• validann

  • Referenced in 0 articles [sw35498]
  • outputs and modelled functions of artificial neural networks (ANNs) in terms of predictive, replicative ... structural validity. Also provides a method for fitting feed-forward ANNs with a single hidden...
  • BetaSCPWeb

  • Referenced in 1 article [sw20703]
  • amino acid sequence and backbone structure. Side-chain prediction (SCP) is an NP-hard energy ... Voronoi diagram of spherical atoms. Its outputs are visual, textual and PDB file format...
  • G4Hunter

  • Referenced in 2 articles [sw27624]
  • negatives) and that other sequences predicted to form G4 structures do not (false positives). Here ... gives a quadruplex propensity score as output. To validate this model, we tested...
  • ANNOTATOR

  • Referenced in 1 article [sw16835]
  • algorithms behind these workflows exhibit complex data structures; they need the ability to spawn subtasks ... individual function prediction algorithms having to transform between differing input and output formats has become...
  • PIntron

  • Referenced in 1 article [sw17148]
  • designing computational methods for predicting the gene structure into exons and introns from a cluster ... sequences obtained from paths of a graph structure, called embedding graph, whose vertices ... size of the output. PIntron, the software tool implementing our methodology, is available ... manageable by other gene structure prediction tools. At the same time, PIntron exhibits high accuracy...
  • LPJ-GUESS

  • Referenced in 0 articles [sw19635]
  • atmospheric carbon dioxide concentrations, it can predict structural, compositional and functional properties of the native ... major climate zones of the Earth. Outputs include vegetation composition and cover in terms...
  • ARAGORN

  • Referenced in 2 articles [sw16999]
  • program employs heuristic algorithms to predict tRNA secondary structure, based on homology with recognized tRNA ... green’ algae lineage are detected. The output of the program reports the proposed tRNA secondary...
  • PONDR-FIT

  • Referenced in 2 articles [sw16904]
  • increasingly recognized in proteomics research. While lacking structure, many regions of disorder have been associated ... intrinsically disordered proteins and regions; nevertheless, the prediction of intrinsic disorder from amino acid sequence ... neural network (ANN) prediction method, which was developed by combining the outputs of several individual...
  • PRALINE

  • Referenced in 2 articles [sw16248]
  • choice of seven different secondary structure prediction programs that can be used individually ... combination as a consensus for integrating structural information into the alignment process. The program ... high confidence alignments. The web-based output is designed to facilitate the comprehensive visualization...
  • DFLpred

  • Referenced in 0 articles [sw25081]
  • linkers/spacers in multi-domain proteins or between structured constituents in domains. They are different from ... directly predict DFLs and they can be found only indirectly by filtering predicted flexible residues ... with predictions of disorder. RESULTS: We conceptualized, developed and empirically assessed a first ... propensities to form certain secondary structures, disordered regions and structured regions, which are processed...
  • ProtPOS

  • Referenced in 0 articles [sw18972]
  • easy-to-use python package that can predict low-energy protein orientations on a surface ... system at hand and provide structural output readily available for further simulation studies. Availability...
  • BEESCOUT

  • Referenced in 2 articles [sw41037]
  • empirical data are available to validate model output. The simulated detection probabilities depend largely ... source locations. Nevertheless, we show that landscape structure and connectivity of food sources can have ... enabling future users to explore how landscape structure and food availability affect the foraging decisions ... bees and, in consequence, to predict colony development and survival...
  • ConfBuster

  • Referenced in 1 article [sw27289]
  • tools that are available to investigate and predict macrocycles 3D conformations are limited in their ... lower energy conformation coordinates is returned as output, as well as PyMOL script and graphics ... tenths of Å of the experimental structures in minutes. To our knowledge, this...
  • oddsratio

  • Referenced in 0 articles [sw17064]
  • Provides structured output (data frame) of all predictors and their corresponding odds ratios for further ... GLMs) which just returns a plain numeric output. For GAM(M)s, odds ratio calculation ... since it takes care of the multiple ’predict()’ calls of the chosen predictor while holding...
  • MetaPSICOV

  • Referenced in 1 article [sw17012]
  • predictor, where the second stage filters the output of the first stage. This two-stage ... additionally evaluated on its ability to accurately predict the long range network of hydrogen bonds ... mean precision of 0.54 for top-L predicted long range contacts—around 60% higher than ... better than CCMpred. In de novo protein structure prediction using FRAGFOLD, MetaPSICOV is able...
  • LTRsift

  • Referenced in 0 articles [sw37851]
  • semi-automatic postprocessing of de novo predicted LTR retrotransposon annotations. Its user-friendly interface offers ... candidate groups, their members and their internal structure in a hierarchical fashion. To ease manual ... postprocessing and refining the output of software for predicting LTR retrotransposons up to the stage...
  • psRNATarget

  • Referenced in 1 article [sw34140]
  • RNAs. Although a number of miRNA target prediction algorithms and programs have been developed, most ... unpaired energy (UPE) required to ‘open’ secondary structure around small RNA’s target site ... preloaded small RNAs and transcript sequences; and outputs a comprehensive list of small RNA/target pairs...
  • CoCoA

  • Referenced in 659 articles [sw00143]
  • CoCoA is a system for Computations in Commutative...
  • C-XSC

  • Referenced in 110 articles [sw00181]
  • C-XSC. A programming environment for verified scientific...
  • KNITRO

  • Referenced in 197 articles [sw00490]
  • KNITRO is a solver for nonlinear optimization. It...