Published in Nucleic Acids Res on July 01, 2006
Reemergence of enterovirus 71 in 2008 in taiwan: dynamics of genetic and antigenic evolution from 1998 to 2008. J Clin Microbiol (2009) 2.40
Isolation and characterization of Alicycliphilus denitrificans strain BC, which grows on benzene with chlorate as the electron acceptor. Appl Environ Microbiol (2008) 1.19
(PS)2-v2: template-based protein structure prediction server. BMC Bioinformatics (2009) 1.15
Computational analysis of KRAS mutations: implications for different effects on the KRAS p.G12D and p.G13D mutations. PLoS One (2013) 1.00
Structure of Est3 reveals a bimodal surface with differential roles in telomere replication. Proc Natl Acad Sci U S A (2013) 0.98
A photolyase-like protein from Agrobacterium tumefaciens with an iron-sulfur cluster. PLoS One (2011) 0.97
SCMCRYS: predicting protein crystallization using an ensemble scoring card method with estimating propensity scores of P-collocated amino acid pairs. PLoS One (2013) 0.90
pKNOT v.2: the protein KNOT web server. Nucleic Acids Res (2012) 0.89
Computational structural and functional analysis of hypothetical proteins of Staphylococcus aureus. Bioinformation (2012) 0.86
A popular engagement at the ends. Nat Struct Mol Biol (2013) 0.85
Modeling of molecular interaction between apoptin, BCR-Abl and CrkL--an alternative approach to conventional rational drug design. PLoS One (2012) 0.85
Chromodomains and LTR retrotransposons in plants. Commun Integr Biol (2009) 0.83
Computational analysis of a novel mutation in ETFDH gene highlights its long-range effects on the FAD-binding motif. BMC Struct Biol (2011) 0.82
In Silico Structural and Functional Annotation of Hypothetical Proteins of Vibrio cholerae O139. Genomics Inform (2015) 0.82
KIDFamMap: a database of kinase-inhibitor-disease family maps for kinase inhibitor selectivity and binding mechanisms. Nucleic Acids Res (2012) 0.81
Pathway-based screening strategy for multitarget inhibitors of diverse proteins in metabolic pathways. PLoS Comput Biol (2013) 0.81
(PS)2: protein structure prediction server version 3.0. Nucleic Acids Res (2015) 0.81
Engineering of the LukS-PV and LukF-PV subunits of Staphylococcus aureus Panton-Valentine leukocidin for diagnostic and therapeutic applications. BMC Biotechnol (2013) 0.80
Exploration of freely available web-interfaces for comparative homology modelling of microbial proteins. Bioinformation (2013) 0.80
Structural insight into the DNA-binding mode of the primosomal proteins PriA, PriB, and DnaT. Biomed Res Int (2014) 0.80
Quality assessment of protein model-structures based on structural and functional similarities. BMC Bioinformatics (2012) 0.80
Homology model and docking studies on porcine β₂ adrenoceptor: description of two binding sites. J Mol Model (2011) 0.79
Structural analysis and epitope prediction of HCV E1 protein isolated in Pakistan: an in-silico approach. Virol J (2013) 0.78
Lack of plasma kallikrein-kinin system cascade in teleosts. PLoS One (2013) 0.78
Different visible colors and green fluorescence were obtained from the mutated purple chromoprotein isolated from sea anemone. Mar Biotechnol (NY) (2014) 0.78
Identifications small molecules inhibitor of p53-mortalin complex for cancer drug using virtual screening. Bioinformation (2012) 0.78
Isolation, characterization and structural studies of amorpha - 4, 11-diene synthase (ADS(3963)) from Artemisia annua L. Bioinformation (2010) 0.78
Ketide Synthase (KS) Domain Prediction and Analysis of Iterative Type II PKS Gene in Marine Sponge-Associated Actinobacteria Producing Biosurfactants and Antimicrobial Agents. Front Microbiol (2016) 0.77
Structure-based computational study of two disease resistance gene homologues (Hm1 and Hm2) in maize (Zea mays L.) with implications in plant-pathogen interactions. PLoS One (2014) 0.77
Molecular cloning and in-silico characterization of high temperature stress responsive pAPX gene isolated from heat tolerant Indian wheat cv. Raj 3765. BMC Res Notes (2014) 0.77
Anti-inflammatory potential of alpha-linolenic acid mediated through selective COX inhibition: computational and experimental data. Inflammation (2014) 0.77
Molecular dynamics simulations of the Bcl-2 protein to predict the structure of its unordered flexible loop domain. J Mol Model (2011) 0.77
Inhibition of a Putative Dihydropyrimidinase from Pseudomonas aeruginosa PAO1 by Flavonoids and Substrates of Cyclic Amidohydrolases. PLoS One (2015) 0.76
In silico determination and validation of baumannii acinetobactin utilization a structure and ligand binding site. Biomed Res Int (2013) 0.76
Computational analysis of cysteine proteases (Clan CA, Family Cl) of Leishmania major to find potential epitopic regions. Genomics Proteomics Bioinformatics (2009) 0.76
Homeobox Is Pivotal for OsWUS Controlling Tiller Development and Female Fertility in Rice. G3 (Bethesda) (2016) 0.75
Insights from molecular modeling and dynamics simulation of pathogen resistance (R) protein from brinjal. Bioinformation (2011) 0.75
Characterization of a thermostable endoglucanase produced by Isoptericola variabilis sp. IDAH9. Braz J Microbiol (2015) 0.75
A hydrophobic spine stabilizes a surface-exposed α-helix according to analysis of the solvent-accessible surface area. BMC Bioinformatics (2016) 0.75
C-terminal domain swapping of SSB changes the size of the ssDNA binding site. Biomed Res Int (2014) 0.75
Identification and validation of immunogenic potential of India specific HPV-16 variant constructs: In-silico &in-vivo insight to vaccine development. Sci Rep (2015) 0.75
In silico sequence analysis, homology modeling and function annotation of leishmanolysin from Leishmania donovani. J Parasit Dis (2015) 0.75
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T-Coffee: A novel method for fast and accurate multiple sequence alignment. J Mol Biol (2000) 57.88
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SWISS-MODEL: An automated protein homology-modeling server. Nucleic Acids Res (2003) 25.86
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The RCSB Protein Data Bank: a redesigned query system and relational database based on the mmCIF schema. Nucleic Acids Res (2005) 7.81
IMPALA: matching a protein sequence against a collection of PSI-BLAST-constructed position-specific score matrices. Bioinformatics (1999) 6.91
GenTHREADER: an efficient and reliable protein fold recognition method for genomic sequences. J Mol Biol (1999) 6.42
Whole genome comparisons of serotype 4b and 1/2a strains of the food-borne pathogen Listeria monocytogenes reveal new insights into the core genome components of this species. Nucleic Acids Res (2004) 4.97
Enhancement of protein modeling by human intervention in applying the automatic programs 3D-JIGSAW and 3D-PSSM. Proteins (2001) 4.85
ESyPred3D: Prediction of proteins 3D structures. Bioinformatics (2002) 4.72
Automated prediction of CASP-5 structures using the Robetta server. Proteins (2003) 3.41
Assessment of predictions submitted for the CASP6 comparative modeling category. Proteins (2005) 2.27
Protein threading using PROSPECT: design and evaluation. Proteins (2000) 2.26
Automatic consensus-based fold recognition using Pcons, ProQ, and Pmodeller. Proteins (2003) 1.46
Determination of the structure of Escherichia coli glyoxalase I suggests a structural basis for differential metal activation. Biochemistry (2000) 1.25
Reaction mechanism of glyoxalase I explored by an X-ray crystallographic analysis of the human enzyme in complex with a transition state analogue. Biochemistry (1999) 1.18
An automatic homology modeling method consisting of database searches and simulated annealing. J Mol Graph Model (2000) 1.13
Mechanism-based competitive inhibitors of glyoxalase I: intracellular delivery, in vitro antitumor activities, and stabilities in human serum and mouse serum. J Med Chem (1999) 1.03
PROTINFO: Secondary and tertiary protein structure prediction. Nucleic Acids Res (2003) 1.01
Prediction of protein subcellular localization. Proteins (2006) 4.46
Three-dimensional reconstruction of brain-wide wiring networks in Drosophila at single-cell resolution. Curr Biol (2010) 4.04
Predicting subcellular localization of proteins for Gram-negative bacteria by support vector machines based on n-peptide compositions. Protein Sci (2004) 3.02
KinasePhos 2.0: a web server for identifying protein kinase-specific phosphorylation sites based on sequences and coupling patterns. Nucleic Acids Res (2007) 2.69
The cAMP receptor-like protein CLP is a novel c-di-GMP receptor linking cell-cell signaling to virulence gene expression in Xanthomonas campestris. J Mol Biol (2009) 1.78
PhosphoPOINT: a comprehensive human kinase interactome and phospho-protein database. Bioinformatics (2008) 1.47
Predicting RNA-binding sites of proteins using support vector machines and evolutionary information. BMC Bioinformatics (2008) 1.39
Kappa-alpha plot derived structural alphabet and BLOSUM-like substitution matrix for rapid search of protein structure database. Genome Biol (2007) 1.30
3D-partner: a web server to infer interacting partners and binding models. Nucleic Acids Res (2007) 1.27
Protein subcellular localization prediction based on compartment-specific features and structure conservation. BMC Bioinformatics (2007) 1.25
Proportion of solvent-exposed amino acids in a protein and rate of protein evolution. Mol Biol Evol (2007) 1.23
Deriving protein dynamical properties from weighted protein contact number. Proteins (2008) 1.23
Aurintricarboxylic acid inhibits influenza virus neuraminidase. Antiviral Res (2008) 1.19
Prediction of the bonding states of cysteines using the support vector machines based on multiple feature vectors and cysteine state sequences. Proteins (2004) 1.19
(PS)2-v2: template-based protein structure prediction server. BMC Bioinformatics (2009) 1.15
Co-evolution positions and rules for antigenic variants of human influenza A/H3N2 viruses. BMC Bioinformatics (2009) 1.13
iGEMDOCK: a graphical environment of enhancing GEMDOCK using pharmacological interactions and post-screening analysis. BMC Bioinformatics (2011) 1.10
pKNOT: the protein KNOT web server. Nucleic Acids Res (2007) 1.08
Relationship between protein structures and disulfide-bonding patterns. Proteins (2003) 1.07
Site-specific structural constraints on protein sequence evolutionary divergence: local packing density versus solvent exposure. Mol Biol Evol (2013) 1.07
A mechanistic stress model of protein evolution accounts for site-specific evolutionary rates and their relationship with packing density and flexibility. BMC Evol Biol (2014) 1.07
An evolutionary algorithm for large traveling salesman problems. IEEE Trans Syst Man Cybern B Cybern (2004) 1.06
Relationship between local structural entropy and protein thermostability. Proteins (2004) 1.04
Computational analysis of KRAS mutations: implications for different effects on the KRAS p.G12D and p.G13D mutations. PLoS One (2013) 1.00
Evolutionary information hidden in a single protein structure. Proteins (2012) 0.99
PPISearch: a web server for searching homologous protein-protein interactions across multiple species. Nucleic Acids Res (2009) 0.99
Fine-grained protein fold assignment by support vector machines using generalized npeptide coding schemes and jury voting from multiple-parameter sets. Proteins (2003) 0.95
Prediction of disulfide connectivity from protein sequences. Proteins (2005) 0.94
SiMMap: a web server for inferring site-moiety map to recognize interaction preferences between protein pockets and compound moieties. Nucleic Acids Res (2010) 0.94
Antigenic sites of H1N1 influenza virus hemagglutinin revealed by natural isolates and inhibition assays. Vaccine (2012) 0.92
Amino acid coupling patterns in thermophilic proteins. Proteins (2005) 0.92
fastSCOP: a fast web server for recognizing protein structural domains and SCOP superfamilies. Nucleic Acids Res (2007) 0.91
Structure-stability-activity relationship in covalently cross-linked N-carbamoyl D-amino acid amidohydrolase and N-acylamino acid racemase. J Mol Biol (2006) 0.90
On the relationship between the protein structure and protein dynamics. Proteins (2008) 0.90
pKNOT v.2: the protein KNOT web server. Nucleic Acids Res (2012) 0.89
Changed epitopes drive the antigenic drift for influenza A (H3N2) viruses. BMC Bioinformatics (2011) 0.88
Codon-usage bias versus gene conversion in the evolution of yeast duplicate genes. Proc Natl Acad Sci U S A (2006) 0.88
Staphylococcus aureus protein SAUGI acts as a uracil-DNA glycosylase inhibitor. Nucleic Acids Res (2013) 0.87
GEM: a Gaussian Evolutionary Method for predicting protein side-chain conformations. Protein Sci (2002) 0.87
Predicting disulfide connectivity patterns. Proteins (2007) 0.86
3D-interologs: an evolution database of physical protein- protein interactions across multiple genomes. BMC Genomics (2010) 0.86
Crystal structure of Helicobacter pylori formamidase AmiF reveals a cysteine-glutamate-lysine catalytic triad. J Biol Chem (2007) 0.86
Deciphering the preference and predicting the viability of circular permutations in proteins. PLoS One (2012) 0.85
Core site-moiety maps reveal inhibitors and binding mechanisms of orthologous proteins by screening compound libraries. PLoS One (2012) 0.85
DNA mimic proteins: functions, structures, and bioinformatic analysis. Biochemistry (2014) 0.85
Synthesis of acylguanidine zanamivir derivatives as neuraminidase inhibitors and the evaluation of their bio-activities. Org Biomol Chem (2013) 0.85
Protein complexity, gene duplicability and gene dispensability in the yeast genome. Gene (2006) 0.84
On the relationship between catalytic residues and their protein contact number. Curr Protein Pept Sci (2011) 0.83
Computational analysis of a novel mutation in ETFDH gene highlights its long-range effects on the FAD-binding motif. BMC Struct Biol (2011) 0.82
On the relationship between the sequence conservation and the packing density profiles of the protein complexes. Proteins (2013) 0.82
A simple way to compute protein dynamics without a mechanical model. Proteins (2007) 0.82
DAPID: a 3D-domain annotated protein-protein interaction database. Genome Inform (2006) 0.82
Crystal structure of a secondary vitamin D3 binding site of milk beta-lactoglobulin. Proteins (2008) 0.81
Roles of amino acids in the Escherichia coli octaprenyl diphosphate synthase active site probed by structure-guided site-directed mutagenesis. Biochemistry (2012) 0.81
Pathway-based screening strategy for multitarget inhibitors of diverse proteins in metabolic pathways. PLoS Comput Biol (2013) 0.81
Detection and alignment of 3D domain swapping proteins using angle-distance image-based secondary structural matching techniques. PLoS One (2010) 0.81
KIDFamMap: a database of kinase-inhibitor-disease family maps for kinase inhibitor selectivity and binding mechanisms. Nucleic Acids Res (2012) 0.81
CAPIH: a Web interface for comparative analyses and visualization of host-HIV protein-protein interactions. BMC Microbiol (2009) 0.80
Structures of Helicobacter pylori shikimate kinase reveal a selective inhibitor-induced-fit mechanism. PLoS One (2012) 0.80
Structural simulation and protein engineering to convert an endo-chitosanase to an exo-chitosanase. Protein Eng Des Sel (2008) 0.80
Crowning proteins: modulating the protein surface properties using crown ethers. Angew Chem Int Ed Engl (2014) 0.79
TSCC: Two-Stage Combinatorial Clustering for virtual screening using protein-ligand interactions and physicochemical features. BMC Genomics (2010) 0.79
Evolutionary conservation of DNA-contact residues in DNA-binding domains. BMC Bioinformatics (2008) 0.79
CPred: a web server for predicting viable circular permutations in proteins. Nucleic Acids Res (2012) 0.79
PCFamily: a web server for searching homologous protein complexes. Nucleic Acids Res (2010) 0.79
Parallel screening of wild-type and drug-resistant targets for anti-resistance neuraminidase inhibitors. PLoS One (2013) 0.79
Space-related pharma-motifs for fast search of protein binding motifs and polypharmacological targets. BMC Genomics (2012) 0.78
PAComplex: a web server to infer peptide antigen families and binding models from TCR-pMHC complexes. Nucleic Acids Res (2011) 0.78
The fragment transformation method to detect the protein structural motifs. Proteins (2006) 0.78
Total synthetic protoapigenone WYC02 inhibits cervical cancer cell proliferation and tumour growth through PIK3 signalling pathway. Basic Clin Pharmacol Toxicol (2013) 0.78
Homopharma: a new concept for exploring the molecular binding mechanisms and drug repurposing. BMC Genomics (2014) 0.78
Diode laser assisted minimal invasive sphenoidotomy for endoscopic transphenoidal pituitary surgery: our technique and results. Lasers Surg Med (2015) 0.77
MoNetFamily: a web server to infer homologous modules and module-module interaction networks in vertebrates. Nucleic Acids Res (2012) 0.77
Molecular dynamics simulation of the enhancement of cobra cardiotoxin and E6 protein binding on mixed self-assembled monolayer molecules. Nanotechnology (2006) 0.77
On the packing density of the unbound protein-protein interaction interface and its implications in dynamics. BMC Bioinformatics (2015) 0.76
Structural transformations in dinuclear zinc complexes involving Zn-Zn bonds. Chem Commun (Camb) (2007) 0.76
7-Chloro-6-piperidin-1-yl-quinoline-5,8-dione (PT-262), a novel ROCK inhibitor blocks cytoskeleton function and cell migration. Biochem Pharmacol (2011) 0.76
LigSeeSVM: ligand-based virtual screening using support vector machines and data fusion. Int J Comput Biol Drug Des (2011) 0.75
Genome-wide structural modelling of TCR-pMHC interactions. BMC Genomics (2013) 0.75
Steric recognition of T-cell receptor contact residues is required to map mutant epitopes by immunoinformatical programmes. Immunology (2012) 0.75
Inferring homologous protein-protein interactions through pair position specific scoring matrix. BMC Bioinformatics (2013) 0.75
Deriving correlated motions in proteins from X-ray structure refinement by using TLS parameters. Gene (2012) 0.75
An evolutionary approach for gene expression patterns. IEEE Trans Inf Technol Biomed (2004) 0.75
Functional investigation of transmembrane helix 3 in H⁺-translocating pyrophosphatase. J Membr Biol (2013) 0.75
Moiety-linkage map reveals selective nonbisphosphonate inhibitors of human geranylgeranyl diphosphate synthase. J Chem Inf Model (2013) 0.75
A three-coordinate and quadruply bonded Mo-Mo complex. J Am Chem Soc (2006) 0.75
Novel Lactulose and Melibiose Targeting Autophagy to Reduce PolyQ Aggregation in Cell Models of Spinocerebellar Ataxia 3. CNS Neurol Disord Drug Targets (2016) 0.75
Computing motif correlations in proteins. J Comput Chem (2003) 0.75
GemAffinity: a scoring function for predicting binding affinity and virtual screening. Int J Data Min Bioinform (2012) 0.75
Numerical performance and throughput benchmark for electronic structure calculations in PC-Linux systems with new architectures, updated compilers, and libraries. J Chem Inf Comput Sci (2004) 0.75