pDOCK: a new technique for rapid and accurate docking of peptide ligands to Major Histocompatibility Complexes. Immunome Res (2010) 0.83
DrugScorePPI knowledge-based potentials used as scoring and objective function in protein-protein docking. PLoS One (2014) 0.81
Docking analysis of transient complexes: interaction of ferredoxin-NADP+ reductase with ferredoxin and flavodoxin. Proteins (2008) 0.80
Protein docking by Rotation-Based Uniform Sampling (RotBUS) with fast computing of intermolecular contact distance and residue desolvation. BMC Bioinformatics (2010) 0.79
Refining near-native protein-protein docking decoys by local resampling and energy minimization. Proteins (2009) 0.79
IFACEwat: the interfacial water-implemented re-ranking algorithm to improve the discrimination of near native structures for protein rigid docking. BMC Bioinformatics (2014) 0.78
Evolutionary Conservation of a GPCR-Independent Mechanism of Trimeric G Protein Activation. Mol Biol Evol (2015) 0.78
Modeling, docking, and fitting of atomic structures to 3D maps from cryo-electron microscopy. Methods Mol Biol (2013) 0.77
Structure-based functional characterization of repressor of toxin (Rot), a central regulator of Staphylococcus aureus virulence. J Bacteriol (2014) 0.77
Predicting protein interactions by Brownian dynamics simulations. J Biomed Biotechnol (2012) 0.77
How to use not-always-reliable binding site information in protein-protein docking prediction. PLoS One (2013) 0.77
Computer applications for prediction of protein-protein interactions and rational drug design. Adv Appl Bioinform Chem (2009) 0.77
Neuronal Porosome-The Secretory Portal at the Nerve Terminal: It's Structure-Function, Composition, and Reconstitution. J Mol Struct (2014) 0.77
Detection and characterization of nonspecific, sparsely populated binding modes in the early stages of complexation. J Comput Chem (2015) 0.77
Experiment-Guided Molecular Modeling of Protein-Protein Complexes Involving GPCRs. Methods Mol Biol (2015) 0.77
Scoring docking conformations using predicted protein interfaces. BMC Bioinformatics (2014) 0.77
Multiscale method for modeling binding phenomena involving large objects: application to kinesin motor domains motion along microtubules. Sci Rep (2016) 0.76
Design of Deinococcus radiodurans thioredoxin reductase with altered thioredoxin specificity using computational alanine mutagenesis. Protein Sci (2011) 0.76
Efficient molecular mechanics simulations of the folding, orientation, and assembly of peptides in lipid bilayers using an implicit atomic solvation model. J Comput Aided Mol Des (2011) 0.75
The neuronal porosome complex in health and disease. Exp Biol Med (Maywood) (2015) 0.75
Software for molecular docking: a review. Biophys Rev (2017) 0.75
Porosome in Cystic Fibrosis. Discoveries (Craiova) (2015) 0.75
Development of a novel bioinformatics tool for in silico validation of protein interactions. J Biomed Biotechnol (2010) 0.75
The Protein Data Bank: a computer-based archival file for macromolecular structures. J Mol Biol (1977) 90.57
The atomic structure of protein-protein recognition sites. J Mol Biol (1999) 12.63
Molecular surface recognition: determination of geometric fit between proteins and their ligands by correlation techniques. Proc Natl Acad Sci U S A (1992) 6.86
Biased probability Monte Carlo conformational searches and electrostatic calculations for peptides and proteins. J Mol Biol (1994) 6.41
A computational procedure for determining energetically favorable binding sites on biologically important macromolecules. J Med Chem (1985) 6.09
Monte Carlo-minimization approach to the multiple-minima problem in protein folding. Proc Natl Acad Sci U S A (1987) 5.84
Molecular structure of the acyl-enzyme intermediate in beta-lactam hydrolysis at 1.7 A resolution. Nature (1992) 5.06
Crystal structure of a complex between electron transfer partners, cytochrome c peroxidase and cytochrome c. Science (1992) 4.82
Modelling protein docking using shape complementarity, electrostatics and biochemical information. J Mol Biol (1997) 4.69
Analysis of protein-protein interaction sites using surface patches. J Mol Biol (1997) 4.51
Large-scale protein structure modeling of the Saccharomyces cerevisiae genome. Proc Natl Acad Sci U S A (1998) 4.17
Correlated mutations contain information about protein-protein interaction. J Mol Biol (1997) 3.11
Atomic solvation parameters applied to molecular dynamics of proteins in solution. Protein Sci (1992) 3.05
Flexible protein-ligand docking by global energy optimization in internal coordinates. Proteins (1997) 3.02
Prediction of protein-protein interaction sites using patch analysis. J Mol Biol (1997) 2.91
A potent new mode of beta-lactamase inhibition revealed by the 1.7 A X-ray crystallographic structure of the TEM-1-BLIP complex. Nat Struct Biol (1996) 2.66
Protein docking for low-resolution structures. Protein Eng (1995) 2.40
Hydrophobic docking: a proposed enhancement to molecular recognition techniques. Proteins (1994) 2.36
Rapid refinement of protein interfaces incorporating solvation: application to the docking problem. J Mol Biol (1998) 2.30
"Soft docking": matching of molecular surface cubes. J Mol Biol (1991) 2.19
Shape complementarity at the hemoglobin alpha 1 beta 1 subunit interface. Biopolymers (1986) 1.95
Scoring docked conformations generated by rigid-body protein-protein docking. Proteins (2000) 1.90
Protein docking and complementarity. J Mol Biol (1991) 1.86
New algorithm to model protein-protein recognition based on surface complementarity. Applications to antibody-antigen docking. J Mol Biol (1992) 1.85
BiGGER: a new (soft) docking algorithm for predicting protein interactions. Proteins (2000) 1.76
An analysis of conformational changes on protein-protein association: implications for predictive docking. Protein Eng (1999) 1.63
Structural and kinetic characterization of a beta-lactamase-inhibitor protein. Nature (1994) 1.53
Molecular docking programs successfully predict the binding of a beta-lactamase inhibitory protein to TEM-1 beta-lactamase. Nat Struct Biol (1996) 1.48
A geometry-based suite of molecular docking processes. J Mol Biol (1995) 1.44
PUZZLE: a new method for automated protein docking based on surface shape complementarity. J Mol Biol (1994) 1.37
Prediction of protein complexes using empirical free energy functions. Protein Sci (1996) 1.33
New methodology for computer-aided modelling of biomolecular structure and dynamics. 1. Non-cyclic structures. J Biomol Struct Dyn (1989) 1.33
A fast method to predict protein interaction sites from sequences. J Mol Biol (2000) 1.33
Detailed ab initio prediction of lysozyme-antibody complex with 1.6 A accuracy. Nat Struct Biol (1994) 1.30
Distance-constrained molecular docking by simulated annealing. Protein Eng (1990) 1.24
Examination of shape complementarity in docking of unbound proteins. Proteins (1999) 1.24
Protein-protein recognition analyzed by docking simulation. Proteins (1991) 1.18
A multiple-start Monte Carlo docking method. Proteins (1992) 1.15
Role of configurational gating in intracomplex electron transfer from cytochrome c to the radical cation in cytochrome c peroxidase. Biochemistry (1999) 1.14
Predictive docking of protein-protein and protein-DNA complexes. Curr Opin Struct Biol (1998) 1.13
Optimal protocol and trajectory visualization for conformational searches of peptides and proteins. J Mol Biol (1992) 1.12
Inhibitor-enhanced electron transfer: copper cytochrome c as a redox-inert probe of ternary complexes. Science (1995) 1.08
Hydrogen bonding and molecular surface shape complementarity as a basis for protein docking. J Mol Biol (1996) 1.03
Docking by least-squares fitting of molecular surface patterns. J Mol Biol (1992) 1.02
Atomic solvation parameters in the analysis of protein-protein docking results. Protein Sci (1995) 1.02
ESCHER: a new docking procedure applied to the reconstruction of protein tertiary structure. Proteins (1997) 1.00
Equilibrium thermodynamics of a physiologically-relevant heme-protein complex. Biochemistry (1999) 0.96
N epsilon,N epsilon-dimethyl-lysine cytochrome c as an NMR probe for lysine involvement in protein-protein complex formation. Biochem J (1998) 0.91
Docking enzyme-inhibitor complexes using a preference-based free-energy surface. Proteins (1996) 0.85
New methodology for computer-aided modelling of biomolecular structure and dynamics. 2. Local deformations and cycles. J Biomol Struct Dyn (1989) 0.85
Cytochrome c/cytochrome c peroxidase complex: effect of binding-site mutations on the thermodynamics of complex formation. Biochemistry (1997) 0.83
XCMS: processing mass spectrometry data for metabolite profiling using nonlinear peak alignment, matching, and identification. Anal Chem (2006) 15.00
Structures of the CXCR4 chemokine GPCR with small-molecule and cyclic peptide antagonists. Science (2010) 10.30
METLIN: a metabolite mass spectral database. Ther Drug Monit (2005) 10.15
Sirtuin 2 inhibitors rescue alpha-synuclein-mediated toxicity in models of Parkinson's disease. Science (2007) 5.49
Structure of the human histamine H1 receptor complex with doxepin. Nature (2011) 3.48
Virtual ligand screening of the p300/CBP histone acetyltransferase: identification of a selective small molecule inhibitor. Chem Biol (2010) 3.38
Comparative study of several algorithms for flexible ligand docking. J Comput Aided Mol Des (2003) 3.29
Pocketome via comprehensive identification and classification of ligand binding envelopes. Mol Cell Proteomics (2005) 2.83
Conserved binding mode of human beta2 adrenergic receptor inverse agonists and antagonist revealed by X-ray crystallography. J Am Chem Soc (2010) 2.62
Flexible ligand docking to multiple receptor conformations: a practical alternative. Curr Opin Struct Biol (2008) 2.38
Status of GPCR modeling and docking as reflected by community-wide GPCR Dock 2010 assessment. Structure (2011) 2.11
Nuclear hormone receptor targeted virtual screening. J Med Chem (2003) 2.05
Analysis of full and partial agonists binding to beta2-adrenergic receptor suggests a role of transmembrane helix V in agonist-specific conformational changes. J Mol Recognit (2009) 2.05
Structure-based discovery of novel chemotypes for adenosine A(2A) receptor antagonists. J Med Chem (2010) 1.88
Identification of protein-protein interaction sites from docking energy landscapes. J Mol Biol (2004) 1.79
The liganding of glycolipid transfer protein is controlled by glycolipid acyl structure. PLoS Biol (2006) 1.70
Optimal docking area: a new method for predicting protein-protein interaction sites. Proteins (2005) 1.69
ADP_EM: fast exhaustive multi-resolution docking for high-throughput coverage. Bioinformatics (2006) 1.68
Statistical analysis and prediction of protein-protein interfaces. Proteins (2005) 1.65
Conserved structural elements in the V3 crown of HIV-1 gp120. Nat Struct Mol Biol (2010) 1.63
ICM-DISCO docking by global energy optimization with fully flexible side-chains. Proteins (2003) 1.63
GPCR 3D homology models for ligand screening: lessons learned from blind predictions of adenosine A2a receptor complex. Proteins (2010) 1.57
Match-only integral distribution (MOID) algorithm for high-density oligonucleotide array analysis. BMC Bioinformatics (2002) 1.56
Disseminating structural genomics data to the public: from a data dump to an animated story. Trends Biochem Sci (2006) 1.55
Waltzing transporters and 'the dance macabre' between humans and bacteria. Nat Rev Drug Discov (2006) 1.55
Four-dimensional docking: a fast and accurate account of discrete receptor flexibility in ligand docking. J Med Chem (2009) 1.54
Discovery of diverse thyroid hormone receptor antagonists by high-throughput docking. Proc Natl Acad Sci U S A (2003) 1.53
Excess polymorphisms in genes for membrane proteins in Plasmodium falciparum. Science (2002) 1.52
The GPCR Network: a large-scale collaboration to determine human GPCR structure and function. Nat Rev Drug Discov (2012) 1.50
Identifying conformational changes of the beta(2) adrenoceptor that enable accurate prediction of ligand/receptor interactions and screening for GPCR modulators. J Comput Aided Mol Des (2009) 1.48
Comprehensive identification of "druggable" protein ligand binding sites. Genome Inform (2004) 1.42
Type-II kinase inhibitor docking, screening, and profiling using modified structures of active kinase states. J Med Chem (2008) 1.38
Docking and scoring with ICM: the benchmarking results and strategies for improvement. J Comput Aided Mol Des (2012) 1.34
Structure based prediction of subtype-selectivity for adenosine receptor antagonists. Neuropharmacology (2010) 1.31
Ab initio prediction of peptide-MHC binding geometry for diverse class I MHC allotypes. Proteins (2006) 1.29
Modeling of the aryl hydrocarbon receptor (AhR) ligand binding domain and its utility in virtual ligand screening to predict new AhR ligands. J Med Chem (2009) 1.28
A new method for publishing three-dimensional content. PLoS One (2009) 1.23
Refinement of glucagon-like peptide 1 docking to its intact receptor using mid-region photolabile probes and molecular modeling. J Biol Chem (2011) 1.22
PIER: protein interface recognition for structural proteomics. Proteins (2007) 1.22
Pocketome: an encyclopedia of small-molecule binding sites in 4D. Nucleic Acids Res (2011) 1.21
Small molecules block the polymerization of Z alpha1-antitrypsin and increase the clearance of intracellular aggregates. J Med Chem (2007) 1.21
Predictions of protein flexibility: first-order measures. Proteins (2004) 1.21
Tyrosine phosphorylation of the Gα-interacting protein GIV promotes activation of phosphoinositide 3-kinase during cell migration. Sci Signal (2011) 1.20
3-Hydroxyanthranilic acid inhibits PDK1 activation and suppresses experimental asthma by inducing T cell apoptosis. Proc Natl Acad Sci U S A (2007) 1.20
Recipes for the selection of experimental protein conformations for virtual screening. J Chem Inf Model (2010) 1.17
Molecular approximations between residues 21 and 23 of secretin and its receptor: development of a model for peptide docking with the amino terminus of the secretin receptor. Mol Pharmacol (2007) 1.16
Structural model of nicotinic acetylcholine receptor isotypes bound to acetylcholine and nicotine. BMC Struct Biol (2002) 1.14
Development of a new physics-based internal coordinate mechanics force field and its application to protein loop modeling. Proteins (2011) 1.13
Cross-clade HIV-1 neutralizing antibodies induced with V3-scaffold protein immunogens following priming with gp120 DNA. J Virol (2011) 1.13
Structure-based discovery of natural-product-like TNF-α inhibitors. Angew Chem Int Ed Engl (2010) 1.13
Mapping spatial approximations between the amino terminus of secretin and each of the extracellular loops of its receptor using cysteine trapping. FASEB J (2012) 1.13
Functional importance of a structurally distinct homodimeric complex of the family B G protein-coupled secretin receptor. Mol Pharmacol (2009) 1.12
Consistent improvement of cross-docking results using binding site ensembles generated with elastic network normal modes. J Chem Inf Model (2009) 1.11
Structure-guided design and immunological characterization of immunogens presenting the HIV-1 gp120 V3 loop on a CTB scaffold. Virology (2010) 1.10
Structural analysis of human and macaque mAbs 2909 and 2.5B: implications for the configuration of the quaternary neutralizing epitope of HIV-1 gp120. Structure (2011) 1.10
FRODOCK: a new approach for fast rotational protein-protein docking. Bioinformatics (2009) 1.09
Defining the CD59-C9 binding interaction. J Biol Chem (2006) 1.09
Viral infection controlled by a calcium-dependent lipid-binding module in ALIX. Dev Cell (2013) 1.07
A new method for ligand docking to flexible receptors by dual alanine scanning and refinement (SCARE). J Comput Aided Mol Des (2008) 1.07
A metal-based inhibitor of tumor necrosis factor-α. Angew Chem Int Ed Engl (2012) 1.06
Molecular basis of secretin docking to its intact receptor using multiple photolabile probes distributed throughout the pharmacophore. J Biol Chem (2011) 1.06
Spatial approximation between secretin residue five and the third extracellular loop of its receptor provides new insight into the molecular basis of natural agonist binding. Mol Pharmacol (2008) 1.06
Determinants of retinoid X receptor transcriptional antagonism. J Med Chem (2004) 1.05
Human anti-V3 HIV-1 monoclonal antibodies encoded by the VH5-51/VL lambda genes define a conserved antigenic structure. PLoS One (2011) 1.04
SGC--structural biology and human health: a new approach to publishing structural biology results. PLoS One (2009) 1.02
Protein-RNA and protein-protein recognition by dual KH1/2 domains of the neuronal splicing factor Nova-1. Structure (2011) 1.01
Secretin occupies a single protomer of the homodimeric secretin receptor complex: insights from photoaffinity labeling studies using dual sites of covalent attachment. J Biol Chem (2010) 1.01
Vaccinia virus virulence factor N1L is a novel promising target for antiviral therapeutic intervention. J Med Chem (2010) 1.00
Systematic exploitation of multiple receptor conformations for virtual ligand screening. PLoS One (2011) 0.99
Predicting pK(a) values of substituted phenols from atomic charges: comparison of different quantum mechanical methods and charge distribution schemes. J Chem Inf Model (2011) 0.99
ICFF: a new method to incorporate implicit flexibility into an internal coordinate force field. J Comput Chem (2003) 0.99
Select small core structure carbamates exhibit high contact toxicity to "carbamate-resistant" strain malaria mosquitoes, Anopheles gambiae (Akron). PLoS One (2012) 0.98
Three-dimensional structure of the EphB2 receptor in complex with an antagonistic peptide reveals a novel mode of inhibition. J Biol Chem (2007) 0.98
Improving CAPRI predictions: optimized desolvation for rigid-body docking. Proteins (2005) 0.97
Fluorescence resonance energy transfer analysis of secretin docking to its receptor: mapping distances between residues distributed throughout the ligand pharmacophore and distinct receptor residues. J Biol Chem (2007) 0.96
The transthyretin-related protein family. Eur J Biochem (2003) 0.96
Lapatinib-binding protein kinases in the African trypanosome: identification of cellular targets for kinase-directed chemical scaffolds. PLoS One (2013) 0.96
Long chain amines and long chain ammonium salts as novel inhibitors of dynamin GTPase activity. Bioorg Med Chem Lett (2004) 0.95
ALiBERO: evolving a team of complementary pocket conformations rather than a single leader. J Chem Inf Model (2012) 0.94
Ligand-guided receptor optimization. Methods Mol Biol (2012) 0.94
Insights into the human CD59 complement binding interface toward engineering new therapeutics. J Biol Chem (2005) 0.94
Optimization of adenosine 5'-carboxamide derivatives as adenosine receptor agonists using structure-based ligand design and fragment screening. J Med Chem (2012) 0.93
GPCR agonist binding revealed by modeling and crystallography. Trends Pharmacol Sci (2011) 0.93
Structure-based ligand discovery targeting orthosteric and allosteric pockets of dopamine receptors. Mol Pharmacol (2013) 0.93