• HHblits

  • Referenced in 2 articles [sw16890]
  • alignment. Sequence-based protein function and structure prediction depends crucially on sequence-search sensitivity...
  • PSICOV

  • Referenced in 5 articles [sw17010]
  • maintaining the native fold of a protein, remains an open problem in the field ... structure and function prediction to name but two benefits. Sequence-based contact predictions are usually ... made by identifying correlated mutations within multiple sequence alignments (MSAs), most commonly through the information ... mutual information between pairs of sites in proteins. These predictions are often inaccurate because...
  • EpiLoc

  • Referenced in 3 articles [sw22452]
  • based system for predicting protein subcellular location. MOTIVATION: Predicting the subcellular location of proteins ... function. Several previous experiments in utilizing text for protein subcellular location prediction varied in methods ... integration of text features into a sequence-based classifier to improve location prediction performance. RESULTS...
  • LIBRUS

  • Referenced in 1 article [sw25078]
  • homology information for sequence-based ligand-binding residue prediction. MOTIVATION: Identifying residues that interact with ... protein function and as an aid to designing small molecules that target the protein ... shown that sequence features are very informative for this type of prediction, while structure features ... structure is available. We develop a sequence-based method, called LIBRUS, that combines homology-based...
  • L1pred

  • Referenced in 1 article [sw25075]
  • L1pred: A Sequence-Based Prediction Tool for Catalytic Residues in Enzymes with the L1-logreg ... Classifier. To understand enzyme functions, identifying the catalytic residues is a usual first step. Moreover ... predict catalytic residues. Here, we developed a new algorithm, L1pred, for catalytic residue prediction ... logreg classifier to integrate eight sequence-based scoring functions. We tested L1pred and compared...
  • PreDisorder

  • Referenced in 2 articles [sw16902]
  • sequence-based prediction of protein disordered regions. Background: Disordered regions are segments of the protein ... have a close relationship with protein expression and functionality. As such, protein disorder prediction...
  • R3P-Loc

  • Referenced in 2 articles [sw22444]
  • Locating proteins within cellular contexts is of paramount significance in elucidating their biological functions. Computational ... methods based on knowledge databases (such as gene ontology annotation (GOA) database) are known ... efficient than sequence-based methods. However, the predominant scenarios of knowledge-based methods are that ... redundant or irrelevant information, causing the prediction systems suffer from overfitting. To address these problems...
  • R

  • Referenced in 7624 articles [sw00771]
  • R is a language and environment for statistical...
  • MIRA

  • Referenced in 1 article [sw02392]
  • MIRA is a multi-pass DNA sequence data...
  • STAR

  • Referenced in 11 articles [sw02515]
  • STAR: ultrafast universal RNA-seq aligner. Motivation: Accurate...
  • Bioconductor

  • Referenced in 281 articles [sw04205]
  • Bioconductor provides tools for the analysis and comprehension...
  • GlobPlot

  • Referenced in 8 articles [sw06213]
  • GlobPlot: exploring protein sequences for globularity and disorder...
  • Biopython

  • Referenced in 16 articles [sw07357]
  • Biopython: freely available Python tools for computational molecular...
  • MAFFT

  • Referenced in 31 articles [sw08304]
  • MAFFT: Multiple alignment program for amino acid or...
  • Soap

  • Referenced in 34 articles [sw08915]
  • SOAP: short oligonucleotide alignment program. We have developed...
  • EMan

  • Referenced in 8 articles [sw09056]
  • EMAN: Semiautomated Software for High-Resolution Single-Particle...
  • PyMOL

  • Referenced in 38 articles [sw09662]
  • PyMOL is a powerful and comprehensive molecular visualization...
  • HMMER

  • Referenced in 17 articles [sw10514]
  • HMMER web server: interactive sequence similarity searching. HMMER...
  • bioperl

  • Referenced in 20 articles [sw10579]
  • The bioperl toolkit: Perl modules for the life...