• TM-align

  • Referenced in 14 articles [sw22248]
  • representative protein chains from the Protein Data Bank (PDB) with a sequence identity cutoff ... homologous proteins in PDB. For both folded and misfolded models, TM-align can almost always...
  • MODELLER

  • Referenced in 32 articles [sw27731]
  • MODELLER is used for homology or comparative modeling of protein three-dimensional structures ... user provides an alignment of a sequence to be modeled with known related structures...
  • RAPTOR

  • Referenced in 19 articles [sw09002]
  • blind and public test by the protein structure prediction community, ranks RAPTOR ... terms of the recognition capability and alignment accuracy for Fold Recognition (FR) family targets. RAPTOR ... performs very well in recognizing the hard Homology Modeling (HM) targets. RAPTOR was implemented...
  • PROMALS3D

  • Referenced in 3 articles [sw16918]
  • used to improve alignment quality. PROMALS3D is a tool for protein MSA construction enhanced with ... homologs from sequence and structure databases for input proteins, derives structure-based constraints from alignments ... consensus alignment enriched with sequence and structural information about input proteins and their homologs. PROMALS3D...
  • BLAT

  • Referenced in 34 articles [sw16891]
  • alignments and 50 times faster for protein alignments at sensitivity settings typically used when comparing ... regions in the genome likely to be homologous to the query sequence. It performs...
  • PROMALS

  • Referenced in 1 article [sw22476]
  • accurate multiple protein sequence alignments. Multiple sequence alignments are essential in homology inference, structure modeling ... constructs multiple protein sequence alignments using PROMALS, a progressive method that improves alignment quality ... homologs from PSI-BLAST searches and secondary structure predictions from PSIPRED. PROMALS shows higher alignment ... PROMALS web server takes FASTA format protein sequences as input. The output includes a colored...
  • LEON

  • Referenced in 2 articles [sw24616]
  • homology between the aligned sequences. If the initial hypothesis of homology is wrong, no subsequent ... LEON, to predict homology between proteins based on a multiple alignment of complete sequences (MACS...
  • ESyPred3D

  • Referenced in 5 articles [sw16876]
  • proteins. It generally consists in four steps: (1) databanks searching to identify the structural homolog ... target–template alignment, (3) model building and optimization, and (4) model evaluation. The target–template ... increased alignment performances of a new alignment strategy. Alignments are obtained by combining, weighting ... screening the results of several multiple alignment programs. The final three-dimensional structure is build...
  • FastLSA

  • Referenced in 3 articles [sw01958]
  • alignment is a fundamental operation for homology search in bioinformatics. For two DNA or protein ... full-matrix (FM), dynamic programming alignment algorithms such as Needleman-Wunsch and Smith-Waterman take...
  • eHive

  • Referenced in 2 articles [sw27408]
  • multiple whole genome alignments and (3) gene trees with protein homology inference. Finally, we show...
  • MICAlign

  • Referenced in 2 articles [sw12010]
  • structure alignment in template-based protein structure modeling for remote homologs remains a difficult problem ... present MICAlign, a sequence-to-structure alignment tool that incorporates multiple sources of information from...
  • COMPASS

  • Referenced in 9 articles [sw23109]
  • quality of local alignments. The method allows prediction of relationships between protein families ... illustrated by the detection of an intricate homology between the DNA-binding domain...
  • HHpred

  • Referenced in 7 articles [sw17271]
  • fast server for remote protein homology detection and structure prediction and is the first ... single query sequence or a multiple alignment as input. Within only a few minutes...
  • FUGUE

  • Referenced in 9 articles [sw16894]
  • FUGUE: sequence-structure homology recognition using environment-specific substitution tables and structure-dependent gap penalties ... Substitutions of an amino acid in a protein structure are constrained by its local structural ... structural alignments in the HOMSTRAD database (http://www-cryst.bioc.cam.ac.uk/homstrad/). (2) Automatic selection of alignment algorithm ... FUGUE uses the global-local algorithm to align a sequence-structure pair when they greatly...
  • FASTA

  • Referenced in 25 articles [sw09655]
  • high scoring library sequences that are homologous to the query sequence, or the search will ... analyzing the G-protein-coupled receptor family, several proteins were found that, because with optimization ... only a careful examination of the sequence alignments that focused on the conserved residues provided...
  • MUMMALS

  • Referenced in 4 articles [sw13110]
  • protein sequence alignment using probabilistic consistency. MUMMALS improves alignment quality by using pairwise alignment hidden ... structure-based alignments. We show that (i) on remote homologs, MUMMALS achieves statistically best accuracy ... automatically computed pairwise structure alignments of divergent protein domains is superior to smaller but carefully...
  • MATRAS

  • Referenced in 4 articles [sw16871]
  • developed a web server for comparing protein 3D structures using the program Matras (http://biunit.aist-nara.ac.jp ... score is designed to detect evolutionarily related (homologous) structural similarities. Our web server has three ... pairwise 3D alignment, which is simply align two structures. A user can assign structures ... service is a multiple 3D alignment, which compares several protein structures. This program employs...
  • CUDAMPF++

  • Referenced in 1 article [sw21326]
  • genomic data grow exponentially, however, most of alignment methods face challenges due to their huge ... widely used for the analysis of homologous protein and nucleotide sequences with high sensitivity, based ... introdues a heuristic pipeline to accelerate the alignment process, which is carried out on central...
  • SWISS-MODEL

  • Referenced in 7 articles [sw17373]
  • SWISS-MODEL: An automated protein homology-modeling server. SWISS-MODEL (http://swissmodel.expasy.org) is a server ... automated comparative modeling of three-dimensional (3D) protein structures. It pioneered the field of automated ... computed 120 000 user requests for 3D protein models. SWISS-MODEL provides several levels ... protein is submitted to build a 3D model. Template selection, alignment and model building...
  • PUDGE

  • Referenced in 2 articles [sw21772]
  • prediction. The construction of a homology model for a protein can involve a number ... modeling pipelines. Pudge is a flexible, interactive protein structure prediction server, which is designed with ... modeling into five stages (template selection, alignment, model building, model refinement and model evaluation...