Announcement: Version 1.0 of PROSPECT
The Computational Protein Structure Group of Oak Ridge National
Laboratory would like to announce the release of PROSPECT Version 1.0.
PROSPECT (PROtein Structure Prediction and Evaluation Computer Toolkit)
is a threading-based protein structure prediction system. PROSPECT is
particularly designed to recognize structural folds whose sequence have
no significant homology to the target sequence. For detailed information
about PROSPECT, please check
PROSPECT has a number of unique features --
* The system guarantees to find the globally-optimal alignments
for a given energy function with any combination of the following
terms: (1) mutation energy (including position-specific score
matrix derived from multiple-sequence alignments), (2) singleton
energy (including matching scores to the predicted secondary
structures), (3) pairwise contact potential (distance dependent or
independent), and (4) alignment gap penalties.
* The system allows users to easily incorporate biological knowledge
and constraints into the threading process to find optimal
alignments under the specified constraints, which may include:
- specified disulfide bonds
- specified active sites
- specified secondary structures
- specified NOE restraints in NMR
- specified gaps with no gap penalties
* The system provides a prediction confidence assessment for each
prediction based on a neural-net method and an evaluation of
compactness of the predicted structure.
* A Web-based interface is available to browse the threading
alignments and 3D structures.
PROSPECT is free of charge to academic users. Please contact the authors
(Ying Xu at xyn at ornl.gov or Dong Xu at xud at ornl.gov) about the download
information. For commercial users, please contact the authors for