• MODELLER

  • Referenced in 34 articles [sw27731]
  • Modeling. MODELLER is used for homology or comparative modeling of protein three-dimensional structures...
  • RAPTOR

  • Referenced in 20 articles [sw09002]
  • very well in recognizing the hard Homology Modeling (HM) targets. RAPTOR was implemented...
  • SWISS-MODEL

  • Referenced in 14 articles [sw17373]
  • SWISS-MODEL: An automated protein homology-modeling server. SWISS-MODEL (http://swissmodel.expasy.org) is a server...
  • HadamardSearch

  • Referenced in 10 articles [sw18675]
  • finite group G for which a homological model hG is known, as described by V.Alvarez...
  • ESyPred3D

  • Referenced in 5 articles [sw16876]
  • proteins 3D structures. Motivation: Homology or comparative modeling is currently the most accurate method ... identify the structural homolog, (2) target–template alignment, (3) model building and optimization ... model evaluation. The target–template alignment step is generally accepted ... most critical step in homology modeling. Results: We present here ESyPred3D, a new automated homology...
  • PatternHunter

  • Referenced in 36 articles [sw20963]
  • homology search algorithm ’PatternHunter’ that uses a novel seed model for increased sensitivity ... sensitivity, PatternHunter is able to find homologies between sequences as large as human chromosomes...
  • SCWRL4

  • Referenced in 7 articles [sw22393]
  • simple command-line interface, designed for homology modeling. To achieve higher accuracy, SCWRL4 is somewhat...
  • VADAR

  • Referenced in 6 articles [sw12496]
  • crystallography, NMR spectroscopy, 3D-threading or homology modelling...
  • TMBpro

  • Referenced in 5 articles [sw11341]
  • tertiary structure of TMB proteins. Traditional homology modeling methods, however, fail on most TMB proteins...
  • CMfinder

  • Referenced in 6 articles [sw17265]
  • importantly, the resulting probabilistic model can be directly used for homology search ... allowing iterative refinement of structural models based on additional homologs. We have used this approach ... models of known RNA motifs based on small numbers of related sequences, which identified homologs...
  • TM-align

  • Referenced in 15 articles [sw22248]
  • match the models predicted by TASSER for solved non-homologous proteins in PDB. For both...
  • Infernal

  • Referenced in 12 articles [sw17000]
  • Infernal 1.1: 100-fold faster RNA homology searches. Summary: Infernal builds probabilistic profiles ... structure of an RNA family called covariance models (CMs) from structurally annotated multiple sequence alignments ... pipeline for RNA homology search based on accelerated profile hidden Markov model (HMM) methods...
  • BetaSCP

  • Referenced in 3 articles [sw08772]
  • important biomolecular applications such as a homology modeling, a docking simulation, a protein design...
  • PROMALS

  • Referenced in 5 articles [sw22476]
  • sequence alignments are essential in homology inference, structure modeling, functional prediction and phylogenetic analysis ... that improves alignment quality by using additional homologs from PSI-BLAST searches and secondary structure...
  • PUDGE

  • Referenced in 2 articles [sw21772]
  • structure prediction. The construction of a homology model for a protein can involve a number...
  • TrpAQP

  • Referenced in 1 article [sw24381]
  • homologs from plants were homology modeled and various simulations have been applied to measure their...
  • BetaSCPWeb

  • Referenced in 1 article [sw20703]
  • Many applications, such as protein design, homology modeling, flexible docking, etc. require the prediction...
  • BetaSCP2

  • Referenced in 1 article [sw09840]
  • protein design, flexible docking of proteins, homology modeling, etc. The SCP-problem can be formulated...
  • MICAlign

  • Referenced in 2 articles [sw12010]
  • template-based protein structure modeling for remote homologs remains a difficult problem even following...
  • TCS

  • Referenced in 1 article [sw24605]
  • procedure when analyzing biological sequences. Homology and evolutionary modeling are the most common applications...