• Q-SiteFinder

  • Referenced in 4 articles [sw35551]
  • appear to show relatively low dependence on protein volume and are similar in volume ... space required for docking and de novo drug design or site comparison. The method ... applied in structural genomics studies where protein binding sites remain uncharacterized since the 86% success...
  • Gene Designer

  • Referenced in 4 articles [sw17359]
  • codon optimized for protein expression in any host organism. Gene Designer also includes features such ... Designer is an expandable Synthetic Biology workbench suitable for molecular biologists interested in the de ... novo creation of genetic constructs...
  • LUDI

  • Referenced in 1 article [sw24443]
  • LUDI: a new method for the de novo design of enzyme inhibitors. A new computer ... which positions small molecules into clefts of protein structures (e.g. an active site...
  • csaw

  • Referenced in 3 articles [sw17944]
  • scientific application is to identify changes in protein binding between different treatment conditions ... package provides a framework for the de novo detection of differentially bound genomic regions ... csaw package can handle arbitrarily complex experimental designs involving biological replicates. It can be applied...
  • AptRank

  • Referenced in 0 articles [sw34196]
  • protein datasets, and compare with four previous methods: GeneMANIA, TMC, ProteinRank and clusDCA. We design ... different validation strategies: missing function prediction, de novo function prediction, guided function prediction and newly...
  • Nebula

  • Referenced in 1 article [sw16944]
  • transcription factors and other DNA-associated proteins. We present a web service, Nebula, which allows ... ChIP-seq data. Results: Nebula was designed for both bioinformaticians and biologists. It is based ... module for immunoprecipitation quality control, (ii) de novo motif discovery with ChIPMunk, (iii) calculation...
  • MetaPSICOV

  • Referenced in 1 article [sw17012]
  • usefulness of contact prediction, we have designed a new meta-predictor (MetaPSICOV) which combines three ... original PSICOV benchmark set of 150 protein families, MetaPSICOV achieves a mean precision ... around 40% better than CCMpred. In de novo protein structure prediction using FRAGFOLD, MetaPSICOV...
  • STAR

  • Referenced in 12 articles [sw02515]
  • STAR: ultrafast universal RNA-seq aligner. Motivation: Accurate...
  • CPLEX

  • Referenced in 2583 articles [sw04082]
  • IBM® ILOG® CPLEX® offers C, C++, Java, .NET...
  • TINKER

  • Referenced in 10 articles [sw04095]
  • TINKER - Software Tools for Molecular Design. The TINKER...
  • alphaBB

  • Referenced in 49 articles [sw06249]
  • alphaBB: A Global Optimization Method for General Constrained...
  • DYANA

  • Referenced in 11 articles [sw08628]
  • Sampling of conformation space in torsion angle dynamics...
  • SOPRA

  • Referenced in 7 articles [sw12607]
  • SOPRA: scaffolding algorithm for paired reads via statistical...
  • Wenxiang

  • Referenced in 15 articles [sw16645]
  • Wenxiang: a web-server for drawing wenxiang diagrams...
  • Orione

  • Referenced in 1 article [sw16940]
  • Orione, a web-based framework for NGS analysis...
  • SSAKE

  • Referenced in 7 articles [sw16990]
  • SSAKE is a de novo assembler for short...
  • TopHat

  • Referenced in 23 articles [sw17157]
  • TopHat2: accurate alignment of transcriptomes in the presence...
  • BLAST

  • Referenced in 245 articles [sw17334]
  • Basic Local Alignment Search Tool. BLAST finds regions...