title: Automated protein motif generation in the structure-based protein function prediction tool ProMOL.
abstract: ProMOL, a plugin for the PyMOL molecular graphics system, is a structure-based protein function prediction tool. ProMOL includes a set of routines for building motif templates that are used for screening query structures for enzyme active sites. Previously, each motif template was generated manually and required supervision in the optimization of parameters for sensitivity and selectivity. We developed an algorithm and workflow for the automation of motif building and testing routines in ProMOL. The algorithm uses a set of empirically derived parameters for optimization and requires little user intervention. The automated motif generation algorithm was first tested in a performance comparison with a set of manually generated motifs based on identical active sites from the same 112 PDB entries. The two sets of motifs were equally effective in identifying alignments with homologs and in rejecting alignments with unrelated structures. A second set of 296 active site motifs were generated automatically, based on Catalytic Site Atlas entries with literature citations, as an expansion of the library of existing manually generated motif templates. The new motif templates exhibited comparable performance to the existing ones in terms of hit rates against native structures, homologs with the same EC and Pfam designations, and randomly selected unrelated structures with a different EC designation at the first EC digit, as well as in terms of RMSD values obtained from local structural alignments of motifs and query structures. This research is supported by NIH grant GM078077.
authors.affiliation: Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester, NY, USA.
authors.forename: Mikhail
authors.initials: M
authors.lastname: Osipovitch
authors.affiliation: School of Chemistry and Materials Science, Rochester Institute of Technology, Rochester, NY, USA.
authors.forename: Mitchell
authors.initials: M
authors.lastname: Lambrecht
authors.affiliation: Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester, NY, USA.
authors.forename: Cameron
authors.initials: C
authors.lastname: Baker
authors.affiliation: Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester, NY, USA.
authors.forename: Shariq
authors.initials: S
authors.lastname: Madha
authors.affiliation: School of Chemistry and Materials Science, Rochester Institute of Technology, Rochester, NY, USA.
authors.forename: Jeffrey L
authors.initials: JL
authors.lastname: Mills
authors.affiliation: School of Chemistry and Materials Science, Rochester Institute of Technology, Rochester, NY, USA. paul.craig@rit.edu.
authors.forename: Paul A
authors.identifier: http://orcid.org/0000-0002-2085-7816
authors.initials: PA
authors.lastname: Craig
authors.affiliation: School of Chemistry and Materials Science, Rochester Institute of Technology, Rochester, NY, USA.
authors.forename: Herbert J
authors.initials: HJ
authors.lastname: Bernstein
mesh_terms: D000465:Algorithms; D020816:Amino Acid Motifs; D000595:Amino Acid Sequence; D020134:Catalytic Domain; D019295:Computational Biology / Q000379:methods; D030562:Databases, Protein; D008958:Models, Molecular; D008969:Molecular Sequence Data; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry*; D016415:Sequence Alignment; D012984:Software; D013329:Structure-Activity Relationship
chemical_list: D011506:Proteins
keywords: Catalytic site motif; Enzyme; Molecular visualization; ProMOL; PyMOL; Structural bioinformatics; Template-based alignment