Published in Proteins on November 22, 2011
The FTMap family of web servers for determining and characterizing ligand-binding hot spots of proteins. Nat Protoc (2015) 1.26
Low-resolution structural modeling of protein interactome. Curr Opin Struct Biol (2013) 1.09
Protein-protein docking: from interaction to interactome. Biophys J (2014) 1.05
Comprehensive experimental and computational analysis of binding energy hot spots at the NF-κB essential modulator/IKKβ protein-protein interface. J Am Chem Soc (2013) 0.91
Rotamer libraries and probabilities of transition between rotamers for the side chains in protein-protein binding. Proteins (2012) 0.86
FTFlex: accounting for binding site flexibility to improve fragment-based identification of druggable hot spots. Bioinformatics (2013) 0.85
A New Distributed Algorithm for Side-Chain Positioning in the Process of Protein Docking(*) Proc IEEE Conf Decis Control (2013) 0.81
The impact of side-chain packing on protein docking refinement. J Chem Inf Model (2015) 0.80
Correlation analysis of the side-chains conformational distribution in bound and unbound proteins. BMC Bioinformatics (2012) 0.80
Challenges in structural approaches to cell modeling. J Mol Biol (2016) 0.78
Pushing the Backbone in Protein-Protein Docking. Structure (2016) 0.78
New Additions to the ClusPro Server Motivated by CAPRI. Proteins (2016) 0.75
CHARMM: the biomolecular simulation program. J Comput Chem (2009) 27.71
The energy landscapes and motions of proteins. Science (1991) 18.93
Application of a Theory of Enzyme Specificity to Protein Synthesis. Proc Natl Acad Sci U S A (1958) 9.18
Protein-protein docking with simultaneous optimization of rigid-body displacement and side-chain conformations. J Mol Biol (2003) 8.35
Ligand binding and co-activator assembly of the peroxisome proliferator-activated receptor-gamma. Nature (1998) 8.33
The role of dynamic conformational ensembles in biomolecular recognition. Nat Chem Biol (2009) 7.36
Backbone-dependent rotamer library for proteins. Application to side-chain prediction. J Mol Biol (1993) 6.26
Diffusion-controlled macromolecular interactions. Annu Rev Biophys Biophys Chem (1985) 4.87
New tools provide new insights in NMR studies of protein dynamics. Science (2006) 4.64
Folding funnels, binding funnels, and protein function. Protein Sci (1999) 4.22
Rotamer libraries in the 21st century. Curr Opin Struct Biol (2002) 4.09
Fundamental aspects of protein-protein association kinetics. Chem Rev (2009) 3.43
Hidden alternative structures of proline isomerase essential for catalysis. Nature (2009) 3.28
Folding funnels and binding mechanisms. Protein Eng (1999) 3.25
Induced fit, conformational selection and independent dynamic segments: an extended view of binding events. Trends Biochem Sci (2010) 2.97
FireDock: fast interaction refinement in molecular docking. Proteins (2007) 2.90
Protein-protein docking benchmark version 3.0. Proteins (2008) 2.54
Flexible ligand docking using conformational ensembles. Protein Sci (1998) 2.43
Flexible ligand docking to multiple receptor conformations: a practical alternative. Curr Opin Struct Biol (2008) 2.38
Anchor residues in protein-protein interactions. Proc Natl Acad Sci U S A (2004) 2.35
Ensemble docking of multiple protein structures: considering protein structural variations in molecular docking. Proteins (2007) 2.03
Kinetics of desolvation-mediated protein-protein binding. Biophys J (2000) 2.03
Convergence and combination of methods in protein-protein docking. Curr Opin Struct Biol (2009) 2.00
Structural conservation of druggable hot spots in protein-protein interfaces. Proc Natl Acad Sci U S A (2011) 1.95
Accommodating protein flexibility in computational drug design. Mol Pharmacol (2000) 1.84
Molecular docking to ensembles of protein structures. J Mol Biol (1997) 1.80
Side-chain flexibility in proteins upon ligand binding. Proteins (2000) 1.70
Protein-protein interactions: hot spots and structurally conserved residues often locate in complemented pockets that pre-organized in the unbound states: implications for docking. J Mol Biol (2004) 1.64
Realistic protein-protein association rates from a simple diffusional model neglecting long-range interactions, free energy barriers, and landscape ruggedness. Protein Sci (2004) 1.47
Dynamical view of the positions of key side chains in protein-protein recognition. Biophys J (2001) 1.42
Antigen recognition by conformational selection. FEBS Lett (1999) 1.42
The relationship between the flexibility of proteins and their conformational states on forming protein-protein complexes with an application to protein-protein docking. J Mol Biol (2005) 1.41
Conformational switching in an aspartic proteinase. Nat Struct Biol (1998) 1.24
Spectroscopic, calorimetric, and kinetic demonstration of conformational adaptation in peptide-antibody recognition. Biochemistry (1995) 1.03
Side-chain conformational changes upon Protein-Protein Association. J Mol Biol (2011) 0.98
Protein conformer selection by ligand binding observed with crystallography. Protein Sci (1998) 0.92
Approaches to solving the rigid receptor problem by identifying a minimal set of flexible residues during ligand docking. Chem Biol (2001) 0.89
Statistically based reduced representation of amino acid side chains. J Chem Inf Comput Sci (2004) 0.77
PISCES: a protein sequence culling server. Bioinformatics (2003) 11.87
A graph-theory algorithm for rapid protein side-chain prediction. Protein Sci (2003) 9.25
Antibacterial and antifungal activity of cicerfuran and related 2-arylbenzofurans and stilbenes. Microbiol Res (2007) 7.16
CAPRI: a Critical Assessment of PRedicted Interactions. Proteins (2003) 6.36
ClusPro: an automated docking and discrimination method for the prediction of protein complexes. Bioinformatics (2004) 6.04
Improved prediction of protein side-chain conformations with SCWRL4. Proteins (2009) 5.67
Formation of MacroH2A-containing senescence-associated heterochromatin foci and senescence driven by ASF1a and HIRA. Dev Cell (2005) 4.83
Cyclic coordinate descent: A robotics algorithm for protein loop closure. Protein Sci (2003) 4.82
PIPER: an FFT-based protein docking program with pairwise potentials. Proteins (2006) 4.31
ClusPro: a fully automated algorithm for protein-protein docking. Nucleic Acids Res (2004) 4.10
PONDR-FIT: a meta-predictor of intrinsically disordered amino acids. Biochim Biophys Acta (2010) 3.62
PISCES: recent improvements to a PDB sequence culling server. Nucleic Acids Res (2005) 3.55
Fragment-based identification of druggable 'hot spots' of proteins using Fourier domain correlation techniques. Bioinformatics (2009) 3.00
A smoothed backbone-dependent rotamer library for proteins derived from adaptive kernel density estimates and regressions. Structure (2011) 2.61
CAFASP3: the third critical assessment of fully automated structure prediction methods. Proteins (2003) 2.60
Anchor residues in protein-protein interactions. Proc Natl Acad Sci U S A (2004) 2.35
Conformation dependence of backbone geometry in proteins. Structure (2009) 2.33
Achieving reliability and high accuracy in automated protein docking: ClusPro, PIPER, SDU, and stability analysis in CAPRI rounds 13-19. Proteins (2010) 2.32
Outcome of a workshop on archiving structural models of biological macromolecules. Structure (2006) 2.32
Outcome of a workshop on applications of protein models in biomedical research. Structure (2009) 2.05
Convergence and combination of methods in protein-protein docking. Curr Opin Struct Biol (2009) 2.00
Structural conservation of druggable hot spots in protein-protein interfaces. Proc Natl Acad Sci U S A (2011) 1.95
Accelerating and focusing protein-protein docking correlations using multi-dimensional rotational FFT generating functions. Bioinformatics (2008) 1.93
Structural profiling of endogenous S-nitrosocysteine residues reveals unique features that accommodate diverse mechanisms for protein S-nitrosylation. Proc Natl Acad Sci U S A (2010) 1.87
Aurora A kinase (AURKA) in normal and pathological cell division. Cell Mol Life Sci (2012) 1.84
A new clustering of antibody CDR loop conformations. J Mol Biol (2010) 1.83
Assignment of protein sequences to existing domain and family classification systems: Pfam and the PDB. Bioinformatics (2012) 1.82
How good is automated protein docking? Proteins (2013) 1.80
SCWRL and MolIDE: computer programs for side-chain conformation prediction and homology modeling. Nat Protoc (2008) 1.79
MxCuBE: a synchrotron beamline control environment customized for macromolecular crystallography experiments. J Synchrotron Radiat (2010) 1.71
Scoring profile-to-profile sequence alignments. Protein Sci (2004) 1.71
Assessment of disorder predictions in CASP6. Proteins (2005) 1.69
Novel druggable hot spots in avian influenza neuraminidase H5N1 revealed by computational solvent mapping of a reduced and representative receptor ensemble. Chem Biol Drug Des (2008) 1.69
Promotion of tumor growth by murine fibroblast activation protein, a serine protease, in an animal model. Cancer Res (2002) 1.66
Identification of hot spots within druggable binding regions by computational solvent mapping of proteins. J Med Chem (2007) 1.63
Optimal clustering for detecting near-native conformations in protein docking. Biophys J (2005) 1.59
Computational mapping identifies the binding sites of organic solvents on proteins. Proc Natl Acad Sci U S A (2002) 1.56
Statistical analysis of interface similarity in crystals of homologous proteins. J Mol Biol (2008) 1.55
Oligomerization of BAK by p53 utilizes conserved residues of the p53 DNA binding domain. J Biol Chem (2008) 1.55
DARS (Decoys As the Reference State) potentials for protein-protein docking. Biophys J (2008) 1.50
ClusPro: performance in CAPRI rounds 6-11 and the new server. Proteins (2007) 1.46
Neighbor-dependent Ramachandran probability distributions of amino acids developed from a hierarchical Dirichlet process model. PLoS Comput Biol (2010) 1.44
Identification of a male-produced aggregation pheromone in the western flower thrips Frankliniella occidentalis. J Chem Ecol (2005) 1.42
Assessment of fold recognition predictions in CASP6. Proteins (2005) 1.41
MollDE: a homology modeling framework you can click with. Bioinformatics (2005) 1.40
Identification of substrate binding sites in enzymes by computational solvent mapping. J Mol Biol (2003) 1.37
Protein docking by the underestimation of free energy funnels in the space of encounter complexes. PLoS Comput Biol (2008) 1.36
Statistical and conformational analysis of the electron density of protein side chains. Proteins (2007) 1.35
Reversing chemoresistance by small molecule inhibition of the translation initiation complex eIF4F. Proc Natl Acad Sci U S A (2010) 1.30
Detection of ligand binding hot spots on protein surfaces via fragment-based methods: application to DJ-1 and glucocerebrosidase. J Comput Aided Mol Des (2009) 1.30
The protein common interface database (ProtCID)--a comprehensive database of interactions of homologous proteins in multiple crystal forms. Nucleic Acids Res (2010) 1.30
Identification and field activity of a male-produced aggregation pheromone in the pine sawyer beetle, Monochamus galloprovincialis. J Chem Ecol (2010) 1.29
Discrimination of near-native structures in protein-protein docking by testing the stability of local minima. Proteins (2008) 1.27
FTSite: high accuracy detection of ligand binding sites on unbound protein structures. Bioinformatics (2011) 1.25
Protein-protein association kinetics and protein docking. Curr Opin Struct Biol (2002) 1.24
Nonplanar peptide bonds in proteins are common and conserved but not biased toward active sites. Proc Natl Acad Sci U S A (2011) 1.23
Analysis of binding site hot spots on the surface of Ras GTPase. J Mol Biol (2011) 1.22
SDU: A Semidefinite Programming-Based Underestimation Method for Stochastic Global Optimization in Protein Docking. IEEE Trans Automat Contr (2007) 1.22
Community-wide evaluation of methods for predicting the effect of mutations on protein-protein interactions. Proteins (2013) 1.20
Crystal structure and DNA-binding analysis of RecO from Deinococcus radiodurans. EMBO J (2005) 1.18
A male-predominant cuticular hydrocarbon, 7-methyltricosane, is used as a contact pheromone in the western flower thrips Frankliniella occidentalis. J Chem Ecol (2013) 1.15
BioDownloader: bioinformatics downloads and updates in a few clicks. Bioinformatics (2007) 1.14
A modified HSP70 inhibitor shows broad activity as an anticancer agent. Mol Cancer Res (2013) 1.14
Rigid Body Energy Minimization on Manifolds for Molecular Docking. J Chem Theory Comput (2012) 1.13
Hot spot analysis for driving the development of hits into leads in fragment-based drug discovery. J Chem Inf Model (2011) 1.13
Ligand binding and activation of PPARγ by Firemaster® 550: effects on adipogenesis and osteogenesis in vitro. Environ Health Perspect (2014) 1.12
A new model for allosteric regulation of phenylalanine hydroxylase: implications for disease and therapeutics. Arch Biochem Biophys (2013) 1.11
ProtBuD: a database of biological unit structures of protein families and superfamilies. Bioinformatics (2006) 1.09
The structural basis of pregnane X receptor binding promiscuity. Biochemistry (2009) 1.09
The role of balanced training and testing data sets for binary classifiers in bioinformatics. PLoS One (2013) 1.09
Application of asymmetric statistical potentials to antibody-protein docking. Bioinformatics (2012) 1.08