• Prodepth

  • Referenced in 0 articles [sw25085]
  • field of protein structure prediction and homology modeling. This method might prove...
  • HHpred

  • Referenced in 7 articles [sw17271]
  • fast server for remote protein homology detection and structure prediction and is the first ... implement pairwise comparison of profile hidden Markov models (HMMs). It allows to search a wide...
  • MATRAS

  • Referenced in 4 articles [sw16871]
  • substitution model of amino acids. This score is designed to detect evolutionarily related (homologous) structural...
  • PAComplex

  • Referenced in 2 articles [sw21769]
  • peptide-TCR interactions and detailed atomic interacting models. PAComplex is the first web server investigating ... interfaces to infer peptide antigens and homologous peptide antigens of a query. This server first ... antigens and homologous peptide antigens of the query and displays detailed interacting models (e.g. hydrogen...
  • SIB-BLAST

  • Referenced in 2 articles [sw21773]
  • sequence-based homology detection. SIB was developed to overcome the model corruption frequently observed...
  • 3DIGARS

  • Referenced in 1 article [sw36904]
  • effective for non-homologous sequence-based structure prediction. Thus, ab initio modeling is indispensable...
  • ChainCon

  • Referenced in 9 articles [sw12058]
  • ChainCon Software: Chain Contractions, Homology and Cohomology Software and Examples. The algorithms described ... primarily intended to serve as a model implementation of the algorithms and concepts introduced ... small amount of code from the Computational Homology Project (CHomP) programming library, and thus...
  • MUMMALS

  • Referenced in 4 articles [sw13110]
  • exploiting explicit structure predictions. Parameters for such models have been estimated from a large library ... alignments. We show that (i) on remote homologs, MUMMALS achieves statistically best accuracy among several...
  • Assemble

  • Referenced in 1 article [sw17136]
  • semi-automated modeling process that can be performed by homology and ab initio with...
  • MEDELLER

  • Referenced in 2 articles [sw17378]
  • homology-based coordinate generation method, MEDELLER, which is optimized to build highly reliable core models...
  • LncADeep

  • Referenced in 1 article [sw34142]
  • intrinsic and homology features into a deep belief network and constructs models targeting both full...
  • TurboFold

  • Referenced in 3 articles [sw17269]
  • analysis between sequences with the thermodynamic folding model. Unlike most other multi-sequence structure prediction ... therefore useful for predicting structures for homologous sequences that have diverged significantly. TurboFold...
  • LocARNAscan

  • Referenced in 2 articles [sw23118]
  • families unrelated by common descent. Current homology search tools for structured RNAs are either based ... date, however, the information contained in covariance models or manually prescribed search patterns is dominated ... secondary structure alone informative for homology search and the detection of novel members...
  • OreAlgebraicAnalysis

  • Referenced in 4 articles [sw15153]
  • over Ore algebras. Physical systems are typically modeled by systems of functional equations; these ... algebraic viewpoint, using D-module theory and homological algebra techniques. The different types of systems...
  • CUDAMPF++

  • Referenced in 1 article [sw21326]
  • homologous protein and nucleotide sequences with high sensitivity, based on profile hidden Markov models (HMMs...
  • StepBrothers

  • Referenced in 1 article [sw34333]
  • related. Of these methods, Markov change-point models currently provide the most coherent framework ... faulty in that the inferred relatedness of homologous sequences across regions divided by recombinant events ... introduce a novel random tips (RT) model. The model springs from the idea that...
  • InterEvDock

  • Referenced in 1 article [sw34229]
  • using the FRODOCK program and the resulting models are re-scored with InterEvScore and SOAP ... thus particularly well suited in case homologous sequences are available for both binding partners ... structures of the most likely consensus models together with 10 predicted residues most likely involved...
  • HOPE

  • Referenced in 4 articles [sw32999]
  • potential energy associated with a protein model. The method uses the minimum energy conformation ... Successful results are presented for pairs of homologous proteins, where HOPE is compared...
  • ElNemo

  • Referenced in 1 article [sw22480]
  • factors). Any number of normal mode perturbed models for MR can be generated for download ... conformations of the same (or a homologous) protein are available, ElNémo identifies the normal modes...
  • FASTSP

  • Referenced in 1 article [sw38911]
  • standard techniques for comparing alignments, Developer, Modeler and Total Column (TC) scores can be derived ... through calculations of the set of homologies that the alignments share. However, the brute-force...