Published in J Comput Aided Mol Des on November 21, 2010
Intermediates in the protein folding process: a computational model. Int J Mol Sci (2011) 0.89
A new protein-ligand binding sites prediction method based on the integration of protein sequence conservation information. BMC Bioinformatics (2011) 0.88
Comparison of different ranking methods in protein-ligand binding site prediction. Int J Mol Sci (2012) 0.76
Structural Interface Forms and Their Involvement in Stabilization of Multidomain Proteins or Protein Complexes. Int J Mol Sci (2016) 0.76
Internal force field in proteins seen by divergence entropy. Bioinformation (2011) 0.75
Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers (1983) 99.69
KEGG for linking genomes to life and the environment. Nucleic Acids Res (2007) 49.37
The interpretation of protein structures: estimation of static accessibility. J Mol Biol (1971) 40.24
CATH--a hierarchic classification of protein domain structures. Structure (1997) 29.95
The Protein Data Bank. Acta Crystallogr D Biol Crystallogr (2002) 14.44
Assessing the accuracy of prediction algorithms for classification: an overview. Bioinformatics (2000) 11.75
The Universal Protein Resource (UniProt). Nucleic Acids Res (2006) 11.50
ConSurf 2005: the projection of evolutionary conservation scores of residues on protein structures. Nucleic Acids Res (2005) 10.60
An evolutionary trace method defines binding surfaces common to protein families. J Mol Biol (1996) 9.31
PQS: a protein quaternary structure file server. Trends Biochem Sci (1998) 9.24
CASTp: computed atlas of surface topography of proteins with structural and topographical mapping of functionally annotated residues. Nucleic Acids Res (2006) 9.19
The Catalytic Site Atlas: a resource of catalytic sites and residues identified in enzymes using structural data. Nucleic Acids Res (2004) 7.21
A simplified representation of protein conformations for rapid simulation of protein folding. J Mol Biol (1976) 7.06
Anatomy of protein pockets and cavities: measurement of binding site geometry and implications for ligand design. Protein Sci (1998) 7.03
Q-SiteFinder: an energy-based method for the prediction of protein-ligand binding sites. Bioinformatics (2005) 6.82
SURFNET: a program for visualizing molecular surfaces, cavities, and intermolecular interactions. J Mol Graph (1995) 6.64
ProFunc: a server for predicting protein function from 3D structure. Nucleic Acids Res (2005) 5.79
The impact of structural genomics: expectations and outcomes. Science (2006) 5.30
CASTp: Computed Atlas of Surface Topography of proteins. Nucleic Acids Res (2003) 4.93
Analysis of catalytic residues in enzyme active sites. J Mol Biol (2002) 4.90
Rate4Site: an algorithmic tool for the identification of functional regions in proteins by surface mapping of evolutionary determinants within their homologues. Bioinformatics (2002) 4.54
Type II restriction endonucleases: structure and mechanism. Cell Mol Life Sci (2005) 4.15
LIGSITE: automatic and efficient detection of potential small molecule-binding sites in proteins. J Mol Graph Model (1997) 3.59
eF-site and PDBjViewer: database and viewer for protein functional sites. Bioinformatics (2004) 3.55
LIGSITEcsc: predicting ligand binding sites using the Connolly surface and degree of conservation. BMC Struct Biol (2006) 3.54
TESS: a geometric hashing algorithm for deriving 3D coordinate templates for searching structural databases. Application to enzyme active sites. Protein Sci (1997) 3.50
Evolutionary predictions of binding surfaces and interactions. Curr Opin Struct Biol (2002) 3.43
Structural and catalytic diversity within the amidohydrolase superfamily. Biochemistry (2005) 3.34
A tour of structural genomics. Nat Rev Genet (2001) 3.18
ConSurf: an algorithmic tool for the identification of functional regions in proteins by surface mapping of phylogenetic information. J Mol Biol (2001) 3.14
Recognition of spatial motifs in protein structures. J Mol Biol (1999) 2.94
An accurate, sensitive, and scalable method to identify functional sites in protein structures. J Mol Biol (2003) 2.87
Fast prediction and visualization of protein binding pockets with PASS. J Comput Aided Mol Des (2000) 2.84
Pocketome via comprehensive identification and classification of ligand binding envelopes. Mol Cell Proteomics (2005) 2.83
An algorithm for constraint-based structural template matching: application to 3D templates with statistical analysis. Bioinformatics (2003) 2.70
Druggability indices for protein targets derived from NMR-based screening data. J Med Chem (2005) 2.67
POCKET: a computer graphics method for identifying and displaying protein cavities and their surrounding amino acids. J Mol Graph (1992) 2.57
Structural clusters of evolutionary trace residues are statistically significant and common in proteins. J Mol Biol (2002) 2.50
Automated structure-based prediction of functional sites in proteins: applications to assessing the validity of inheriting protein function from homology in genome annotation and to protein docking. J Mol Biol (2001) 2.46
Recognition of functional sites in protein structures. J Mol Biol (2004) 2.32
Prediction of functionally important residues based solely on the computed energetics of protein structure. J Mol Biol (2001) 2.28
Three-dimensional cluster analysis identifies interfaces and functional residue clusters in proteins. J Mol Biol (2001) 2.17
THEMATICS: a simple computational predictor of enzyme function from structure. Proc Natl Acad Sci U S A (2001) 2.17
Annotation in three dimensions. PINTS: Patterns in Non-homologous Tertiary Structures. Nucleic Acids Res (2003) 2.14
Protein function prediction using local 3D templates. J Mol Biol (2005) 2.13
The ConSurf-DB: pre-calculated evolutionary conservation profiles of protein structures. Nucleic Acids Res (2008) 2.04
A model for statistical significance of local similarities in structure. J Mol Biol (2003) 2.01
Multiple conformational changes in enzyme catalysis. Biochemistry (2002) 1.90
Using a neural network and spatial clustering to predict the location of active sites in enzymes. J Mol Biol (2003) 1.88
Lipases at interfaces: a review. Adv Colloid Interface Sci (2008) 1.86
Mechanistic insights into glycosidase chemistry. Curr Opin Chem Biol (2008) 1.85
Identification of protein functions from a molecular surface database, eF-site. J Struct Funct Genomics (2002) 1.79
Crystal structure of gingipain R: an Arg-specific bacterial cysteine proteinase with a caspase-like fold. EMBO J (1999) 1.79
The automatic search for ligand binding sites in proteins of known three-dimensional structure using only geometric criteria. J Mol Biol (1996) 1.71
Predicting protein druggability. Drug Discov Today (2005) 1.66
Identification of hot spots within druggable binding regions by computational solvent mapping of proteins. J Med Chem (2007) 1.63
A new bioinformatic approach to detect common 3D sites in protein structures. Proteins (2003) 1.62
LigBase: a database of families of aligned ligand binding sites in known protein sequences and structures. Bioinformatics (2002) 1.62
Recognizing protein binding sites using statistical descriptions of their 3D environments. Pac Symp Biocomput (1998) 1.57
MACiE (Mechanism, Annotation and Classification in Enzymes): novel tools for searching catalytic mechanisms. Nucleic Acids Res (2006) 1.57
Ribonuclease H: molecular diversities, substrate binding domains, and catalytic mechanism of the prokaryotic enzymes. FEBS J (2009) 1.48
sc-PDB: an annotated database of druggable binding sites from the Protein Data Bank. J Chem Inf Model (2006) 1.47
Crystal structure of Escherichia coli RNase HI in complex with Mg2+ at 2.8 A resolution: proof for a single Mg(2+)-binding site. Proteins (1993) 1.46
The Cfr10I restriction enzyme is functional as a tetramer. J Mol Biol (1999) 1.46
Comprehensive identification of "druggable" protein ligand binding sites. Genome Inform (2004) 1.42
The SuMo server: 3D search for protein functional sites. Bioinformatics (2005) 1.41
Analysis and prediction of carbohydrate binding sites. Protein Eng (2000) 1.39
Evaluation of features for catalytic residue prediction in novel folds. Protein Sci (2006) 1.39
Functional sites in protein families uncovered via an objective and automated graph theoretic approach. J Mol Biol (2003) 1.37
Methods for the prediction of protein-ligand binding sites for structure-based drug design and virtual ligand screening. Curr Protein Pept Sci (2006) 1.36
Crystal structure of the polysialic acid-degrading endosialidase of bacteriophage K1F. Nat Struct Mol Biol (2004) 1.36
WebFEATURE: An interactive web tool for identifying and visualizing functional sites on macromolecular structures. Nucleic Acids Res (2003) 1.35
From fold predictions to function predictions: automation of functional site conservation analysis for functional genome predictions. Protein Sci (1999) 1.33
Understanding the functional roles of amino acid residues in enzyme catalysis. J Mol Biol (2009) 1.33
Structure and mechanism of metallocarboxypeptidases. Crit Rev Biochem Mol Biol (2008) 1.32
Searching for patterns of amino acids in 3D protein structures. J Chem Inf Comput Sci (2003) 1.28
Accurate sequence-based prediction of catalytic residues. Bioinformatics (2008) 1.20
Characterization of protein-ligand interaction sites using experimental and computational methods. Curr Opin Drug Discov Devel (2006) 1.19
In silico identification of functional regions in proteins. Bioinformatics (2005) 1.18
Structural genomics: keeping up with expanding knowledge of the protein universe. Curr Opin Struct Biol (2007) 1.17
Role of histidine 124 in the catalytic function of ribonuclease HI from Escherichia coli. J Biol Chem (1993) 1.14
Using the radial distributions of physical features to compare amino acid environments and align amino acid sequences. Pac Symp Biocomput (1997) 1.10
MEDock: a web server for efficient prediction of ligand binding sites based on a novel optimization algorithm. Nucleic Acids Res (2005) 1.10
Prediction of functional sites based on the fuzzy oil drop model. PLoS Comput Biol (2007) 1.08
The scientific impact of the Structural Genomics Consortium: a protein family and ligand-centered approach to medically-relevant human proteins. J Struct Funct Genomics (2007) 1.07
Conformational dynamics and enzyme activity. Biochimie (1998) 1.06
PDBLIG: classification of small molecular protein binding in the Protein Data Bank. J Med Chem (2004) 1.04
An improved prediction of catalytic residues in enzyme structures. Protein Eng Des Sel (2008) 1.02
Domain-based small molecule binding site annotation. BMC Bioinformatics (2006) 1.01
Structural genomics and drug discovery: all in the family. Curr Opin Chem Biol (2008) 0.99
Identification of single Mn(2+) binding sites required for activation of the mutant proteins of E.coli RNase HI at Glu48 and/or Asp134 by X-ray crystallography. J Mol Biol (2004) 0.97
SCOWLP classification: structural comparison and analysis of protein binding regions. BMC Bioinformatics (2008) 0.97
Finding functional sites in structural genomics proteins. Structure (2004) 0.96
Mapping of protein surface cavities and prediction of enzyme class by a self-organizing neural network. Protein Eng (2000) 0.95
Accurate detection of protein:ligand binding sites using molecular dynamics simulations. Structure (2004) 0.94
Identification of catalytic residues from protein structure using support vector machine with sequence and structural features. Biochem Biophys Res Commun (2008) 0.92
The expanding diversity of serine hydrolases. Curr Opin Struct Biol (2007) 0.88
Breaking open a protein barrel. Proc Natl Acad Sci U S A (2001) 0.81
Characterization of the cofactor-binding site in the SPOUT-fold methyltransferases by computational docking of S-adenosylmethionine to three crystal structures. BMC Bioinformatics (2003) 0.81
Prediction of catalytic residues using the variation of stereochemical properties. Protein J (2009) 0.81
Hydrophobic collapse in (in silico) protein folding. Comput Biol Chem (2006) 1.16
Fuzzy-oil-drop hydrophobic force field--a model to represent late-stage folding (in silico) of lysozyme. J Biomol Struct Dyn (2006) 1.12
Gauss-function-Based model of hydrophobicity density in proteins. In Silico Biol (2006) 1.10
Prediction of functional sites based on the fuzzy oil drop model. PLoS Comput Biol (2007) 1.08
Hydrophobic collapse in late-stage folding (in silico) of bovine pancreatic trypsin inhibitor. Biochimie (2006) 1.03
Is the protein folding an aim-oriented process? Human haemoglobin as example. Int J Bioinform Res Appl (2007) 0.98
Induction of a tumor-metastasis-receptive microenvironment as an unwanted and underestimated side effect of treatment by chemotherapy or radiotherapy. J Ovarian Res (2013) 0.95
The structure and protein binding of amyloid-specific dye reagents. Acta Biochim Pol (2003) 0.91
Ligation site in proteins recognized in silico. Bioinformation (2006) 0.91
Conformational subspace in simulation of early-stage protein folding. Proteins (2004) 0.90
New advances in stem cell research: practical implications for regenerative medicine. Pol Arch Med Wewn (2014) 0.89
The indirect generation of long-distance structural changes in antibodies upon their binding to antigen. Chem Biol Drug Des (2006) 0.88
Mobilization of CD34+CXCR4+ stem/progenitor cells and the parameters of left ventricular function and remodeling in 1-year follow-up of patients with acute myocardial infarction. Mediators Inflamm (2012) 0.88
Albumin binds self-assembling dyes as specific polymolecular ligands. Int J Biol Macromol (2006) 0.88
Fuzzy oil drop model to interpret the structure of antifreeze proteins and their mutants. J Mol Model (2011) 0.86
Localization of ligand binding site in proteins identified in silico. J Mol Model (2007) 0.84
Early-stage folding in proteins (in silico) sequence-to-structure relation. J Biomed Biotechnol (2005) 0.84
Hypothetical in silico model of the early-stage intermediate in protein folding. J Mol Model (2013) 0.84
Application of the fuzzy-oil-drop model to membrane protein simulation. Proteins (2009) 0.83
Search for structural similarity in proteins. Bioinformatics (2003) 0.82
Circulating very small embryonic-like stem cells in cardiovascular disease. J Cardiovasc Transl Res (2010) 0.82
Very small embryonic-like stem cells in cardiovascular repair. Pharmacol Ther (2010) 0.82
An approach to understand the complexation of supramolecular dye Congo red with immunoglobulin L chain lambda. Biopolymers (2005) 0.81
The use of rigid, fibrillar Congo red nanostructures for scaffolding protein assemblies and inducing the formation of amyloid-like arrangement of molecules. Chem Biol Drug Des (2007) 0.80
"Fuzzy oil drop" model applied to individual small proteins built of 70 amino acids. J Mol Model (2010) 0.80
Local and long-range structural effects caused by the removal of the N-terminal polypeptide fragment from immunoglobulin L chain lambda. Biopolymers (2003) 0.79
Influence of the electric field on supramolecular structure and properties of amyloid-specific reagent Congo red. Eur Biophys J (2011) 0.78
Sequence-structure-function relation characterized in silico. In Silico Biol (2006) 0.78
The increased flexibility of CDR loops generated in antibodies by Congo red complexation favors antigen binding. J Biomol Struct Dyn (2006) 0.78
Conservative secondary structure motifs already present in early-stage folding (in silico) as found in serpines family. J Theor Biol (2007) 0.77
Instability of monoclonal myeloma protein may be identified as susceptibility to penetration and binding by newly synthesized Congo red derivatives. Biochimie (2004) 0.77
Force-field parametrization and molecular dynamics simulations of Congo red. J Comput Aided Mol Des (2004) 0.77
Analysis of correlated domain motions in IgG light chain reveals possible mechanisms of immunological signal transduction. Proteins (2005) 0.77
In silico structural study of random amino acid sequence proteins not present in nature. Chem Biodivers (2009) 0.77
Functional characteristics of small proteins (70 amino acid residues) forming protein-nucleic acid complexes. J Biomol Struct Dyn (2009) 0.77
Protein distorsion-derived mechanism of signal discrimination in monocytes revealed using Congo red to stain activated cells. Folia Histochem Cytobiol (2003) 0.76
The structural abnormality of myeloma immunoglobulins tested by Congo red binding. Med Sci Monit (2003) 0.76
SPI--structure predictability index for protein sequences. In Silico Biol (2004) 0.76
In vivo accumulation of self-assembling dye Congo red in an area marked by specific immune complexes: possible relevance to chemotherapy. Folia Histochem Cytobiol (2004) 0.76
Never born proteins as a test case for ab initio protein structures prediction. Bioinformation (2008) 0.75
"Fuzzy oil drop" model verified positively. Bioinformation (2011) 0.75
Internal force field in proteins seen by divergence entropy. Bioinformation (2011) 0.75
Chaperonin structure: the large multi-subunit protein complex. Int J Mol Sci (2009) 0.75
Statistical dictionaries for hypothetical in silico model of the early-stage intermediate in protein folding. J Comput Aided Mol Des (2015) 0.75
The use of supramolecular structures as protein ligands. J Mol Model (2013) 0.75
Recognition of protein complexation based on hydrophobicity distribution. Bioinformation (2009) 0.75
A tabular approach to the sequence-to-structure relation in proteins (tetrapeptide representation) for de novo protein design. Med Sci Monit (2006) 0.75
ST segment elevation myocardial infarction caused by post-traumatic coronary artery perforation. Kardiol Pol (2017) 0.75
[Selected problems concerning anaemia in systemic lupus erythematosus patients]. Pol Merkur Lekarski (2009) 0.75
The use of the Congo red-related dye DBACR to recognize the heavy chain-derived abnormality of myeloma immunoglobulins. Arch Immunol Ther Exp (Warsz) (2006) 0.75
Serum albumin complexation of acetylsalicylic acid metabolites. Curr Drug Metab (2009) 0.75
Tandemly repeated trinucleotides - comparative analysis. Acta Biochim Pol (2006) 0.75
Electromechanical mapping of the left ventricle for stem cell injection in a patient with permanent atrial fibrillation. Kardiol Pol (2015) 0.75
Hydrophobic core formation in protein complex of cathepsin. J Biomol Struct Dyn (2013) 0.75
Optical Coherence Tomography of De Novo Lesions and In-Stent Restenosis in Coronary Saphenous Vein Grafts (OCTOPUS Study). Circ J (2016) 0.75