• ViennaRNA

  • Referenced in 20 articles [sw10504]
  • programs for the prediction and comparison of RNA secondary structures. RNA secondary structure prediction through ... optimal energy. For secondary structure comparison, the package contains several measures of distance (dissimilarities) using ... algorithm to design sequences with a predefined structure (inverse folding...
  • MODELLER

  • Referenced in 33 articles [sw27731]
  • clustering, searching of sequence databases, comparison of protein structures, etc. MODELLER is available for download...
  • MAMMOTH

  • Referenced in 11 articles [sw26215]
  • automated method for model comparison. Advances in structural genomics and protein structure prediction require ... presented that allows comparison of an experimental protein structure with an arbitrary low-resolution protein ... good tool for protein structure comparisons in structural genomics applications. MAMMOTH is available from...
  • TM-align

  • Referenced in 14 articles [sw22248]
  • applied to an all-against-all structure comparison of 10 515 representative protein chains from ... align can almost always find close structural analogs, with an average root mean square deviation...
  • FUGUE

  • Referenced in 9 articles [sw16894]
  • recognizing distant homologues by sequence-structure comparison (http://www-cryst.bioc.cam.ac.uk/fugue/), has three key features ... amino acid in a protein structure are constrained by its local structural environment, which...
  • DaliLite

  • Referenced in 5 articles [sw35907]
  • DaliLite workbench for protein structure comparison. Summary: DaliLite is a program for pairwise structure comparison...
  • TreeJuxtaposer

  • Referenced in 5 articles [sw18623]
  • using focus+context with guaranteed visibility. Structural comparison of large trees is a difficult task ... TreeJuxtaposer, a system designed to support the comparison task for large trees of several hundred ... propose a new methodology for detailed structural comparison between two trees and provide ... audience of biologists who must understand the structural details of many phylogenetic, or evolutionary, trees...
  • MARNA

  • Referenced in 5 articles [sw35539]
  • prediction of RNAs based on sequence structure comparisons. Results: We describe a novel approach ... consideration both the primary and the secondary structures ... based on pairwise sequence–structure comparisons of RNAs. From these sequence–structure alignments, libraries...
  • 3DCoffee

  • Referenced in 6 articles [sw12008]
  • pairwise sequence alignments and pairwise structure comparison methods to generate multiple sequence alignments. We benchmarked ... subset of HOMSTRAD, the collection of reference structural alignments. We found that combining TCoffee with...
  • MCQ4Structures

  • Referenced in 4 articles [sw15705]
  • MCQ4Structures to compute similarity of molecule structures. Comparison of molecular structures in order to identify ... structural similarity computation based on molecule tertiary structure representation in torsional angle space. We discuss ... experimental use in comparison of a number of 3D structures as well as evaluation...
  • GenThreader

  • Referenced in 10 articles [sw35746]
  • profiles or perform profile-profile comparison. Layer on structural information. GenThreader is a family...
  • STRSCNE

  • Referenced in 56 articles [sw00922]
  • steps of the method is discussed. The structure and the usage of STRSCNE are described ... numerical experiments. The results of a comparison with high quality codes for nonlinear optimization...
  • TetGen

  • Referenced in 151 articles [sw04046]
  • TetGen, including an efficient tetrahedral mesh data structure, a set of enhanced local mesh operations ... mesh generation. Experimental examples as well as comparisons with other softwares are presented...
  • FATCAT

  • Referenced in 2 articles [sw32830]
  • FATCAT: a web server for flexible structure comparison and structure similarity searching. Protein structure comparison ... implements the recently developed flexible protein structure comparison algorithm FATCAT, which automatically identifies hinges ... algorithms: FATCAT-pairwise for pairwise flexible structure comparison and FATCAT-search for database searching...
  • MATRAS

  • Referenced in 4 articles [sw16871]
  • MATRAS: a program for protein 3D structure comparison. The recent accumulation of large amounts...
  • MultRoot

  • Referenced in 98 articles [sw00604]
  • backward error, estimated forward error, and the structure-preserving condition number. The most significant features ... included for numerical experiments and performance comparison...
  • FRASS

  • Referenced in 2 articles [sw15707]
  • FRASS: the web-server for RNA structural comparison. Background: The impressive increase of novel ... years, demands automated methods for structure comparison. While many algorithms handle only small motifs ... LaJolla) are available for the structural comparison of large and intact RNA molecules. Results ... Gauss integrals and allows one to compare structures of RNA chains and to find similar...
  • ProCKSI

  • Referenced in 3 articles [sw35361]
  • decision support system for Protein (Structure) Comparison, Knowledge, Similarity and Information. Results: We present ProCKSI ... structures could have a large deviation from one another. To perform this type of comparison ... protein kinases, originally derived by sequence comparison by Hanks and Hunter, but here ... consensus similarity measure based on structures. In the third experiment using the Rost and Sander...
  • SMART

  • Referenced in 16 articles [sw17187]
  • protein domain structure, and to align these displays to provide schematic comparisons of orthologous genes ... query SMART by Gene Ontology terms, improved structure database searching and batch retrieval of multiple...
  • CasANOVA

  • Referenced in 24 articles [sw13555]
  • levels of the significant factors. Level comparisons are done via a post-hoc analysis based ... also leads to the identification of a structure within each factor, as levels ... groups. In contrast to the traditional pairwise comparison methods, these groups are necessarily nonoverlapping ... performs as well as if the exact structure were known beforehand. A simulation and real...