Published in Proteins on July 01, 2000
MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res (2004) 168.89
MUSCLE: a multiple sequence alignment method with reduced time and space complexity. BMC Bioinformatics (2004) 50.89
Improving the accuracy of PSI-BLAST protein database searches with composition-based statistics and other refinements. Nucleic Acids Res (2001) 22.33
ProbCons: Probabilistic consistency-based multiple sequence alignment. Genome Res (2005) 11.90
Comparative protein structure modeling using Modeller. Curr Protoc Bioinformatics (2006) 8.72
Cyclic coordinate descent: A robotics algorithm for protein loop closure. Protein Sci (2003) 4.82
Comprehensive evaluation of protein structure alignment methods: scoring by geometric measures. J Mol Biol (2005) 4.02
Benchmarking tools for the alignment of functional noncoding DNA. BMC Bioinformatics (2004) 4.00
PISCES: recent improvements to a PDB sequence culling server. Nucleic Acids Res (2005) 3.55
Pcons: a neural-network-based consensus predictor that improves fold recognition. Protein Sci (2001) 2.90
Domain enhanced lookup time accelerated BLAST. Biol Direct (2012) 2.87
Alignment of protein sequences by their profiles. Protein Sci (2004) 2.80
The accuracy of several multiple sequence alignment programs for proteins. BMC Bioinformatics (2006) 2.52
Structural evolution of the protein kinase-like superfamily. PLoS Comput Biol (2005) 2.48
Quality measures for protein alignment benchmarks. Nucleic Acids Res (2010) 2.23
Homology modeling using parametric alignment ensemble generation with consensus and energy-based model selection. Nucleic Acids Res (2006) 1.96
CASP9 assessment of free modeling target predictions. Proteins (2011) 1.90
A consensus view of fold space: combining SCOP, CATH, and the Dali Domain Dictionary. Protein Sci (2003) 1.89
Finding weak similarities between proteins by sequence profile comparison. Nucleic Acids Res (2003) 1.88
SCWRL and MolIDE: computer programs for side-chain conformation prediction and homology modeling. Nat Protoc (2008) 1.79
Scoring profile-to-profile sequence alignments. Protein Sci (2004) 1.71
How well can the accuracy of comparative protein structure models be predicted? Protein Sci (2008) 1.52
Advances in homology protein structure modeling. Curr Protein Pept Sci (2006) 1.39
A database and tools for 3-D protein structure comparison and alignment using the Combinatorial Extension (CE) algorithm. Nucleic Acids Res (2001) 1.34
Evaluation of PSI-BLAST alignment accuracy in comparison to structural alignments. Protein Sci (2000) 1.33
Evolutionary constraints on structural similarity in orthologs and paralogs. Protein Sci (2009) 1.23
Sequence-based prediction of protein domains. Nucleic Acids Res (2004) 1.21
Molecular modeling of the von Willebrand factor A2 Domain and the effects of associated type 2A von Willebrand disease mutations. J Mol Model (2004) 1.15
Domain mapping of the Rad51 paralog protein complexes. Nucleic Acids Res (2004) 1.14
Accuracy of structure-based sequence alignment of automatic methods. BMC Bioinformatics (2007) 1.14
A comparison of position-specific score matrices based on sequence and structure alignments. Protein Sci (2002) 1.13
Defining functional distance using manifold embeddings of gene ontology annotations. Proc Natl Acad Sci U S A (2007) 1.08
Combining multiple structure and sequence alignments to improve sequence detection and alignment: application to the SH2 domains of Janus kinases. Proc Natl Acad Sci U S A (2001) 1.08
Including biological literature improves homology search. Pac Symp Biocomput (2001) 1.07
Sequence variations within protein families are linearly related to structural variations. J Mol Biol (2002) 1.06
Application of protein structure alignments to iterated hidden Markov model protocols for structure prediction. BMC Bioinformatics (2006) 1.05
A comprehensive system for evaluation of remote sequence similarity detection. BMC Bioinformatics (2007) 1.05
Protein structural similarity search by Ramachandran codes. BMC Bioinformatics (2007) 1.04
CPSARST: an efficient circular permutation search tool applied to the detection of novel protein structural relationships. Genome Biol (2008) 1.03
Analysis of protein sequence/structure similarity relationships. Biophys J (2002) 1.01
Phylogenetic simulation of promoter evolution: estimation and modeling of binding site turnover events and assessment of their impact on alignment tools. Genome Biol (2007) 0.99
Systematic analysis of the effect of multiple templates on the accuracy of comparative models of protein structure. BMC Struct Biol (2008) 0.98
A comparative assessment and analysis of 20 representative sequence alignment methods for protein structure prediction. Sci Rep (2013) 0.97
Comparative Protein Structure Modeling Using MODELLER. Curr Protoc Bioinformatics (2016) 0.95
Accuracy analysis of multiple structure alignments. Protein Sci (2009) 0.95
Current Methods for Automated Filtering of Multiple Sequence Alignments Frequently Worsen Single-Gene Phylogenetic Inference. Syst Biol (2015) 0.94
BCL::Align-sequence alignment and fold recognition with a custom scoring function online. Gene (2008) 0.90
Structural alphabets for protein structure classification: a comparison study. J Mol Biol (2008) 0.90
Evolutionary inference via the Poisson Indel Process. Proc Natl Acad Sci U S A (2012) 0.89
Protein sequence alignment with family-specific amino acid similarity matrices. BMC Res Notes (2011) 0.89
iSARST: an integrated SARST web server for rapid protein structural similarity searches. Nucleic Acids Res (2009) 0.89
Revisiting gap locations in amino acid sequence alignments and a proposal for a method to improve them by introducing solvent accessibility. Proteins (2011) 0.89
Homology modeling a fast tool for drug discovery: current perspectives. Indian J Pharm Sci (2012) 0.87
Template-based protein structure modeling. Methods Mol Biol (2010) 0.86
PASS2 version 4: an update to the database of structure-based sequence alignments of structural domain superfamilies. Nucleic Acids Res (2011) 0.86
DECIPHER: harnessing local sequence context to improve protein multiple sequence alignment. BMC Bioinformatics (2015) 0.83
Detection and alignment of 3D domain swapping proteins using angle-distance image-based secondary structural matching techniques. PLoS One (2010) 0.81
Fast and robust multiple sequence alignment with phylogeny-aware gap placement. BMC Bioinformatics (2012) 0.81
MaxMod: a hidden Markov model based novel interface to MODELLER for improved prediction of protein 3D models. J Mol Model (2015) 0.80
Systematic assessment of accuracy of comparative model of proteins belonging to different structural fold classes. J Mol Model (2011) 0.79
CORAL: aligning conserved core regions across domain families. Bioinformatics (2009) 0.79
Using structure to explore the sequence alignment space of remote homologs. PLoS Comput Biol (2011) 0.79
Evolution of structural shape in bacterial globin-related proteins. J Mol Evol (2006) 0.77
The distance-profile representation and its application to detection of distantly related protein families. BMC Bioinformatics (2005) 0.77
Next-Generation Sequencing Techniques Reveal that Genomic Imprinting Is Absent in Day-Old Gallus gallus domesticus Brains. PLoS One (2015) 0.76
MTRAP: pairwise sequence alignment algorithm by a new measure based on transition probability between two consecutive pairs of residues. BMC Bioinformatics (2010) 0.76
AlignStat: a web-tool and R package for statistical comparison of alternative multiple sequence alignments. BMC Bioinformatics (2016) 0.75
ReformAlign: improved multiple sequence alignments using a profile-based meta-alignment approach. BMC Bioinformatics (2014) 0.75
An integrated Java tool for generating amino acid sequence alignments with mapped secondary structure elements. 3 Biotech (2014) 0.75
PR2ALIGN: a stand-alone software program and a web-server for protein sequence alignment using weighted biochemical properties of amino acids. BMC Res Notes (2015) 0.75
An efficient algorithm for protein structure comparison using elastic shape analysis. Algorithms Mol Biol (2016) 0.75
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Genomic fold assignment and rational modeling of proteins of biological interest. Proc Int Conf Intell Syst Mol Biol (2000) 1.47
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Identification and structural analysis of human RBM8A and RBM8B: two highly conserved RNA-binding motif proteins that interact with OVCA1, a candidate tumor suppressor. Genomics (2000) 0.95
Biochemical characteristics and inhibitor selectivity of mouse indoleamine 2,3-dioxygenase-2. Amino Acids (2010) 0.90
An inhibitory monoclonal antibody binds at the turn of the helix-turn-helix motif in the N-terminal domain of HIV-1 integrase. J Biol Chem (2000) 0.82
Modeling of substrate specificity of the Alzheimer's disease amyloid precursor protein beta-secretase. J Mol Biol (2000) 0.81
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