Fri, Feb 27, 2004: PROSPECT PRO Perl API Available to Academic Community
BSI is delighted to announce that Perl API scripts are now available to PROSPECT PRO user community. Cavanagh and Hart, from the Bioinformatics Department, Genentech Inc., have released to the public Bio::Prospect::, an object-oriented Perl Application Programming Interface (API) for the protein threading application PROSPECT (see "A Perl API for Prospect").
PROSPECT PRO is an award-winning and top ranked automated protein structure prediction software from Bioinformatics Solutions (BSI) see "PROSPECT PRO"). Protein structure prediction is difficult, but key to the success of worldwide proteomics efforts," said President, Ming Li, We are very pleased these modules for PROSPECT have been made public and they will definitely benefit our users engaged in high-throughput discovery and identification of potentially novel protein candidates.?
According to Hart/Cavanaugh, Although various incarnations of fold recognition software exist, most are either not distributed or are inaccessible to commercial users. PROSPECT has been a consistent performer at the CASP - Critical Assessments of Structure Prediction (Moult, et al., 2003) and is available to both academic and commercial users. Whereas most users execute PROSPECT on one or a few sequences of interest, we use PROSPECT and other methods as a discovery tool for identifying potentially novel candidates of therapeutically relevant families from a very large number of sequences.? The Bio::PROSPECT:: modules serves three main objectives: running PROSPECT locally or remotely, parsing the resulting alignments and preparing the alignments for viewing.
Li said that some experts go as far as saying "any breakthrough in the high-throughput protein folding would cause revolutionary change in ways people do research and in the pharmaceutical industry? At present, the low-throughput method used in the wet labs can take one scientist as long as six months to determine the structure of one protein, deploying X-ray crystallography or NMR (nuclear magnetic resonance) technologies. Automated computer prediction like PROSPECT PRO is urgently needed," Li said, noting that hundreds of top research groups in the world have been working on the challenge for over a decade. We are pleased PROSPECT acts as a tool in helping scientists to move forward in resolving the protein folding challenge, which has benefits for all mankind.?
PROSPECT PRO 3.0 offers several new features for the protein structure enthusiast. The program now has a PyMOL-based alignment viewer, PROView, which allows users to visualize and manipulate structure and sequence alignment data, an up-to-date PDB library, an automated batch command line, and much more. See "PROSPECT PRO") for more information.
Whether you are using PROSPECT PRO in a high-throughput environment or need a local and remote execution via a consistent interface, the Bio::Prospect:: modules are now available to academic users at "Modules").
