• MSMBuilder

  • Referenced in 2 articles [sw23802]
  • atomistic simulations of biomolecular dynamics such as protein folding and conformational change. MSMBuilder is named ... construct Markov state models (MSMs), a class of models that has gained favor among computational ... such as hidden Markov models and time-structure based independent component analysis. MSMBuilder boasts...
  • PPI_SVM

  • Referenced in 2 articles [sw30744]
  • challenging, especially when the three-dimensional structure of interacting partners is not known. Recently ... protein sequences by exploiting their domain information. We trained a two-class support vector machine...
  • GtRNAdb

  • Referenced in 2 articles [sw23001]
  • represent the largest, most ubiquitous class of non-protein coding RNA genes found ... tRNA functional prediction, non-canonical features, predicted structural impacts from sequence variants and minimum free...
  • TargetSpy

  • Referenced in 2 articles [sw29586]
  • selection using a wide spectrum of compositional, structural, and base pairing features covering current biological ... conserved seed match requirement. TargetSpy predictions for classes II and III are generated by appropriate ... human dataset revealing fold-change in protein production for five selected microRNAs our method shows...
  • DeepAffinity

  • Referenced in 1 article [sw39160]
  • based approaches. Under novel representations of structurally-annotated protein sequences, a semi-supervised deep learning ... test cases and 20-fold for protein classes not included for training. Performances...
  • VaxiJen

  • Referenced in 3 articles [sw26855]
  • sequence similarity, although they may share similar structures and biological properties. The antigenicity ... auto cross covariance (ACC) transformation of protein sequences into uniform vectors of principal amino acid ... tumour protein datasets were used to derive models for prediction of whole protein antigenicity. Every ... additional five training sets for each class of antigens were used to test the stability...
  • MesoBioNano

  • Referenced in 1 article [sw18198]
  • compute system’s energy, to optimize molecular structure as well as to consider the molecular ... such as atomic clusters, fullerenes, nanotubes, polypeptides, proteins, DNA, composite systems, nanofractals ... existing codes are developed for particular classes of molecular systems and do not permit multiscale...
  • MinRMS

  • Referenced in 2 articles [sw26877]
  • fewer than  800 residues) on current workstation-class computers, and therefore addresses the need ... multiple plausible shape similarities between two proteins using a widely accepted comparison metric. MinRMS generates ... matched residue pairs. That is, for two proteins of sequence length ... even possible to find a single ”best” structural alignment. The figure below shows the results...
  • iMUSIC

  • Referenced in 1 article [sw27869]
  • this paper introduces a new and simpler class of alternatives to MUSIC. This new family ... demonstrated on examples that include repeats in protein and DNA sequences. The iMUSIC algorithms ... signal space bases are non-Vandermonde in structure. Consequently, many aspects of classical MUSIC that...
  • iBitter-SCM

  • Referenced in 1 article [sw40046]
  • propensity scores of dipeptides. In general, hydrolyzed proteins, plant-derived alkaloids and toxins displays unpleasant ... attracted great attention as a new drug class. The successful identification and characterization of bitter ... dependence on their functional domain or structural information. iBitter-SCM is a simple and effective...
  • CGAL

  • Referenced in 394 articles [sw00118]
  • The goal of the CGAL Open Source Project...
  • GAP

  • Referenced in 3189 articles [sw00320]
  • GAP is a system for computational discrete algebra...
  • LAPACK

  • Referenced in 1702 articles [sw00503]
  • LAPACK is written in Fortran 90 and provides...
  • LEDA

  • Referenced in 263 articles [sw00509]
  • In the core computer science areas -- data structures...
  • Maple

  • Referenced in 5373 articles [sw00545]
  • The result of over 30 years of cutting...
  • Mathematica

  • Referenced in 6355 articles [sw00554]
  • Almost any workflow involves computing results, and that...
  • Matlab

  • Referenced in 13544 articles [sw00558]
  • MATLAB® is a high-level language and interactive...
  • mclust

  • Referenced in 309 articles [sw00563]
  • R package mclust: Normal Mixture Modeling for Model...
  • NITSOL

  • Referenced in 99 articles [sw00623]
  • We introduce a well-developed Newton iterative (truncated...