title: An efficient visualization tool for the analysis of protein mutation matrices.
abstract: BACKGROUND
  It is useful to develop a tool that would effectively describe protein mutation matrices specifically geared towards the identification of mutations that produce either wanted or unwanted effects, such as an increase or decrease in affinity, or a predisposition towards misfolding. Here, we describe a tool where such mutations are efficiently identified, categorized and visualized. To categorize the mutations, amino acids in a mutation matrix are arranged according to one of three sets of physicochemical characteristics, namely hydrophilicity, size and polarizability, and charge and polarity. The magnitude and frequencies of mutations for an alignment are subsequently described using color information and scaling factors.
  
  
  RESULTS
  To illustrate the capabilities of our approach, the technique is used to visualize and to compare mutation patterns in evolving sequences with diametrically opposite characteristics. Results show the emergence of distinct patterns not immediately discernible from the raw matrices.
  
  
  CONCLUSIONS
  Our technique enables effective categorization and visualization of mutations by using specifically-arranged mutation matrices. This tool has a number of possible applications in protein engineering, notably in simplifying the identification of mutations and/or mutation trends that are associated with specific engineered protein characteristics and behavior.
authors.affiliation: Computational Science Research Center, University of the Philippines, Diliman 1101, Philippines. maria_pamela.david@up.edu.ph
authors.forename: Maria Pamela C
authors.initials: MP
authors.lastname: David
authors.forename: Carlo M
authors.initials: CM
authors.lastname: Lapid
authors.forename: Vincent Ricardo M
authors.initials: VR
authors.lastname: Daria
mesh_terms: D000596:Amino Acids / Q000737:chemistry* / Q000145:classification*; D000682:Amyloid / Q000276:immunology; D000818:Animals; D000906:Antibodies / Q000032:analysis / Q000235:genetics; D001296:Audiovisual Aids; D003196:Computer Graphics; D030562:Databases, Protein; D025802:Electric Capacitance; D006388:Hemagglutinins / Q000032:analysis / Q000235:genetics; D006801:Humans; D057927:Hydrophobic and Hydrophilic Interactions; D007453:Iodide Peroxidase / Q000276:immunology; D016296:Mutagenesis; D009154:Mutation; D017510:Protein Folding; D011506:Proteins / Q000737:chemistry / Q000235:genetics*; D018035:Receptors, Odorant / Q000032:analysis / Q000235:genetics; D012107:Research Design; D016415:Sequence Alignment; D020539:Sequence Analysis, Protein; D055672:Static Electricity; D014584:User-Computer Interface
chemical_list: D000596:Amino Acids; D000682:Amyloid; D000906:Antibodies; D006388:Hemagglutinins; D011506:Proteins; D018035:Receptors, Odorant; D007453:Iodide Peroxidase