Published in Proteins on January 01, 2003
Comparative protein structure modeling using Modeller. Curr Protoc Bioinformatics (2006) 8.72
LOMETS: a local meta-threading-server for protein structure prediction. Nucleic Acids Res (2007) 5.30
MUSTER: Improving protein sequence profile-profile alignments by using multiple sources of structure information. Proteins (2008) 3.38
JPred4: a protein secondary structure prediction server. Nucleic Acids Res (2015) 2.37
Gene3D: merging structure and function for a Thousand genomes. Nucleic Acids Res (2009) 2.34
A comprehensive assessment of sequence-based and template-based methods for protein contact prediction. Bioinformatics (2008) 2.08
Fido, a novel AMPylation domain common to fic, doc, and AvrB. PLoS One (2009) 1.92
Automated protein subfamily identification and classification. PLoS Comput Biol (2007) 1.89
Natural history of S-adenosylmethionine-binding proteins. BMC Struct Biol (2005) 1.85
De novo high-resolution protein structure determination from sparse spin-labeling EPR data. Structure (2008) 1.84
SAM-T08, HMM-based protein structure prediction. Nucleic Acids Res (2009) 1.82
Structural and evolutionary bioinformatics of the SPOUT superfamily of methyltransferases. BMC Bioinformatics (2007) 1.74
Improving the accuracy of protein secondary structure prediction using structural alignment. BMC Bioinformatics (2006) 1.66
Automated protein structure modeling in CASP9 by I-TASSER pipeline combined with QUARK-based ab initio folding and FG-MD-based structure refinement. Proteins (2011) 1.58
Phylogenomic analysis of the GIY-YIG nuclease superfamily. BMC Genomics (2006) 1.56
LEAping to conclusions: a computational reanalysis of late embryogenesis abundant proteins and their possible roles. BMC Bioinformatics (2003) 1.52
Structural and evolutionary classification of Type II restriction enzymes based on theoretical and experimental analyses. Nucleic Acids Res (2008) 1.49
The PD-(D/E)XK superfamily revisited: identification of new members among proteins involved in DNA metabolism and functional predictions for domains of (hitherto) unknown function. BMC Bioinformatics (2005) 1.46
Structure of the Plasmodium falciparum circumsporozoite protein, a leading malaria vaccine candidate. J Biol Chem (2009) 1.41
Antiviral activity of the interferon-induced cellular protein BST-2/tetherin. AIDS Res Hum Retroviruses (2009) 1.35
Pcons.net: protein structure prediction meta server. Nucleic Acids Res (2007) 1.28
Applying undertaker cost functions to model quality assessment. Proteins (2009) 1.23
Rigorous performance evaluation in protein structure modelling and implications for computational biology. Philos Trans R Soc Lond B Biol Sci (2006) 1.22
Shaping up the protein folding funnel by local interaction: lesson from a structure prediction study. Proc Natl Acad Sci U S A (2006) 1.22
Resolution-adapted recombination of structural features significantly improves sampling in restraint-guided structure calculation. Proteins (2012) 1.21
Evaluation of 3D-Jury on CASP7 models. BMC Bioinformatics (2007) 1.18
Structure of the head of the Bartonella adhesin BadA. PLoS Pathog (2008) 1.17
COMPASS server for remote homology inference. Nucleic Acids Res (2007) 1.16
Improved protein structure selection using decoy-dependent discriminatory functions. BMC Struct Biol (2004) 1.15
Prp8, the pivotal protein of the spliceosomal catalytic center, evolved from a retroelement-encoded reverse transcriptase. RNA (2011) 1.13
Molecular phylogenetics and comparative modeling of HEN1, a methyltransferase involved in plant microRNA biogenesis. BMC Evol Biol (2006) 1.12
Model quality assessment using distance constraints from alignments. Proteins (2009) 1.12
PREDICT-2ND: a tool for generalized protein local structure prediction. Bioinformatics (2008) 1.10
Identification of a bifunctional enzyme MnmC involved in the biosynthesis of a hypermodified uridine in the wobble position of tRNA. RNA (2004) 1.10
NMR structure of the pseudo-receiver domain of CikA. Protein Sci (2007) 1.06
Structural insight into repair of alkylated DNA by a new superfamily of DNA glycosylases comprising HEAT-like repeats. Nucleic Acids Res (2007) 1.06
Avl9p, a member of a novel protein superfamily, functions in the late secretory pathway. Mol Biol Cell (2007) 1.05
Cloning, characterisation and comparative analysis of a starch synthase IV gene in wheat: functional and evolutionary implications. BMC Plant Biol (2008) 1.03
Human sirt-1: molecular modeling and structure-function relationships of an unordered protein. PLoS One (2008) 1.01
Domain-based small molecule binding site annotation. BMC Bioinformatics (2006) 1.01
Structural model for the multisubunit Type IC restriction-modification DNA methyltransferase M.EcoR124I in complex with DNA. Nucleic Acids Res (2006) 0.97
Identification of a new family of putative PD-(D/E)XK nucleases with unusual phylogenomic distribution and a new type of the active site. BMC Genomics (2005) 0.97
A comparative assessment and analysis of 20 representative sequence alignment methods for protein structure prediction. Sci Rep (2013) 0.97
Dihydroorotase from the hyperthermophile Aquifex aeolicus is activated by stoichiometric association with aspartate transcarbamoylase and forms a one-pot reactor for pyrimidine biosynthesis. Biochemistry (2009) 0.96
Comparative Protein Structure Modeling Using MODELLER. Curr Protoc Bioinformatics (2016) 0.95
Double mutant cycle analysis identified a critical leucine residue in the IIS4S5 linker for the activation of the Ca(V)2.3 calcium channel. J Biol Chem (2011) 0.94
Improved chemical shift based fragment selection for CS-Rosetta using Rosetta3 fragment picker. J Biomol NMR (2013) 0.93
The MULTICOM toolbox for protein structure prediction. BMC Bioinformatics (2012) 0.93
Highly sensitive detection of individual HEAT and ARM repeats with HHpred and COACH. PLoS One (2009) 0.91
A homology model of restriction endonuclease SfiI in complex with DNA. BMC Struct Biol (2005) 0.90
Generalized pattern search algorithm for Peptide structure prediction. Biophys J (2008) 0.89
The Laminin 511/521-binding site on the Lutheran blood group glycoprotein is located at the flexible junction of Ig domains 2 and 3. Blood (2007) 0.88
Protein structure prediction by all-atom free-energy refinement. BMC Struct Biol (2007) 0.87
Characterization of the structure of RAMP1 by mutagenesis and molecular modeling. Biophys J (2006) 0.86
EVAcon: a protein contact prediction evaluation service. Nucleic Acids Res (2005) 0.86
Evolutionary and structural analyses of alpha-papillomavirus capsid proteins yields novel insights into L2 structure and interaction with L1. Virol J (2008) 0.84
Mammaglobin as a potential molecular target for breast cancer drug delivery. Cancer Cell Int (2009) 0.84
Bioinformatics resources for cancer research with an emphasis on gene function and structure prediction tools. Cancer Inform (2007) 0.83
Characterization of the interactions between the nucleoprotein and the phosphoprotein of Henipavirus. J Biol Chem (2011) 0.82
Three-dimensional structure of the catalytic domain of the yeast beta-(1,3)-glucan transferase Gas1: a molecular modeling investigation. J Mol Model (2005) 0.82
Efficient sampling in fragment-based protein structure prediction using an estimation of distribution algorithm. PLoS One (2013) 0.82
Retrieving backbone string neighbors provides insights into structural modeling of membrane proteins. Mol Cell Proteomics (2012) 0.81
HHsvm: fast and accurate classification of profile-profile matches identified by HHsearch. Bioinformatics (2009) 0.80
Fold-recognition and comparative modeling of human alpha2,3-sialyltransferases reveal their sequence and structural similarities to CstII from Campylobacter jejuni. BMC Struct Biol (2006) 0.80
Tip-alpha (hp0596 gene product) is a highly immunogenic Helicobacter pylori protein involved in colonization of mouse gastric mucosa. Curr Microbiol (2008) 0.80
Applying Undertaker to quality assessment. Proteins (2009) 0.79
Evolution of new function through a single amino acid change in the yeast repressor Sum1p. Mol Cell Biol (2008) 0.78
The electrostatic profile of consecutive Cβ atoms applied to protein structure quality assessment. F1000Res (2013) 0.77
A score of the ability of a three-dimensional protein model to retrieve its own sequence as a quantitative measure of its quality and appropriateness. PLoS One (2010) 0.77
In silico and in vivo studies of an Arabidopsis thaliana gene, ACR2, putatively involved in arsenic accumulation in plants. J Mol Model (2012) 0.77
Improved predictions by Pcons.net using multiple templates. Bioinformatics (2010) 0.77
Calcium-induced tertiary structure modifications of endo-beta-1,3-glucanase from Pyrococcus furiosus in 7.9 M guanidinium chloride. Biochem J (2005) 0.77
Alternative approach to protein structure prediction based on sequential similarity of physical properties. Proc Natl Acad Sci U S A (2015) 0.76
Enhancement of E. coli acyl-CoA synthetase FadD activity on medium chain fatty acids. PeerJ (2015) 0.76
The Inner Membrane Protein PilG Interacts with DNA and the Secretin PilQ in Transformation. PLoS One (2015) 0.76
Cell Wall Anchoring of the Campylobacter Antigens to Lactococcus lactis. Front Microbiol (2016) 0.76
Fallacy of the Unique Genome: Sequence Diversity within Single Helicobacter pylori Strains. MBio (2017) 0.76
In silico and in vivo studies of molecular structures and mechanisms of AtPCS1 protein involved in binding arsenite and/or cadmium in plant cells. J Mol Model (2014) 0.76
From local structure to a global framework: recognition of protein folds. J R Soc Interface (2014) 0.76
Cysteine-Rich Atrial Secretory Protein from the Snail Achatina achatina: Purification and Structural Characterization. PLoS One (2015) 0.75
A sequence sub-sampling algorithm increases the power to detect distant homologues. Nucleic Acids Res (2005) 0.75
Deciphering peculiar protein-protein interacting modules in Deinococcus radiodurans. Biol Direct (2009) 0.75
Initial sequencing and comparative analysis of the mouse genome. Nature (2002) 96.15
An integrated genomic analysis of human glioblastoma multiforme. Science (2008) 51.36
The genomic landscapes of human breast and colorectal cancers. Science (2007) 38.12
Core signaling pathways in human pancreatic cancers revealed by global genomic analyses. Science (2008) 36.02
GENCODE: the reference human genome annotation for The ENCODE Project. Genome Res (2012) 19.19
The UCSC Genome Browser database: update 2010. Nucleic Acids Res (2009) 16.58
The UCSC Genome Browser database: update 2011. Nucleic Acids Res (2010) 16.24
The consensus coding sequence (CCDS) project: Identifying a common protein-coding gene set for the human and mouse genomes. Genome Res (2009) 14.90
The UCSC Known Genes. Bioinformatics (2006) 14.67
Covariation in frequencies of substitution, deletion, transposition, and recombination during eutherian evolution. Genome Res (2003) 11.12
The UCSC Genome Browser database: extensions and updates 2013. Nucleic Acids Res (2012) 9.02
Assemblathon 1: a competitive assessment of de novo short read assembly methods. Genome Res (2011) 8.38
The genetic landscape of the childhood cancer medulloblastoma. Science (2010) 8.34
The UCSC Genome Browser database: extensions and updates 2011. Nucleic Acids Res (2011) 6.88
The UCSC Genome Browser database: 2014 update. Nucleic Acids Res (2013) 6.54
28-way vertebrate alignment and conservation track in the UCSC Genome Browser. Genome Res (2007) 6.42
ENCODE data in the UCSC Genome Browser: year 5 update. Nucleic Acids Res (2012) 6.29
Using native and syntenically mapped cDNA alignments to improve de novo gene finding. Bioinformatics (2008) 5.46
Cancer-specific high-throughput annotation of somatic mutations: computational prediction of driver missense mutations. Cancer Res (2009) 4.92
Accumulation of driver and passenger mutations during tumor progression. Proc Natl Acad Sci U S A (2010) 4.47
The GENCODE pseudogene resource. Genome Biol (2012) 4.18
ENCODE whole-genome data in the UCSC Genome Browser: update 2012. Nucleic Acids Res (2011) 4.00
MODBASE: a database of annotated comparative protein structure models and associated resources. Nucleic Acids Res (2006) 3.56
Whole-exome sequencing of neoplastic cysts of the pancreas reveals recurrent mutations in components of ubiquitin-dependent pathways. Proc Natl Acad Sci U S A (2011) 3.51
Detection and measurement of alternative splicing using splicing-sensitive microarrays. Methods (2005) 3.21
LS-SNP: large-scale annotation of coding non-synonymous SNPs based on multiple information sources. Bioinformatics (2005) 3.05
The UCSC Proteome Browser. Nucleic Acids Res (2005) 3.03
Human bile contains microRNA-laden extracellular vesicles that can be used for cholangiocarcinoma diagnosis. Hepatology (2014) 2.98
Defining the disease liability of variants in the cystic fibrosis transmembrane conductance regulator gene. Nat Genet (2013) 2.91
Annotating nucleic acid-binding function based on protein structure. J Mol Biol (2003) 2.46
Prioritization of driver mutations in pancreatic cancer using cancer-specific high-throughput annotation of somatic mutations (CHASM). Cancer Biol Ther (2010) 2.33
Mutational signature of aristolochic acid exposure as revealed by whole-exome sequencing. Sci Transl Med (2013) 2.30
Whole-exome sequencing combined with functional genomics reveals novel candidate driver cancer genes in endometrial cancer. Genome Res (2012) 2.27
The completion of the Mammalian Gene Collection (MGC). Genome Res (2009) 2.21
Current status and new features of the Consensus Coding Sequence database. Nucleic Acids Res (2013) 2.19
The UCSC Cancer Genomics Browser: update 2013. Nucleic Acids Res (2012) 2.18
Comparative genomics search for losses of long-established genes on the human lineage. PLoS Comput Biol (2007) 2.07
Cactus: Algorithms for genome multiple sequence alignment. Genome Res (2011) 2.03
Discriminative prediction of mammalian enhancers from DNA sequence. Genome Res (2011) 2.02
MODBASE, a database of annotated comparative protein structure models and associated resources. Nucleic Acids Res (2008) 2.02
Retrocopy contributions to the evolution of the human genome. BMC Genomics (2008) 1.95
Determination of cancer risk associated with germ line BRCA1 missense variants by functional analysis. Cancer Res (2007) 1.89
Exploring functional relationships between components of the gene expression machinery. Nat Struct Mol Biol (2005) 1.87
Viral photosynthetic reaction center genes and transcripts in the marine environment. ISME J (2007) 1.84
Hidden Markov models that use predicted local structure for fold recognition: alphabets of backbone geometry. Proteins (2003) 1.84
Correlation of somatic mutation and expression identifies genes important in human glioblastoma progression and survival. Cancer Res (2011) 1.83
Targeted discovery of novel human exons by comparative genomics. Genome Res (2007) 1.79
Tracking and coordinating an international curation effort for the CCDS Project. Database (Oxford) (2012) 1.78
Computational approaches to identify functional genetic variants in cancer genomes. Nat Methods (2013) 1.64
Identifying Mendelian disease genes with the variant effect scoring tool. BMC Genomics (2013) 1.64
LS-SNP/PDB: annotated non-synonymous SNPs mapped to Protein Data Bank structures. Bioinformatics (2009) 1.61
Alternative splicing regulation at tandem 3' splice sites. Nucleic Acids Res (2006) 1.53
Analysis of human mRNAs with the reference genome sequence reveals potential errors, polymorphisms, and RNA editing. Genome Res (2004) 1.51
Calibrating E-values for hidden Markov models using reverse-sequence null models. Bioinformatics (2005) 1.50
Using bioinformatics to predict the functional impact of SNVs. Bioinformatics (2010) 1.49
SAM-T04: what is new in protein-structure prediction for CASP6. Proteins (2005) 1.49
CRAVAT: cancer-related analysis of variants toolkit. Bioinformatics (2013) 1.43
Whole-genome sequencing identifies a recurrent functional synonymous mutation in melanoma. Proc Natl Acad Sci U S A (2013) 1.35
Predicting reliable regions in protein sequence alignments. Bioinformatics (2002) 1.34
SFmap: a web server for motif analysis and prediction of splicing factor binding sites. Nucleic Acids Res (2010) 1.33
Classifying RNA-binding proteins based on electrostatic properties. PLoS Comput Biol (2008) 1.29
A computational approach for genome-wide mapping of splicing factor binding sites. Genome Biol (2009) 1.25
Cactus graphs for genome comparisons. J Comput Biol (2011) 1.24
Collections of simultaneously altered genes as biomarkers of cancer cell drug response. Cancer Res (2013) 1.23
Charting the landscape of tandem BRCT domain-mediated protein interactions. Sci Signal (2012) 1.19
CHASM and SNVBox: toolkit for detecting biologically important single nucleotide mutations in cancer. Bioinformatics (2011) 1.18
Patch Finder Plus (PFplus): a web server for extracting and displaying positive electrostatic patches on protein surfaces. Nucleic Acids Res (2007) 1.17
Integrating diverse genomic data using gene sets. Genome Biol (2011) 1.13
PREDICT-2ND: a tool for generalized protein local structure prediction. Bioinformatics (2008) 1.10
Somatic mutations in the Notch, NF-KB, PIK3CA, and Hedgehog pathways in human breast cancers. Genes Chromosomes Cancer (2012) 1.06
Covariation between homeodomain transcription factors and the shape of their DNA binding sites. Nucleic Acids Res (2013) 1.05
MuPIT interactive: webserver for mapping variant positions to annotated, interactive 3D structures. Hum Genet (2013) 0.99
Regions of extreme synonymous codon selection in mammalian genes. Nucleic Acids Res (2006) 0.97
The Saccharomyces cerevisiae GSK-3 beta homologs. Curr Drug Targets (2006) 0.97
Roles of DNA polymerase I in leading and lagging-strand replication defined by a high-resolution mutation footprint of ColE1 plasmid replication. Nucleic Acids Res (2011) 0.94
DRIMust: a web server for discovering rank imbalanced motifs using suffix trees. Nucleic Acids Res (2013) 0.93
A supervised learning approach for taxonomic classification of core-photosystem-II genes and transcripts in the marine environment. BMC Genomics (2009) 0.93
Analysis of a set of missense, frameshift, and in-frame deletion variants of BRCA1. Mutat Res (2008) 0.91
Characterization of coding synonymous and non-synonymous variants in ADAMTS13 using ex vivo and in silico approaches. PLoS One (2012) 0.91
Experimental assessment of splicing variants using expression minigenes and comparison with in silico predictions. Hum Mutat (2014) 0.90
Cyanophage tRNAs may have a role in cross-infectivity of oceanic Prochlorococcus and Synechococcus hosts. ISME J (2011) 0.90
The hnRNP F/H homologue of Trypanosoma brucei is differentially expressed in the two life cycle stages of the parasite and regulates splicing and mRNA stability. Nucleic Acids Res (2013) 0.90
Heterogeneous nuclear ribonucleoprotein H1/H2-dependent unsplicing of thymidine phosphorylase results in anticancer drug resistance. J Biol Chem (2010) 0.89
Network models of TEM β-lactamase mutations coevolving under antibiotic selection show modular structure and anticipate evolutionary trajectories. PLoS Comput Biol (2011) 0.89
Detecting species-site dependencies in large multiple sequence alignments. Nucleic Acids Res (2009) 0.89
A structural-based statistical approach suggests a cooperative activity of PUM1 and miR-410 in human 3'-untranslated regions. Silence (2010) 0.89
Predicting and controlling the reactivity of immune cell populations against cancer. Mol Syst Biol (2009) 0.88
An integrated regulatory network reveals pervasive cross-regulation among transcription and splicing factors. PLoS Comput Biol (2012) 0.88
Does distance matter? Variations in alternative 3' splicing regulation. Nucleic Acids Res (2007) 0.87
Divergent RNA binding specificity of yeast Puf2p. RNA (2011) 0.87
From face to interface recognition: a differential geometric approach to distinguish DNA from RNA binding surfaces. Nucleic Acids Res (2011) 0.87
PIK3CA somatic mutations in breast cancer: Mechanistic insights from Langevin dynamics simulations. Proteins (2009) 0.86
Ancient diversity of splicing motifs and protein surfaces in the wild emmer wheat (Triticum dicoccoides) LR10 coiled coil (CC) and leucine-rich repeat (LRR) domains. Mol Plant Pathol (2011) 0.86