title: MODexplorer: an integrated tool for exploring protein sequence, structure and function relationships.
abstract: CONCLUSIONS
  MODexplorer is an integrated tool aimed at exploring the sequence, structural and functional diversity in protein families useful in homology modeling and in analyzing protein families in general. It takes as input either the sequence or the structure of a protein and provides alignments with its homologs along with a variety of structural and functional annotations through an interactive interface. The annotations include sequence conservation, similarity scores, ligand-, DNA- and RNA-binding sites, secondary structure, disorder, crystallographic structure resolution and quality scores of models implied by the alignments to the homologs of known structure. MODexplorer can be used to analyze sequence and structural conservation among the structures of similar proteins, to find structures of homologs solved in different conformational state or with different ligands and to transfer functional annotations. Furthermore, if the structure of the query is not known, MODexplorer can be used to select the modeling templates taking all this information into account and to build a comparative model.
  
  
  METHODS
  Freely available on the web at http://modorama.biocomputing.it/modexplorer. Website implemented in HTML and JavaScript with all major browsers supported.
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
authors: Department of Physics, Sapienza University, 00185 Rome, Italy.
authors: Jan
authors: J
authors: Kosinski
authors: Alessandro
authors: A
authors: Barbato
authors: Anna
authors: A
authors: Tramontano
mesh_terms: D000595:Amino Acid Sequence; D001665:Binding Sites; D017124:Conserved Sequence; D020407:Internet; D008024:Ligands; D008958:Models, Molecular; D058977:Molecular Sequence Annotation; D017433:Protein Structure, Secondary; D011506:Proteins / Q000737:chemistry* / Q000145:classification* / Q000502:physiology; D016415:Sequence Alignment; D020539:Sequence Analysis, Protein; D012984:Software; D040681:Structural Homology, Protein; D013329:Structure-Activity Relationship
chemical_list: D008024:Ligands; D011506:Proteins
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