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Software

• Concavity
  Predict ligand-binding sites from structure. Download source code or use online.
• SPICi
  A fast, greedy approach for finding dense subnetworks within weighted graphs. Download source code or use online.
• Princeton LC-MS/MS Proteomics Data Viewer
  Download source code.
• Finding maximal exact matches in large sequence data sets using sparse suffix arrays.
  Download source code for use within the MUMmer 3 system.
• Predicting C2H2 DNA binding sites. Evaluate a C2H2 zinc finger transcription factor for binding to a DNA sequence.
  Download or use online.
• NetGrep.
  Find matches to user-supplied pathway, domain-domain, or other network schema queries. Download or use online.
• Side-chain positioning.
  Download software to generate LP/IPs for solving the side-chain positioning problem.
• MotifSearch.
  Search for DNA binding sites, using one of several methods. (Webform and software download.)
• Inferring ancestral amino acid content.
  Download software to infer ancestral amino acid usage for a set of protein sequences.
• bZIP Partner Prediction Program Webpage.
  Score potential bZIP coiled-coil protein interactions.
• Viral Membrane-Fusion Proteins Program Webpage.
  Detect “hairpin” coiled-coil-like structures in viral membrane fusion proteins.
• Histidine Kinase Program Webpage.
  Analyze putative coiled-coil-like domains in histidine kinases.