title: DINAMO: interactive protein alignment and model building.
abstract: BACKGROUND
  To facilitate the process of structure prediction by both comparative modeling and fold recognition, we describe DINAMO, an interactive protein alignment building and model evaluation tool that dynamically couples a multiple sequence alignment editor to a molecular graphics display. DINAMO allows the user to optimize the alignment and model to satisfy the known heuristics of protein structure by means of a set of analysis tools. The analysis tools return information to both the alignment editor and graphics model in the form of visual cues (color, shape), allowing for rapid evaluation. Several analysis tools may be employed, including residue conservation, residue properties (charge, hydrophobicity, volume), residue environmental preference, and secondary structure propensity.
  
  
  RESULTS
  We demonstrate DINAMO by building a model for submission in the 3rd annual Critical Assessment of Techniques for Protein Structure Prediction (CASP3) contest.
  
  
  BACKGROUND
  DINAMO is freely available as a local application or Web-based Java applet at http://tito.ucsc.edu/dinamo
mesh_terms: D000595:Amino Acid Sequence; D003196:Computer Graphics; D003198:Computer Simulation; D008958:Models, Molecular; D008969:Molecular Sequence Data; D011506:Proteins / Q000737:chemistry*; D016415:Sequence Alignment / Q000379:methods*; D012984:Software