Published in J Mol Model on September 09, 2007
Dynamic interaction of the measles virus hemagglutinin with its receptor signaling lymphocytic activation molecule (SLAM, CD150). J Biol Chem (2008) 1.29
Base of the measles virus fusion trimer head receives the signal that triggers membrane fusion. J Biol Chem (2012) 1.18
InterProSurf: a web server for predicting interacting sites on protein surfaces. Bioinformatics (2007) 1.14
Automated detection of conformational epitopes using phage display Peptide sequences. Bioinform Biol Insights (2009) 1.09
Joint evolutionary trees: a large-scale method to predict protein interfaces based on sequence sampling. PLoS Comput Biol (2009) 1.07
Engineering cytochrome P450 biocatalysts for biotechnology, medicine and bioremediation. Expert Opin Drug Metab Toxicol (2010) 1.07
The role of entropy and polarity in intermolecular contacts in protein crystals. Acta Crystallogr D Biol Crystallogr (2009) 1.06
Comprehensive 3D-modeling of allergenic proteins and amino acid composition of potential conformational IgE epitopes. Mol Immunol (2008) 1.05
Protein docking prediction using predicted protein-protein interface. BMC Bioinformatics (2012) 1.00
Linking genotype and phenotype of Saccharomyces cerevisiae strains reveals metabolic engineering targets and leads to triterpene hyper-producers. PLoS One (2011) 0.94
Overcoming Chemical, Biological, and Computational Challenges in the Development of Inhibitors Targeting Protein-Protein Interactions. Chem Biol (2015) 0.91
Structural analysis of linear and conformational epitopes of allergens. Regul Toxicol Pharmacol (2008) 0.85
Protein-protein interaction site predictions with three-dimensional probability distributions of interacting atoms on protein surfaces. PLoS One (2012) 0.82
Progress and challenges in predicting protein interfaces. Brief Bioinform (2015) 0.81
Local Geometry and Evolutionary Conservation of Protein Surfaces Reveal the Multiple Recognition Patches in Protein-Protein Interactions. PLoS Comput Biol (2015) 0.81
AllerTOP v.2--a server for in silico prediction of allergens. J Mol Model (2014) 0.76
CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res (1994) 392.47
BIND: the Biomolecular Interaction Network Database. Nucleic Acids Res (2003) 18.75
DIP, the Database of Interacting Proteins: a research tool for studying cellular networks of protein interactions. Nucleic Acids Res (2002) 15.70
Principles of protein-protein interactions. Proc Natl Acad Sci U S A (1996) 14.51
The atomic structure of protein-protein recognition sites. J Mol Biol (1999) 12.63
Assessing the accuracy of prediction algorithms for classification: an overview. Bioinformatics (2000) 11.75
ConSurf 2005: the projection of evolutionary conservation scores of residues on protein structures. Nucleic Acids Res (2005) 10.60
A hot spot of binding energy in a hormone-receptor interface. Science (1995) 10.41
Anatomy of hot spots in protein interfaces. J Mol Biol (1998) 9.70
ConSurf: identification of functional regions in proteins by surface-mapping of phylogenetic information. Bioinformatics (2003) 7.83
A simple physical model for binding energy hot spots in protein-protein complexes. Proc Natl Acad Sci U S A (2002) 6.18
Unraveling hot spots in binding interfaces: progress and challenges. Curr Opin Struct Biol (2002) 6.06
Protein interaction databases. Curr Opin Biotechnol (2001) 5.22
The structure of protein-protein recognition sites. J Biol Chem (1990) 4.55
Dissecting protein-protein recognition sites. Proteins (2002) 4.51
Analysis of protein-protein interaction sites using surface patches. J Mol Biol (1997) 4.51
Convergent solutions to binding at a protein-protein interface. Science (2000) 4.47
The crystal structure of the human hepatitis B virus capsid. Mol Cell (1999) 4.36
Protein-protein interactions: a review of protein dimer structures. Prog Biophys Mol Biol (1995) 3.98
A dissection of specific and non-specific protein-protein interfaces. J Mol Biol (2004) 3.77
Protein-protein interactions: structurally conserved residues distinguish between binding sites and exposed protein surfaces. Proc Natl Acad Sci U S A (2003) 3.42
Computational alanine scanning of protein-protein interfaces. Sci STKE (2004) 3.41
ProMate: a structure based prediction program to identify the location of protein-protein binding sites. J Mol Biol (2004) 3.18
Residue frequencies and pairing preferences at protein-protein interfaces. Proteins (2001) 3.09
Studies of protein-protein interfaces: a statistical analysis of the hydrophobic effect. Protein Sci (1997) 3.00
Improved prediction of protein-protein binding sites using a support vector machines approach. Bioinformatics (2004) 2.93
Prediction of protein-protein interaction sites using patch analysis. J Mol Biol (1997) 2.91
An accurate, sensitive, and scalable method to identify functional sites in protein structures. J Mol Biol (2003) 2.87
Predicting protein--protein interactions from primary structure. Bioinformatics (2001) 2.82
Structure-based assignment of the biochemical function of a hypothetical protein: a test case of structural genomics. Proc Natl Acad Sci U S A (1998) 2.70
ASEdb: a database of alanine mutations and their effects on the free energy of binding in protein interactions. Bioinformatics (2001) 2.60
Conservation of polar residues as hot spots at protein interfaces. Proteins (2000) 2.42
Delaunay tessellation of proteins: four body nearest-neighbor propensities of amino acid residues. J Comput Biol (1996) 2.29
Prediction of protein interaction sites from sequence profile and residue neighbor list. Proteins (2001) 2.21
Three-dimensional cluster analysis identifies interfaces and functional residue clusters in proteins. J Mol Biol (2001) 2.17
PRISM: protein interactions by structural matching. Nucleic Acids Res (2005) 2.11
Combinatorial alanine-scanning. Curr Opin Chem Biol (2001) 1.82
Prediction of protein--protein interaction sites in heterocomplexes with neural networks. Eur J Biochem (2002) 1.74
Electrostatic complementarity at protein/protein interfaces. J Mol Biol (1997) 1.67
Statistical analysis and prediction of protein-protein interfaces. Proteins (2005) 1.65
Prediction of protein-protein interaction sites using support vector machines. Protein Eng Des Sel (2004) 1.54
Protein domain interfaces: characterization and comparison with oligomeric protein interfaces. Protein Eng (2000) 1.43
Structure-based method for analyzing protein-protein interfaces. J Mol Model (2003) 1.35
A fast method to predict protein interaction sites from sequences. J Mol Biol (2000) 1.33
Evolutionary trace report_maker: a new type of service for comparative analysis of proteins. Bioinformatics (2006) 1.30
SHARP2: protein-protein interaction predictions using patch analysis. Bioinformatics (2006) 1.25
Analysis of homodimeric protein interfaces by graph-spectral methods. Protein Eng (2002) 1.22
Strong hydrophobic nature of cysteine residues in proteins. FEBS Lett (1999) 1.22
Protein-protein interactions as a target for drugs in proteomics. Proteomics (2003) 1.19
Identifying property based sequence motifs in protein families and superfamilies: application to DNase-1 related endonucleases. Bioinformatics (2003) 1.15
Protein informatics towards function identification. Curr Opin Struct Biol (2003) 1.10
Determining functionally important amino acid residues of the E1 protein of Venezuelan equine encephalitis virus. J Mol Model (2006) 1.00
Atom density in protein structures. Proc Natl Acad Sci U S A (1999) 0.88
Construction of protein binding sites in scaffold structures. Biopolymers (2000) 0.82
The enhanced LBG algorithm. Neural Netw (2001) 0.76
Selectively receptor-blind measles viruses: Identification of residues necessary for SLAM- or CD46-induced fusion and their localization on a new hemagglutinin structural model. J Virol (2004) 2.42
Measles virus blind to its epithelial cell receptor remains virulent in rhesus monkeys but cannot cross the airway epithelium and is not shed. J Clin Invest (2008) 2.21
SDAP: database and computational tools for allergenic proteins. Nucleic Acids Res (2003) 1.61
The heads of the measles virus attachment protein move to transmit the fusion-triggering signal. Nat Struct Mol Biol (2011) 1.61
Conformational flexibility of mammalian cytochrome P450 2B4 in binding imidazole inhibitors with different ring chemistry and side chains. Solution thermodynamics and molecular modeling. J Biol Chem (2006) 1.35
Dynamic interaction of the measles virus hemagglutinin with its receptor signaling lymphocytic activation molecule (SLAM, CD150). J Biol Chem (2008) 1.29
Host S-nitrosylation inhibits clostridial small molecule-activated glucosylating toxins. Nat Med (2011) 1.19
Base of the measles virus fusion trimer head receives the signal that triggers membrane fusion. J Biol Chem (2012) 1.18
Nearby clusters of hemagglutinin residues sustain SLAM-dependent canine distemper virus entry in peripheral blood mononuclear cells. J Virol (2005) 1.17
A "moving metal mechanism" for substrate cleavage by the DNA repair endonuclease APE-1. Proteins (2007) 1.16
Identifying property based sequence motifs in protein families and superfamilies: application to DNase-1 related endonucleases. Bioinformatics (2003) 1.15
InterProSurf: a web server for predicting interacting sites on protein surfaces. Bioinformatics (2007) 1.14
Data mining of sequences and 3D structures of allergenic proteins. Bioinformatics (2002) 1.10
Automated detection of conformational epitopes using phage display Peptide sequences. Bioinform Biol Insights (2009) 1.09
Membrane-protein interactions contribute to efficient 27-hydroxylation of cholesterol by mitochondrial cytochrome P450 27A1. J Biol Chem (2002) 1.08
Membrane fusion triggering: three modules with different structure and function in the upper half of the measles virus attachment protein stalk. J Biol Chem (2012) 1.07
Molego-based definition of the architecture and specificity of metal-binding sites. Proteins (2005) 1.05
Comprehensive 3D-modeling of allergenic proteins and amino acid composition of potential conformational IgE epitopes. Mol Immunol (2008) 1.05
Major linear IgE epitopes of mountain cedar pollen allergen Jun a 1 map to the pectate lyase catalytic site. Mol Immunol (2003) 1.02
Determining functionally important amino acid residues of the E1 protein of Venezuelan equine encephalitis virus. J Mol Model (2006) 1.00
The property distance index PD predicts peptides that cross-react with IgE antibodies. Mol Immunol (2008) 0.99
NMR structure of the viral peptide linked to the genome (VPg) of poliovirus. Peptides (2006) 0.99
Characteristic motifs for families of allergenic proteins. Mol Immunol (2008) 0.98
Stereophysicochemical variability plots highlight conserved antigenic areas in Flaviviruses. Virol J (2005) 0.98
Using property based sequence motifs and 3D modeling to determine structure and functional regions of proteins. Curr Med Chem (2004) 0.98
Effects of backbone contacts 3' to the abasic site on the cleavage and the product binding by human apurinic/apyrimidinic endonuclease (APE1). Biochemistry (2004) 0.97
Unusual role of a cysteine residue in substrate binding and activity of human AP-endonuclease 1. J Mol Biol (2008) 0.94
Common physical-chemical properties correlate with similar structure of the IgE epitopes of peanut allergens. J Agric Food Chem (2005) 0.94
Bioinformatics approaches to classifying allergens and predicting cross-reactivity. Immunol Allergy Clin North Am (2007) 0.94
Structural basis for epitope sharing between group 1 allergens of cedar pollen. Mol Immunol (2005) 0.91
Detecting potential IgE-reactive sites on food proteins using a sequence and structure database, SDAP-food. J Agric Food Chem (2003) 0.90
Structural and functional analysis of Aplysia attractins, a family of water-borne protein pheromones with interspecific attractiveness. Proc Natl Acad Sci U S A (2004) 0.90
Total sequence decomposition distinguishes functional modules, "molegos" in apurinic/apyrimidinic endonucleases. BMC Bioinformatics (2002) 0.89
Identification and analysis of conserved sequence motifs in cytochrome P450 family 2. Functional and structural role of a motif 187RFDYKD192 in CYP2B enzymes. J Biol Chem (2008) 0.87
Validation of a phage display and computational algorithm by mapping a conformational epitope of Bla g 2. Int Arch Allergy Immunol (2011) 0.87
A multimeric model for murine anti-apoptotic protein Bcl-2 and structural insights for its regulation by post-translational modification. J Mol Model (2003) 0.86
Mechanical stability and differentially conserved physical-chemical properties of titin Ig-domains. Proteins (2009) 0.86
Structural analysis of linear and conformational epitopes of allergens. Regul Toxicol Pharmacol (2008) 0.85
NMR solution structure of attractin, a water-borne protein pheromone from the mollusk Aplysia californica. Biochemistry (2003) 0.84
An Allergen Portrait Gallery: Representative Structures and an Overview of IgE Binding Surfaces. Bioinform Biol Insights (2010) 0.83
NMR solution structure of poliovirus uridylyated peptide linked to the genome (VPgpU). Peptides (2010) 0.82
MD simulation and experimental evidence for Mg²+ binding at the B site in human AP endonuclease 1. Bioinformation (2011) 0.80
Automated assignment and 3D structure calculations using combinations of 2D homonuclear and 3D heteronuclear NOESY spectra. J Biomol NMR (2002) 0.80
Co-localization of glyceraldehyde-3-phosphate dehydrogenase with ferredoxin-NADP reductase in pea leaf chloroplasts. J Struct Biol (2007) 0.80
Clostridial toxins: sensing a target in a hostile gut environment. Gut Microbes (2012) 0.80
Molluscan attractins, a family of water-borne protein pheromones with interspecific attractiveness. Peptides (2005) 0.77
Robust quantitative modeling of peptide binding affinities for MHC molecules using physical-chemical descriptors. Protein Pept Lett (2007) 0.77
Assessment of 3D models for allergen research. Proteins (2013) 0.76
Engineering proteins with enhanced mechanical stability by force-specific sequence motifs. Proteins (2012) 0.75
AllerML: markup language for allergens. Regul Toxicol Pharmacol (2011) 0.75
Cross-React: a new structural bioinformatics method for predicting allergen cross-reactivity. Bioinformatics (2017) 0.75
D-graph clusters flaviviruses and β-coronaviruses according to their hosts, disease type and human cell receptors. bioRxiv (2020) 0.75