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- W1795671280 abstract "ProMOL, a plugin for the molecular graphics system PyMOL, was designed to characterize protein structures that lack functional annotation; there are currently over 3700 PDB entries with “unknown” functions. ProMOL was created, and is constantly being revised, by members of the RIT and Dowling College communities. ProMOL compares query protein structures against a library of active site motif templates, calculates Levenshtein distances and RMSD values, and generates a 3D visual alignment between query and motif template. The best results are then submitted to BLAST, Dali and Pfam for analysis. If the data produced by these four bioinformatics programs lead to a preliminary conclusion concerning the function of an uncharacterized structure, the behavior of the protein is then tested in vitro. To date, we have found >90 significant “hits” for uncharacterized protein structures using ProMOL’s motif library. These structures are currently being analyzed via BLAST, Dali, and Pfam. To date the most promising alignments include PDB entries 2HRZ (proposed as isomerase/NAD-dependent epimerase), 4EZI (confirmed as an esterase; see the related poster by Kaitlin Hart), 3L1W (proposed as a nuclease), and 2O14 (proposed as a hydrolase/aminopeptidase). This work has been supported in part by National Institute of General Medical Sciences 2R15GM078077-02, 3R15GM078077-02S1. Grant Funding Source: Supported by NIGMS 2R15GM078077-02, 3R15GM078077-02S1" @default.
- W1795671280 created "2016-06-24" @default.
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- W1795671280 date "2014-04-01" @default.
- W1795671280 modified "2023-10-16" @default.
- W1795671280 title "Protein function prediction using ProMOL and PyMOL (777.3)" @default.
- W1795671280 doi "https://doi.org/10.1096/fasebj.28.1_supplement.777.3" @default.
- W1795671280 hasPublicationYear "2014" @default.
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