Published in J Mol Biol on February 07, 2003
MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res (2004) 168.89
The HHpred interactive server for protein homology detection and structure prediction. Nucleic Acids Res (2005) 21.68
Comparative protein structure modeling using Modeller. Curr Protoc Bioinformatics (2006) 8.72
Local homology recognition and distance measures in linear time using compressed amino acid alphabets. Nucleic Acids Res (2004) 6.42
MODBASE, a database of annotated comparative protein structure models, and associated resources. Nucleic Acids Res (2004) 4.54
SCOOP: a simple method for identification of novel protein superfamily relationships. Bioinformatics (2007) 4.19
Structure prediction for CASP8 with all-atom refinement using Rosetta. Proteins (2009) 3.64
PISCES: recent improvements to a PDB sequence culling server. Nucleic Acids Res (2005) 3.55
Progress and challenges in protein structure prediction. Curr Opin Struct Biol (2008) 3.48
Alignment of protein sequences by their profiles. Protein Sci (2004) 2.80
The GAAS metagenomic tool and its estimations of viral and microbial average genome size in four major biomes. PLoS Comput Biol (2009) 2.61
Sequence context-specific profiles for homology searching. Proc Natl Acad Sci U S A (2009) 2.05
Homology modeling using parametric alignment ensemble generation with consensus and energy-based model selection. Nucleic Acids Res (2006) 1.96
Fido, a novel AMPylation domain common to fic, doc, and AvrB. PLoS One (2009) 1.92
Detecting distant homology with Meta-BASIC. Nucleic Acids Res (2004) 1.86
Natural history of S-adenosylmethionine-binding proteins. BMC Struct Biol (2005) 1.85
MUMMALS: multiple sequence alignment improved by using hidden Markov models with local structural information. Nucleic Acids Res (2006) 1.85
Berkeley Phylogenomics Group web servers: resources for structural phylogenomic analysis. Nucleic Acids Res (2007) 1.79
A primer on python for life science researchers. PLoS Comput Biol (2007) 1.78
Scoring profile-to-profile sequence alignments. Protein Sci (2004) 1.71
The CATH hierarchy revisited-structural divergence in domain superfamilies and the continuity of fold space. Structure (2009) 1.62
A multi-template combination algorithm for protein comparative modeling. BMC Struct Biol (2008) 1.62
PROMALS3D: multiple protein sequence alignment enhanced with evolutionary and three-dimensional structural information. Methods Mol Biol (2014) 1.59
The limits of protein sequence comparison? Curr Opin Struct Biol (2005) 1.57
PhyLAT: a phylogenetic local alignment tool. Bioinformatics (2012) 1.54
The construction and use of log-odds substitution scores for multiple sequence alignment. PLoS Comput Biol (2010) 1.54
GeMMA: functional subfamily classification within superfamilies of predicted protein structural domains. Nucleic Acids Res (2009) 1.50
Homology-extended sequence alignment. Nucleic Acids Res (2005) 1.40
Advances in homology protein structure modeling. Curr Protein Pept Sci (2006) 1.39
Analysis of CASP8 targets, predictions and assessment methods. Database (Oxford) (2009) 1.38
Improved profile HMM performance by assessment of critical algorithmic features in SAM and HMMER. BMC Bioinformatics (2005) 1.33
MULTICOM: a multi-level combination approach to protein structure prediction and its assessments in CASP8. Bioinformatics (2010) 1.30
Gene and genome duplication in Acanthamoeba polyphaga Mimivirus. J Virol (2005) 1.30
Accurate statistical model of comparison between multiple sequence alignments. Nucleic Acids Res (2008) 1.28
Profile-profile comparisons by COMPASS predict intricate homologies between protein families. Protein Sci (2003) 1.26
@TOME-2: a new pipeline for comparative modeling of protein-ligand complexes. Nucleic Acids Res (2009) 1.26
Refining homology models by combining replica-exchange molecular dynamics and statistical potentials. Proteins (2008) 1.25
Practical lessons from protein structure prediction. Nucleic Acids Res (2005) 1.25
4SCOPmap: automated assignment of protein structures to evolutionary superfamilies. BMC Bioinformatics (2004) 1.25
Discrete-continuous duality of protein structure space. Curr Opin Struct Biol (2009) 1.24
PROCAIN: protein profile comparison with assisting information. Nucleic Acids Res (2009) 1.17
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
Protein function prediction using domain families. BMC Bioinformatics (2013) 1.15
Longin-like folds identified in CHiPS and DUF254 proteins: vesicle trafficking complexes conserved in eukaryotic evolution. Protein Sci (2006) 1.15
Predicting cis-acting elements of Lactobacillus plantarum by comparative genomics with different taxonomic subgroups. Nucleic Acids Res (2006) 1.12
Evolutionary relationships of microbial aromatic prenyltransferases. PLoS One (2011) 1.09
Discrimination between distant homologs and structural analogs: lessons from manually constructed, reliable data sets. J Mol Biol (2008) 1.08
Essential roles for imuA'- and imuB-encoded accessory factors in DnaE2-dependent mutagenesis in Mycobacterium tuberculosis. Proc Natl Acad Sci U S A (2010) 1.07
A galaxy of folds. Protein Sci (2010) 1.05
A comprehensive system for evaluation of remote sequence similarity detection. BMC Bioinformatics (2007) 1.05
Divergent evolution within protein superfolds inferred from profile-based phylogenetics. J Mol Biol (2005) 1.04
Protein subcellular localization prediction of eukaryotes using a knowledge-based approach. BMC Bioinformatics (2009) 1.02
Functional site plasticity in domain superfamilies. Biochim Biophys Acta (2013) 1.00
Highly divergent mitochondrial ATP synthase complexes in Tetrahymena thermophila. PLoS Biol (2010) 0.96
MALISAM: a database of structurally analogous motifs in proteins. Nucleic Acids Res (2007) 0.96
Detection of distant evolutionary relationships between protein families using theory of sequence profile-profile comparison. BMC Bioinformatics (2010) 0.96
Comparative Protein Structure Modeling Using MODELLER. Curr Protoc Bioinformatics (2016) 0.95
ProfNet, a method to derive profile-profile alignment scoring functions that improves the alignments of distantly related proteins. BMC Bioinformatics (2005) 0.94
Identification of plant RAD52 homologs and characterization of the Arabidopsis thaliana RAD52-like genes. Plant Cell (2011) 0.94
Mammalian BEX, WEX and GASP genes: coding and non-coding chimaerism sustained by gene conversion events. BMC Evol Biol (2005) 0.94
Identification of homologs in insignificant blast hits by exploiting extrinsic gene properties. BMC Bioinformatics (2007) 0.93
Improving protein secondary structure prediction using a simple k-mer model. Bioinformatics (2010) 0.93
Analysis of superfamily specific profile-profile recognition accuracy. BMC Bioinformatics (2004) 0.93
Alternating evolutionary pressure in a genetic algorithm facilitates protein model selection. BMC Struct Biol (2008) 0.92
PHOG-BLAST--a new generation tool for fast similarity search of protein families. BMC Evol Biol (2006) 0.91
COMPASS server for homology detection: improved statistical accuracy, speed and functionality. Nucleic Acids Res (2009) 0.90
DescFold: a web server for protein fold recognition. BMC Bioinformatics (2009) 0.90
MRFalign: protein homology detection through alignment of Markov random fields. PLoS Comput Biol (2014) 0.89
Hepatitis C virus NS4B carboxy terminal domain is a membrane binding domain. Virol J (2009) 0.89
dRHP-PseRA: detecting remote homology proteins using profile-based pseudo protein sequence and rank aggregation. Sci Rep (2016) 0.88
webPRC: the Profile Comparer for alignment-based searching of public domain databases. Nucleic Acids Res (2009) 0.88
Designing and benchmarking the MULTICOM protein structure prediction system. BMC Struct Biol (2013) 0.88
GraphClust: alignment-free structural clustering of local RNA secondary structures. Bioinformatics (2012) 0.88
Functional classification of CATH superfamilies: a domain-based approach for protein function annotation. Bioinformatics (2015) 0.87
Island method for estimating the statistical significance of profile-profile alignment scores. BMC Bioinformatics (2009) 0.87
Large-scale sequence analysis of hemagglutinin of influenza A virus identifies conserved regions suitable for targeting an anti-viral response. PLoS One (2010) 0.87
Improving protein fold recognition by random forest. BMC Bioinformatics (2014) 0.86
Detection of biochemical pathways by probabilistic matching of phyletic vectors. PLoS One (2009) 0.86
eFindSite: improved prediction of ligand binding sites in protein models using meta-threading, machine learning and auxiliary ligands. J Comput Aided Mol Des (2013) 0.86
Incorporation of local structural preference potential improves fold recognition. PLoS One (2011) 0.85
An assessment of substitution scores for protein profile-profile comparison. Bioinformatics (2011) 0.85
Application of nonnegative matrix factorization to improve profile-profile alignment features for fold recognition and remote homolog detection. BMC Bioinformatics (2008) 0.85
The presence of the iron-sulfur motif is important for the conformational stability of the antiviral protein, Viperin. PLoS One (2012) 0.85
eThread: a highly optimized machine learning-based approach to meta-threading and the modeling of protein tertiary structures. PLoS One (2012) 0.85
Effect of using suboptimal alignments in template-based protein structure prediction. Proteins (2011) 0.84
Consensus sequences improve PSI-BLAST through mimicking profile-profile alignments. Nucleic Acids Res (2007) 0.84
The CATH database. Hum Genomics (2010) 0.84
AlignHUSH: alignment of HMMs using structure and hydrophobicity information. BMC Bioinformatics (2011) 0.83
One-Block CYRCA: an automated procedure for identifying multiple-block alignments from single block queries. Nucleic Acids Res (2005) 0.83
Recursive protein modeling: a divide and conquer strategy for Protein Structure Prediction and its case study in CASP9. J Bioinform Comput Biol (2012) 0.82
A large-scale conformation sampling and evaluation server for protein tertiary structure prediction and its assessment in CASP11. BMC Bioinformatics (2015) 0.81
Refining intra-protein contact prediction by graph analysis. BMC Bioinformatics (2007) 0.81
Beyond the E-Value: Stratified Statistics for Protein Domain Prediction. PLoS Comput Biol (2015) 0.80
HHsvm: fast and accurate classification of profile-profile matches identified by HHsearch. Bioinformatics (2009) 0.80
Unleashing the power of meta-threading for evolution/structure-based function inference of proteins. Front Genet (2013) 0.80
Proteases in malaria parasites - a phylogenomic perspective. Curr Genomics (2011) 0.79
Refinement by shifting secondary structure elements improves sequence alignments. Proteins (2015) 0.79
Using homology relations within a database markedly boosts protein sequence similarity search. Proc Natl Acad Sci U S A (2015) 0.79
The arginine methyltransferase NDUFAF7 is essential for complex I assembly and early vertebrate embryogenesis. Hum Mol Genet (2014) 0.79
BAP1 loss defines a new class of renal cell carcinoma. Nat Genet (2012) 4.97
Probabilistic scoring measures for profile-profile comparison yield more accurate short seed alignments. Bioinformatics (2003) 1.18
Nuclear envelope phosphatase 1-regulatory subunit 1 (formerly TMEM188) is the metazoan Spo7p ortholog and functions in the lipin activation pathway. J Biol Chem (2011) 1.17
Protein side chain modeling with orientation-dependent atomic force fields derived by series expansions. J Comput Chem (2011) 0.90
Sequences in the nonconsensus nucleotide-binding domain of ABCG5/ABCG8 required for sterol transport. J Biol Chem (2011) 0.85
Platelet-derived growth factor/vascular endothelial growth factor receptor inactivation by sunitinib results in Tsc1/Tsc2-dependent inhibition of TORC1. Mol Cell Biol (2013) 0.78
Sequences and topology: evolution of proteins and evolution of computational approaches. Curr Opin Struct Biol (2010) 0.77