• EAT

  • Referenced in 17 articles [sw09167]
  • goal was the computation of the first homology groups of some loop spaces, for which ... just designed to illustrate our methods of Effective Homology by a concrete experimental program...
  • Homology

  • Referenced in 30 articles [sw04871]
  • Computing simplicial homology based on efficient Smith normal form algorithms Geometric properties of topological spaces ... paper focuses on methods for the computer calculation of the homology of finite simplicial complexes...
  • PurityFiltration

  • Referenced in 10 articles [sw07656]
  • explicitly characterized by means of elementary methods of homological algebra. Our approach avoids using sophisticated...
  • Perseus

  • Referenced in 25 articles [sw08778]
  • linear time while preserving all the underlying homological information. In this talk, we outline ... scope and limitations of such Morse-theoretic methods. We also provide a brief overview ... which implements these methods in order to efficiently compute persistent homology of various types...
  • CHomP

  • Referenced in 47 articles [sw09358]
  • nonlinear spaces and functions, within which homology is perhaps the most computable subset. In particular ... apply efficient and effective topologically based methods to the analysis of nonlinear systems...
  • RedHom

  • Referenced in 12 articles [sw08776]
  • homology of sets. The library implements algorithms based on geometric and algebraic reduction methods: acyclic ... speed up the classical Smith diagonalization method, which is unsatisfactorily slow for large inputs ... used to compute Betti numbers, torsion coefficients, homology generators, persistence intervals and maps induced ... homology. The library is based on C++ templates. This allows us to have one efficient...
  • TMBpro

  • Referenced in 5 articles [sw11341]
  • tertiary structure of TMB proteins. Traditional homology modeling methods, however, fail on most TMB proteins ... since very few non-homologous TMB structures have been determined. Yet, because TMB structures conform ... possible for methods that do not depend on target-template homology to be applied successfully...
  • ESyPred3D

  • Referenced in 5 articles [sw16876]
  • structures. Motivation: Homology or comparative modeling is currently the most accurate method to predict ... databanks searching to identify the structural homolog, (2) target–template alignment, (3) model building ... here ESyPred3D, a new automated homology modeling program. The method gets benefit of the increased...
  • Infernal

  • Referenced in 12 articles [sw17000]
  • homology search based on accelerated profile hidden Markov model (HMM) methods and HMM-banded...
  • Quasidegrees

  • Referenced in 2 articles [sw30289]
  • Matusevich, Ezra Miller, and Uli Walther. Homological methods for hypergeometric families. J. Am. Math...
  • ProCARs

  • Referenced in 1 article [sw29623]
  • main computational approaches: rearrangement-based, and homology-based methods. The rearrangement-based methods consist ... branches of a species tree. The homology-based methods consist in the detection ... this paper, we present a new homology-based method that uses a progressive approach ... comparison with three other homology-based methods: AnGeS, InferCARs and GapAdj. The program, written...
  • PFRES

  • Referenced in 6 articles [sw26875]
  • Present tertiary structure prediction methods behave well when a homologous structure is predicted, but give ... poorer results when no homologous templates are available. At the same time, some proteins that ... tertiary structures. RESULTS: The proposed PFRES method for automated protein fold classification from low identity...
  • GOASVM

  • Referenced in 6 articles [sw22445]
  • method called GOASVM that exploits the information from the GO term frequencies and distant homologs ... Chou’s pseudo-amino acid composition. The method first selects a subset of relevant ... method uses the accession number (AC) of the protein or the ACs of its homologs...
  • VFC package

  • Referenced in 16 articles [sw16729]
  • methods we introduce by giving definitions of Gromov-Witten invariants and Hamiltonian Floer homology over...
  • PROMALS

  • Referenced in 5 articles [sw22476]
  • alignments. Multiple sequence alignments are essential in homology inference, structure modeling, functional prediction and phylogenetic ... PROMALS, a progressive method that improves alignment quality by using additional homologs from PSI-BLAST ... shows higher alignment accuracy than other advanced methods, such as MUMMALS, ProbCons, MAFFT and SPEM...
  • MEDELLER

  • Referenced in 2 articles [sw17378]
  • relatively few examples. Existing homology-based structure prediction methods are designed for globular, water-soluble ... structures to justify the development of a homology-based approach specifically for them. Results ... present a MP-specific homology-based coordinate generation method, MEDELLER, which is optimized to build...
  • SCPRED

  • Referenced in 6 articles [sw26876]
  • Background: Protein structure prediction methods provide accurate results when a homologous protein is predicted, while ... predictions are obtained in the absence of homologous templates. However, some protein chains that share ... structural class. Current structural class prediction methods that predict the four structural classes defined...
  • iMembrane

  • Referenced in 2 articles [sw17379]
  • proteins. Summary: iMembrane is a homology-based method, which predicts a membrane protein’s position...
  • Footprinter

  • Referenced in 9 articles [sw09003]
  • method for the discovery of regulatory elements in a set of homologous regulatory regions, usually...
  • MEGA

  • Referenced in 34 articles [sw09078]
  • desktop application designed for comparative analysis of homologous gene sequences either from multigene families ... analyze large data set using new computational methods...