Published in Nucleic Acids Res on November 27, 2006
Fr-TM-align: a new protein structural alignment method based on fragment alignments and the TM-score. BMC Bioinformatics (2008) 1.50
Prediction of enzyme function based on 3D templates of evolutionarily important amino acids. BMC Bioinformatics (2008) 1.41
De-orphaning the structural proteome through reciprocal comparison of evolutionarily important structural features. PLoS One (2008) 1.20
Comparison of structure-based and threading-based approaches to protein functional annotation. Proteins (2010) 1.11
Protein function prediction: towards integration of similarity metrics. Curr Opin Struct Biol (2011) 1.00
Sequence and structure continuity of evolutionary importance improves protein functional site discovery and annotation. Protein Sci (2010) 0.96
The SALAMI protein structure search server. Nucleic Acids Res (2009) 0.94
Exploring protein dynamics space: the dynasome as the missing link between protein structure and function. PLoS One (2012) 0.93
Constructing de novo biosynthetic pathways for chemical synthesis inside living cells. Biochemistry (2011) 0.91
Improving protein secondary structure prediction based on short subsequences with local structure similarity. BMC Genomics (2010) 0.88
deconSTRUCT: general purpose protein database search on the substructure level. Nucleic Acids Res (2010) 0.85
Reduced representation of protein structure: implications on efficiency and scope of detection of structural similarity. BMC Bioinformatics (2010) 0.84
Protein sequence and structure alignments within one framework. Algorithms Mol Biol (2008) 0.80
Recent advances in functional region prediction by using structural and evolutionary information - Remaining problems and future extensions. Comput Struct Biotechnol J (2013) 0.80
GOSSIP: a method for fast and accurate global alignment of protein structures. Bioinformatics (2011) 0.80
Alignment-free local structural search by writhe decomposition. Bioinformatics (2010) 0.79
Exploring representations of protein structure for automated remote homology detection and mapping of protein structure space. BMC Bioinformatics (2014) 0.78
Random amino acid mutations and protein misfolding lead to Shannon limit in sequence-structure communication. PLoS One (2008) 0.75
Basic local alignment search tool. J Mol Biol (1990) 659.07
The Protein Data Bank. Nucleic Acids Res (2000) 187.10
The Gene Ontology (GO) database and informatics resource. Nucleic Acids Res (2004) 54.37
NCBI Reference Sequence (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Res (2005) 37.39
Protein structure comparison by alignment of distance matrices. J Mol Biol (1993) 34.74
Secondary-structure matching (SSM), a new tool for fast protein structure alignment in three dimensions. Acta Crystallogr D Biol Crystallogr (2004) 31.52
Protein structure alignment by incremental combinatorial extension (CE) of the optimal path. Protein Eng (1998) 28.09
Surprising similarities in structure comparison. Curr Opin Struct Biol (1996) 22.27
Design of a novel globular protein fold with atomic-level accuracy. Science (2003) 13.06
Enlarged representative set of protein structures. Protein Sci (1994) 7.98
Evolution of function in protein superfamilies, from a structural perspective. J Mol Biol (2001) 6.63
Computational design of receptor and sensor proteins with novel functions. Nature (2003) 5.48
Threading a database of protein cores. Proteins (1995) 5.38
The impact of structural genomics: expectations and outcomes. Science (2006) 5.30
Predicting protein function from sequence and structural data. Curr Opin Struct Biol (2005) 4.31
Comprehensive evaluation of protein structure alignment methods: scoring by geometric measures. J Mol Biol (2005) 4.02
One fold with many functions: the evolutionary relationships between TIM barrel families based on their sequences, structures and functions. J Mol Biol (2002) 3.88
Searching protein structure databases has come of age. Proteins (1994) 3.87
Thioredoxin--a fold for all reasons. Structure (1995) 3.85
Retracted Computational design of a biologically active enzyme. Science (2004) 3.25
Protein structure comparison using the markov transition model of evolution. Proteins (2000) 2.94
Functional proteins from a random-sequence library. Nature (2001) 2.81
Computational thermostabilization of an enzyme. Science (2005) 2.79
The protein structure prediction problem could be solved using the current PDB library. Proc Natl Acad Sci U S A (2005) 2.75
The structural alignment between two proteins: is there a unique answer? Protein Sci (1996) 2.50
FATCAT: a web server for flexible structure comparison and structure similarity searching. Nucleic Acids Res (2004) 2.49
Evolution of protein structures and functions. Curr Opin Struct Biol (2002) 2.38
Protein structure comparison: implications for the nature of 'fold space', and structure and function prediction. Curr Opin Struct Biol (2006) 2.37
FAST: a novel protein structure alignment algorithm. Proteins (2005) 2.27
Recovery of protein structure from contact maps. Fold Des (1997) 2.25
Detection of protein three-dimensional side-chain patterns: new examples of convergent evolution. J Mol Biol (1998) 2.15
The protein threading problem with sequence amino acid interaction preferences is NP-complete. Protein Eng (1994) 2.05
Automatic classification of protein structure by using Gauss integrals. Proc Natl Acad Sci U S A (2002) 2.03
From structure to function: approaches and limitations. Nat Struct Biol (2000) 1.96
Evaluation of protein fold comparison servers. Proteins (2004) 1.94
Protein structure similarities. Curr Opin Struct Biol (2001) 1.89
More than the sum of their parts: on the evolution of proteins from peptides. Bioessays (2003) 1.83
Assessing the performance of fold recognition methods by means of a comprehensive benchmark. Pac Symp Biocomput (1996) 1.75
From protein structure to function. Curr Opin Struct Biol (1999) 1.58
Protein fold similarity estimated by a probabilistic approach based on C(alpha)-C(alpha) distance comparison. J Mol Biol (2002) 1.56
Hierarchical protein structure superposition using both secondary structure and atomic representations. Proc Int Conf Intell Syst Mol Biol (1997) 1.54
Motif-based searching in TOPS protein topology databases. Bioinformatics (1999) 1.47
The CATH protein family database: a resource for structural and functional annotation of genomes. Proteomics (2002) 1.33
The ups and downs of protein topology; rapid comparison of protein structure. Protein Eng (2000) 1.27
The structure of the C4C4 ring finger of human NOT4 reveals features distinct from those of C3HC4 RING fingers. J Biol Chem (2000) 1.25
The impact of structural genomics on the protein data bank. Am J Pharmacogenomics (2004) 1.21
Definitions of enzyme function for the structural genomics era. Curr Opin Chem Biol (2003) 1.19
Superfamily active site templates. Proteins (2004) 1.15
Structurally analogous proteins do exist! Structure (2004) 1.12
Déjà vu all over again: finding and analyzing protein structure similarities. Structure (2004) 1.10
CASP3 comparative modeling evaluation. Proteins (1999) 1.09
Recurrent use of evolutionary importance for functional annotation of proteins based on local structural similarity. Protein Sci (2006) 1.08
Reconstruction of protein structures from a vectorial representation. Phys Rev Lett (2004) 1.06
Efficient recognition of folds in protein 3D structures by the improved PRIDE algorithm. Bioinformatics (2005) 1.02
Prediction of protein function in the absence of significant sequence similarity. Curr Med Chem (2004) 1.00
Recoverable one-dimensional encoding of three-dimensional protein structures. Bioinformatics (2005) 0.99
Crystal structure of the hyperthermophilic archaeal DNA-binding protein Sso10b2 at a resolution of 1.85 Angstroms. J Bacteriol (2003) 0.98
Finding functional sites in structural genomics proteins. Structure (2004) 0.96
A novel ADP- and zinc-binding fold from function-directed in vitro evolution. Nat Struct Mol Biol (2004) 0.94
PROuST: a comparison method of three-dimensional structures of proteins using indexing techniques. J Comput Biol (2004) 0.93
Structural analysis of carboxypeptidase A and its complexes with inhibitors as a basis for modeling enzyme recognition and specificity. Biopolymers (1985) 0.92
Thermal stability and DNA binding activity of a variant form of the Sso7d protein from the archeon Sulfolobus solfataricus truncated at leucine 54. Biochemistry (2003) 0.84
Prediction of protein function from structure: insights from methods for the detection of local structural similarities. Biotechniques (2005) 0.83
beta-arrestin-dependent, G protein-independent ERK1/2 activation by the beta2 adrenergic receptor. J Biol Chem (2005) 4.91
A large-scale evaluation of computational protein function prediction. Nat Methods (2013) 4.61
Identification of a candidate therapeutic autophagy-inducing peptide. Nature (2013) 3.76
An accurate, sensitive, and scalable method to identify functional sites in protein structures. J Mol Biol (2003) 2.87
Structural clusters of evolutionary trace residues are statistically significant and common in proteins. J Mol Biol (2002) 2.50
Mitochondrial neurogastrointestinal encephalopathy due to mutations in RRM2B. Arch Neurol (2009) 1.85
Evolutionary trace of G protein-coupled receptors reveals clusters of residues that determine global and class-specific functions. J Biol Chem (2003) 1.65
Distinct faces of the Ku heterodimer mediate DNA repair and telomeric functions. Nat Struct Mol Biol (2007) 1.55
ET viewer: an application for predicting and visualizing functional sites in protein structures. Bioinformatics (2006) 1.55
Characterization of retinal guanylate cyclase-activating protein 3 (GCAP3) from zebrafish to man. Eur J Neurosci (2002) 1.52
Identity and function of a large gene network underlying mutagenic repair of DNA breaks. Science (2012) 1.52
An AT-hook domain in MeCP2 determines the clinical course of Rett syndrome and related disorders. Cell (2013) 1.49
Prediction of enzyme function based on 3D templates of evolutionarily important amino acids. BMC Bioinformatics (2008) 1.41
Evolution-guided discovery and recoding of allosteric pathway specificity determinants in psychoactive bioamine receptors. Proc Natl Acad Sci U S A (2010) 1.32
Essential helix interactions in the anion transporter domain of prestin revealed by evolutionary trace analysis. J Neurosci (2006) 1.22
De-orphaning the structural proteome through reciprocal comparison of evolutionarily important structural features. PLoS One (2008) 1.20
Evolutionary trace annotation of protein function in the structural proteome. J Mol Biol (2009) 1.16
Evolutionary trace-based peptides identify a novel asymmetric interaction that mediates oligomerization in nuclear receptors. J Biol Chem (2005) 1.10
Graph sharpening plus graph integration: a synergy that improves protein functional classification. Bioinformatics (2007) 1.10
Recurrent use of evolutionary importance for functional annotation of proteins based on local structural similarity. Protein Sci (2006) 1.08
Evolution of neural precursor selection: functional divergence of proneural proteins. Development (2004) 1.07
Separation of recombination and SOS response in Escherichia coli RecA suggests LexA interaction sites. PLoS Genet (2011) 1.07
Role for the regulator of G-protein signaling homology domain of G protein-coupled receptor kinases 5 and 6 in beta 2-adrenergic receptor and rhodopsin phosphorylation. Mol Pharmacol (2009) 1.05
Molecular defects in human carbamoy phosphate synthetase I: mutational spectrum, diagnostic and protein structure considerations. Hum Mutat (2011) 1.04
Functional rescue of beta-adrenoceptor dimerization and trafficking by pharmacological chaperones. Traffic (2009) 1.03
Protein function prediction: towards integration of similarity metrics. Curr Opin Struct Biol (2011) 1.00
Evolutionary Trace Annotation Server: automated enzyme function prediction in protein structures using 3D templates. Bioinformatics (2009) 1.00
Rank information: a structure-independent measure of evolutionary trace quality that improves identification of protein functional sites. Proteins (2006) 0.97
Single nucleotide variations: biological impact and theoretical interpretation. Protein Sci (2014) 0.97
Accurate protein structure annotation through competitive diffusion of enzymatic functions over a network of local evolutionary similarities. PLoS One (2010) 0.96
PyETV: a PyMOL evolutionary trace viewer to analyze functional site predictions in protein complexes. Bioinformatics (2010) 0.94
Correlated evolutionary pressure at interacting transcription factors and DNA response elements can guide the rational engineering of DNA binding specificity. J Mol Biol (2005) 0.94
Evolutionary trace for prediction and redesign of protein functional sites. Methods Mol Biol (2012) 0.94
Algorithms for structural comparison and statistical analysis of 3D protein motifs. Pac Symp Biocomput (2005) 0.93
The MASH pipeline for protein function prediction and an algorithm for the geometric refinement of 3D motifs. J Comput Biol (2007) 0.92
Accounting for epistatic interactions improves the functional analysis of protein structures. Bioinformatics (2013) 0.92
Desmosterolosis-phenotypic and molecular characterization of a third case and review of the literature. Am J Med Genet A (2011) 0.91
Character and evolution of protein-protein interfaces. Phys Biol (2005) 0.90
The use of evolutionary patterns in protein annotation. Curr Opin Struct Biol (2012) 0.87
Prediction and experimental validation of enzyme substrate specificity in protein structures. Proc Natl Acad Sci U S A (2013) 0.87
The maternal-to-zygotic transition targets actin to promote robustness during morphogenesis. PLoS Genet (2013) 0.86
Regulation of Ras localization and cell transformation by evolutionarily conserved palmitoyltransferases. Mol Cell Biol (2013) 0.84
Cavity-aware motifs reduce false positives in protein function prediction. Comput Syst Bioinformatics Conf (2006) 0.84
Protein kinase A and phosphodiesterase-4D3 binding to coding polymorphisms of cardiac muscle anchoring protein (mAKAP). J Mol Biol (2013) 0.83
Evolutionary identification of a subtype specific functional site in the ligand binding domain of steroid receptors. Proteins (2006) 0.83
Cavity scaling: automated refinement of cavity-aware motifs in protein function prediction. J Bioinform Comput Biol (2007) 0.82
Computational and biochemical identification of a nuclear pore complex binding site on the nuclear transport carrier NTF2. J Mol Biol (2004) 0.81
REPURPOSING GERMLINE EXOMES OF THE CANCER GENOME ATLAS DEMANDS A CAUTIOUS APPROACH AND SAMPLE-SPECIFIC VARIANT FILTERING. Pac Symp Biocomput (2016) 0.81
Lysine 270 in the third intracellular domain of the oxytocin receptor is an important determinant for G alpha(q) coupling specificity. Mol Endocrinol (2002) 0.81
Identification of functionally important residues/domains in membrane proteins using an evolutionary approach coupled with systematic mutational analysis. Methods Mol Biol (2009) 0.80
An angiotensin II type 1 receptor activation switch patch revealed through evolutionary trace analysis. Biochem Pharmacol (2010) 0.80
Function prediction from networks of local evolutionary similarity in protein structure. BMC Bioinformatics (2013) 0.80
ETAscape: analyzing protein networks to predict enzymatic function and substrates in Cytoscape. Bioinformatics (2012) 0.79
Conserved motifs in somatostatin, D2-dopamine, and alpha 2B-adrenergic receptors for inhibiting the Na-H exchanger, NHE1. J Biol Chem (2003) 0.79
Role of transmembrane domain/transmembrane domain interfaces of P-glycoprotein (ABCB1) in solute transport. Convergent information from photoaffinity labeling, site directed mutagenesis and in silico importance prediction. Curr Med Chem (2006) 0.78
Composite motifs integrating multiple protein structures increase sensitivity for function prediction. Comput Syst Bioinformatics Conf (2007) 0.77
DISCOVERY OF FUNCTIONAL AND DISEASE PATHWAYS BY COMMUNITY DETECTION IN PROTEIN-PROTEIN INTERACTION NETWORKS. Pac Symp Biocomput (2016) 0.75
Untangling complex networks: risk minimization in financial markets through accessible spin glass ground states. Physica A (2010) 0.75
COMPUTING THERAPY FOR PRECISION MEDICINE: COLLABORATIVE FILTERING INTEGRATES AND PREDICTS MULTI-ENTITY INTERACTIONS. Pac Symp Biocomput (2016) 0.75
HUMAN KINASES DISPLAY MUTATIONAL HOTSPOTS AT COGNATE POSITIONS WITHIN CANCER. Pac Symp Biocomput (2016) 0.75
Deleterious Effect of RAS and Evolutionary High-risk TP53 Double Mutation in Colorectal Liver Metastases. Ann Surg (2017) 0.75