Atom depth in protein structure and function.

Neutron diffraction studies of Escherichia coli dihydrofolate reductase complexed with methotrexate. Proc Natl Acad Sci U S A (2006) 1.70

Prediction of the general transcription factors associated with RNA polymerase II in Plasmodium falciparum: conserved features and differences relative to other eukaryotes. BMC Genomics (2005) 1.53

DEPTH: a web server to compute depth and predict small-molecule binding cavities in proteins. Nucleic Acids Res (2011) 1.12

Depth: a web server to compute depth, cavity sizes, detect potential small-molecule ligand-binding cavities and predict the pKa of ionizable residues in proteins. Nucleic Acids Res (2013) 1.01

A generalized analysis of hydrophobic and loop clusters within globular protein sequences. BMC Struct Biol (2007) 0.96

Prodepth: predict residue depth by support vector regression approach from protein sequences only. PLoS One (2009) 0.87

Reconstructing protein structure from solvent exposure using tabu search. Algorithms Mol Biol (2006) 0.81

ComQXPA quorum sensing systems may not be unique to Bacillus subtilis: a census in prokaryotic genomes. PLoS One (2014) 0.81

A stringent test for hydrophobicity scales: two proteins with 88% sequence identity but different structure and function. Proc Natl Acad Sci U S A (2008) 0.78

Prediction of functionally important residues in globular proteins from unusual central distances of amino acids. BMC Struct Biol (2011) 0.77

Dancing through Life: Molecular Dynamics Simulations and Network-Centric Modeling of Allosteric Mechanisms in Hsp70 and Hsp110 Chaperone Proteins. PLoS One (2015) 0.76

Shape and evolution of thermostable protein structure. Proteins (2010) 0.76

Analysis of Conformational B-Cell Epitopes in the Antibody-Antigen Complex Using the Depth Function and the Convex Hull. PLoS One (2015) 0.76

The fundamental tradeoff in genomes and proteomes of prokaryotes established by the genetic code, codon entropy, and physics of nucleic acids and proteins. Biol Direct (2014) 0.76

Dataset of eye disease-related proteins analyzed using the unfolding mutation screen. Sci Data (2016) 0.75

Characterization of non-trivial neighborhood fold constraints from protein sequences using generalized topohydrophobicity. Bioinform Biol Insights (2008) 0.75

DBAC: a simple prediction method for protein binding hot spots based on burial levels and deeply buried atomic contacts. BMC Syst Biol (2011) 0.75

A local average distance descriptor for flexible protein structure comparison. BMC Bioinformatics (2014) 0.75

The efficiency of multi-target drugs: the network approach might help drug design. Trends Pharmacol Sci (2005) 3.02

The quest for orthologs: finding the corresponding gene across genomes. Trends Genet (2008) 2.86

ROC analysis: applications to the classification of biological sequences and 3D structures. Brief Bioinform (2008) 2.01

DNA analysis servers: plot.it, bend.it, model.it and IS. Nucleic Acids Res (2003) 1.70

Protein fold similarity estimated by a probabilistic approach based on C(alpha)-C(alpha) distance comparison. J Mol Biol (2002) 1.56

Vicinal disulfide turns. Protein Eng (2003) 1.50

A Mek1-Mek2 heterodimer determines the strength and duration of the Erk signal. Nat Struct Mol Biol (2009) 1.48

Increased hydrophobicity at the N terminus/membrane interface impairs gating of the severe combined immunodeficiency-related ORAI1 mutant. J Biol Chem (2009) 1.39

CX, an algorithm that identifies protruding atoms in proteins. Bioinformatics (2002) 1.33

DPX: for the analysis of the protein core. Bioinformatics (2003) 1.29

Atom depth as a descriptor of the protein interior. Biophys J (2003) 1.24

Multiple weak hits confuse complex systems: a transcriptional regulatory network as an example. Phys Rev E Stat Nonlin Soft Matter Phys (2005) 1.19

ProGMap: an integrated annotation resource for protein orthology. Nucleic Acids Res (2009) 1.17

Unique features of the sodC-encoded superoxide dismutase from Mycobacterium tuberculosis, a fully functional copper-containing enzyme lacking zinc in the active site. J Biol Chem (2004) 1.15

Co-swarming and local collapse: quorum sensing conveys resilience to bacterial communities by localizing cheater mutants in Pseudomonas aeruginosa. PLoS One (2010) 1.13

Vicinal disulfide bridge conformers by experimental methods and by ab initio and DFT molecular computations. Proteins (2004) 1.13

Application of compression-based distance measures to protein sequence classification: a methodological study. Bioinformatics (2005) 1.06

Fragmentation pathways of N(G)-methylated and unmodified arginine residues in peptides studied by ESI-MS/MS and MALDI-MS. J Am Soc Mass Spectrom (2004) 1.03

Efficient recognition of folds in protein 3D structures by the improved PRIDE algorithm. Bioinformatics (2005) 1.02

Benchmarking protein classification algorithms via supervised cross-validation. J Biochem Biophys Methods (2007) 1.01

A Protein Classification Benchmark collection for machine learning. Nucleic Acids Res (2006) 1.01

From autoinhibition to inhibition in trans: the Raf-1 regulatory domain inhibits Rok-alpha kinase activity. J Cell Biol (2009) 1.01

Alanine-scanning mutagenesis of the predicted rRNA-binding domain of ErmC' redefines the substrate-binding site and suggests a model for protein-RNA interactions. Nucleic Acids Res (2003) 0.99

The evolution of structural databases. Trends Biotechnol (2002) 0.99

Repair of a minimal DNA double-strand break by NHEJ requires DNA-PKcs and is controlled by the ATM/ATR checkpoint. Nucleic Acids Res (2003) 0.98

Mutational analysis defines the roles of conserved amino acid residues in the predicted catalytic pocket of the rRNA:m6A methyltransferase ErmC'. J Mol Biol (2003) 0.97

A simple model for the early events of quorum sensing in Pseudomonas aeruginosa: modeling bacterial swarming as the movement of an "activation zone". Biol Direct (2009) 0.97

Crystal structure of human filamin C domain 23 and small angle scattering model for filamin C 23-24 dimer. J Mol Biol (2007) 0.96

The virtue of temperance: built-in negative regulators of quorum sensing in Pseudomonas. Mol Microbiol (2011) 0.94

The intracellular region of Notch ligands: does the tail make the difference? Biol Direct (2007) 0.93

Targeted proteolysis of plectin isoform 1a accounts for hemidesmosome dysfunction in mice mimicking the dominant skin blistering disease EBS-Ogna. PLoS Genet (2011) 0.93

Consensus prediction of protein conformational disorder from amino acidic sequence. Open Biochem J (2008) 0.93

Repeats with variations: accelerated evolution of the Pin2 family of proteinase inhibitors. Trends Genet (2002) 0.92

Classifying the topology of AHL-driven quorum sensing circuits in proteobacterial genomes. Sensors (Basel) (2012) 0.91

The organization of the quorum sensing luxI/R family genes in Burkholderia. Int J Mol Sci (2013) 0.89

The SBASE domain sequence resource, release 12: prediction of protein domain-architecture using support vector machines. Nucleic Acids Res (2005) 0.89

The "first in-last out" hypothesis on protein folding revisited. Proteins (2005) 0.88

Chromosomal Arrangement of AHL-Driven Quorum Sensing Circuits in Pseudomonas. ISRN Microbiol (2012) 0.88

Functional aspects of cHH C-terminal amidation in crayfish species. Regul Pept (2008) 0.88

IS: a web-site for intron statistics. Bioinformatics (2003) 0.87

Protein sequence redundancy reduction: comparison of various method. Bioinformation (2010) 0.87

Stability of multispecies bacterial communities: signaling networks may stabilize microbiomes. PLoS One (2013) 0.87

Locality versus globality in bacterial signalling: can local communication stabilize bacterial communities? Biol Direct (2010) 0.87

FRASS: the web-server for RNA structural comparison. BMC Bioinformatics (2010) 0.86

Prevalence of intrinsic disorder in the intracellular region of human single-pass type I proteins: the case of the notch ligand Delta-4. J Proteome Res (2008) 0.86

Evolution of robust and efficient system topologies. Cell Immunol (2007) 0.85

The SBASE domain sequence library, release 10: domain architecture prediction. Nucleic Acids Res (2003) 0.85

CX, DPX and PRIDE: WWW servers for the analysis and comparison of protein 3D structures. Nucleic Acids Res (2005) 0.84

Exon 6 of human Jagged-1 encodes an autonomously folding unit. FEBS Lett (2004) 0.84

The tetralogy of Fallot-associated G274D mutation impairs folding of the second epidermal growth factor repeat in Jagged-1. FEBS J (2009) 0.84

Minor group human rhinovirus-receptor interactions: geometry of multimodular attachment and basis of recognition. FEBS Lett (2008) 0.84

Systematic comparison of crystal and NMR protein structures deposited in the protein data bank. Open Biochem J (2010) 0.84

Efficient synthesis and comparative studies of the arginine and Nomega,Nomega-dimethylarginine forms of the human nucleolin glycine/arginine rich domain. J Pept Sci (2005) 0.84

Progress in the PRIDE technique for rapidly comparing protein three-dimensional structures. BMC Res Notes (2008) 0.83

JBioWH: an open-source Java framework for bioinformatics data integration. Database (Oxford) (2013) 0.81

Synthesis, Structure, and Reactivity of Model Complexes of Copper Nitrite Reductase. Inorg Chem (1996) 0.81

Oxidative folding intermediates with nonnative disulfide bridges between adjacent cysteine residues. Proc Natl Acad Sci U S A (2003) 0.81

Gene synthesis, expression, purification, and characterization of human Jagged-1 intracellular region. Protein Expr Purif (2005) 0.80

The SBASE protein domain library, release 9.0: an online resource for protein domain identification. Nucleic Acids Res (2002) 0.80

Application of a simple likelihood ratio approximant to protein sequence classification. Bioinformatics (2006) 0.80

Computational approaches to protein-protein interaction. J Struct Funct Genomics (2003) 0.79

The interaction of Jagged-1 cytoplasmic tail with afadin PDZ domain is local, folding-independent, and tuned by phosphorylation. J Mol Recognit (2011) 0.79

Predictive bioinformatic identification of minor receptor group human rhinoviruses. FEBS Lett (2009) 0.79

Structural portrait of filamin interaction mechanisms. Curr Protein Pept Sci (2010) 0.79

Novel protocol for the chemical synthesis of crustacean hyperglycemic hormone analogues--an efficient experimental tool for studying their functions. PLoS One (2012) 0.79

The intracellular region of the Notch ligand Jagged-1 gains partial structure upon binding to synthetic membranes. FEBS J (2007) 0.79

Structural and biochemical studies on ATP binding and hydrolysis by the Escherichia coli RNA chaperone Hfq. PLoS One (2012) 0.78

Detecting atypical examples of known domain types by sequence similarity searching: the SBASE domain library approach. Curr Protein Pept Sci (2010) 0.78

Balanced ROC analysis (BAROC) protocol for the evaluation of protein similarities. J Biochem Biophys Methods (2007) 0.78

Structural similarity between native proteins and chimera constructs obtained by inverting the amino Acid sequence. Acta Chim Slov (2010) 0.78

Exon 6 of human JAG1 encodes a conserved structural unit. BMC Struct Biol (2009) 0.78

Multi-netclust: an efficient tool for finding connected clusters in multi-parametric networks. Bioinformatics (2010) 0.78

Jagged-1 juxtamembrane region: biochemical characterization and cleavage by ADAM17 (TACE) catalytic domain. Biochem Biophys Res Commun (2013) 0.78

Oxidative folding of Amaranthus alpha-amylase inhibitor: disulfide bond formation and conformational folding. J Biol Chem (2004) 0.77

Hydration sites of unpaired RNA bases: a statistical analysis of the PDB structures. BMC Struct Biol (2011) 0.77

Folding of epidermal growth factor-like repeats from human tenascin studied through a sequence frame-shift approach. Eur J Biochem (2004) 0.77

Probing dynamic protein ensembles with atomic proximity measures. Curr Protein Pept Sci (2010) 0.77

DNA-mediated assembly of weakly interacting DNA-binding protein subunits: in vitro recruitment of phage 434 repressor and yeast GCN4 DNA-binding domains. Nucleic Acids Res (2004) 0.77

The G-M-N motif determines ion selectivity in the yeast magnesium channel Mrs2p. Metallomics (2013) 0.77

Different degrees of structural order in distinct regions of the transcriptional repressor HES-1. Biochim Biophys Acta (2010) 0.77

Structural and functional characterization of the N-terminal domain of the yeast Mg2+ channel Mrs2. Acta Crystallogr D Biol Crystallogr (2013) 0.77

Graph-representation of oxidative folding pathways. BMC Bioinformatics (2005) 0.77

Flexibility of the PDZ-binding motif in the micelle-bound form of Jagged-1 cytoplasmic tail. Biochim Biophys Acta (2012) 0.76

Fast protein fold estimation from NMR-derived distance restraints. Bioinformatics (2007) 0.76

Protein domain boundary predictions: a structural biology perspective. Open Biochem J (2009) 0.75

CARON--average RMSD of NMR structure ensembles. Bioinformation (2009) 0.75

PTMTreeSearch: a novel two-stage tree-search algorithm with pruning rules for the identification of post-translational modification of proteins in MS/MS spectra. Bioinformatics (2013) 0.75

Chemical rule-based filtering of MS/MS spectra. Bioinformatics (2013) 0.75

Protein classification based on propagation of unrooted binary trees. Protein Pept Lett (2008) 0.75

Prediction of new abiotic stress genes in Arabidopsis thaliana and Oryza sativa according to enumeration-based statistical analysis. Mol Genet Genomics (2011) 0.75

Multi-netclust: an efficient tool for finding connected clusters in multi-parametric networks. Bioinformatics (2015) 0.75

The basic helix-loop-helix region of the transcriptional repressor hairy and enhancer of split 1 is preorganized to bind DNA. Proteins (2014) 0.75

Non-random features of loop-size chromatin fragmentation. J Cell Biochem (2003) 0.75

Modeling bacterial quorum sensing in open and closed environments: potential discrepancies between agar plate and culture flask experiments. J Mol Model (2014) 0.75