Bioinformatics Tools


Graphics & Modeling

Sequence Evaluation and Comparison

  • ExPASy Bioinformatics: calculate a theoretical MW or pI, perform a sequence alignment, predict cleavage sites, and much more
  • EMBL-EBI Services: European Bioinformatics Institute, capable of DNA, protein multiple sequence alignments
  • NCBI RefSeq: A comprehensive, integrated, non-redundant, well-annotated set of reference sequences including genomic, transcript, and protein
  • MATTFash: multiple sequence alignments
  • SEEKQUENCHER: pulls sequences from databanks
  • EMBOSS: suite of bioinformatic tools
  • ESPript 3: pretty sequence alignments for publications, lots of colors
  • SMART: Simple Modular Architecture Research Tool
  • Disulfide by Design: application for the rational design of disulfide bonds in proteins. For a given protein structural model, all residue pairs are rapidly assessed for proximity and geometry consistent with disulfide formation – assuming the residues were mutated to cysteines
  • HMMER: biosequence analysis using profile hidden Markov models

Structural Evaluation and Comparison

  • List of Surface and Volume Programs
  • Protein Data Bank: data base for 3-D structures of proteins
  • Phobius: transmembrane topology and signal peptide predictor, FASTA input
  • Naccess: calculates the accessible area of a molecule from a PDB (Protein Data Bank) format file. It can calculate the atomic and residue accessibilities for both proteins and nucleic acids.
  • Protein Interaction Server : surface calculations
  • Monster:  non-covalant interactions in proteins
  • VADAR: Volume, Area, Dihedral Angle Reporter
  • PARVATI: anisotropic displacement parameters statistics
  • CASTp: identification and measurements of surface accessible pockets as well as interior inaccessible cavities
  • BBCU binding site prediction and docking 
  • Database of Macromolecular Movements with Associated Tools for Flexibility and Geometric Analysis
  • FATCAT: structure alignment is formulated as the AFPs (aligned fragment pairs) chaining process allowing at most t twists, and the flexible structure alignment is transformed into a rigid structure alignment when t is forced to be 0.
  • SCOPe: Structural Classification of Proteins
  • SiteEngine: functional site search engine; recognizes regions on the surface of one protein that resemble a specific binding site of another
  • POSA (Partial Order Structure Alignment): A flexible multiple structure alignment approach