Estimation of protein function using template-based alignment of enzyme active sites

Abstract

BackgroundThe accumulation of protein structural data occurs more rapidly than it can be characterized by traditional laboratory means. This has motivated widespread efforts to predict enzyme function computationally. The most useful/accurate strategies employed to date are based on the detection of motifs in novel structures that correspond to a specific function. Functional residues are critical components of predictively useful motifs. We have implemented a novel method, to complement current approaches, which detects motifs solely on the basis of distance restraints between catalytic residues.ResultsProMOL is a plugin for the PyMOL molecular graphics environment that can be used to create active site motifs for enzymes. A library of 181 active site motifs has been created with ProMOL, based on definitions published in the Catalytic Site Atlas (CSA). Searches with ProMOL produce better than 50% useful Enzyme Commission (EC) class suggestions for level 1 searches in EC classes 1, 4 and 5, and produce some useful results for other classes. 261 additional motifs automatically translated from Jonathan Barker’s JESS motif set [Bioinformatics 19:1644–1649, 2003] and a set of NMR motifs is under development. Alignments are evaluated by visual superposition, Levenshtein distance and root-mean-square deviation (RMSD) and are reasonably consistent with related search methods.ConclusionThe ProMOL plugin for PyMOL provides ready access to template-based local alignments. Recent improvements to ProMOL, including the expanded motif library, RMSD calculations and output selection formatting, have greatly increased the program’s usability and speed, and have improved the way that the results are presented.

Automated protein motif generation in the structure-based protein function prediction tool ProMOL

“…The two motif sets based on the same set of native structures but generated with different methods exhibited similar hit rates against homologous structures (70.25% and 71.59% for the P Set and the AP Set, respectively) and against unrelated structures (3.79% and 4.32% for the P Set and the AP Set, respectively). The true positive rate for both sets of motifs is different from the 62.63% value reported previously for the full P set of 181 motifs [1]. The differences result from the following changes in the matching algorithm: (1) the use of a more restricted definition of a true positive to be one with a Levenshtein distances ≤ 1, rather than accepting Levenshtein distances of 2 and 3 as in the prior results, (2) the use in the present instance of a smaller set of the most reliable 112 motifs for which positive results with Levenshtein distances ≤ 1 could be achieved, and (3) restricting the definition of a homolog to be a molecule agreeing in both EC number and Pfam family, rather than the EC number alone.…”

“…As part of the Structural Biology Extensible Visualization Scripting Language (SBEVSL) initiative, ProMOL [1] is a plugin for the molecular graphics system PyMOL [2]. ProMOL is written in Python 2.7 and utilizes a template-based function prediction method in an attempt to classify proteins of known structure but unknown function [1].…”

“…ProMOL is written in Python 2.7 and utilizes a template-based function prediction method in an attempt to classify proteins of known structure but unknown function [1]. The method involves compilation of an extensive library of structural motif templates based on well characterized enzyme structures with active sites that are defined in the Catalytic Site Atlas (CSA) [3].…”

Annotation of proteins of unknown function: initial enzyme results

“…Structures were selected based on the availability of literature definitions of active sites in the Catalytic Site Atlas [15]. Two sets of motif templates make up the current library: roughly half were generated manually with the Motif Maker tool in ProMOL [11], which can be used to create motif templates based on residue name, residue number and chain identifier for the residues in the active site of an enzyme structure found in the PDB. The remaining motif templates were generated automatically with a script that tests the motif template against itself, homologs and random PDB structures to provide sensitivity and specificity data for each new motif template [manuscript in preparation].…”

“…We have developed the ProMOL [11] plugin for PyMOL [12], a tool used to explore the catalytic site structural homologies between proteins of known function and those for which functions are not yet known. ProMOL uses template-based alignment of these structures with a current library of 388 active site motifs as reported in the Catalytic Site Atlas [13].…”