# PROSPECT: A Computer System for Globally-Optimal Threading

## Abstract

This paper presents a new computer system, PROSPECT, for protein threading. PROSPECT employs an energy function that consists of three additive terms: (1) a singleton fitness term, (2) a distance-dependent pairwise-interaction preference term, and (3) alignment gap penalty; and currently uses FSSP as its threading template database. PROSPECT uses a divide-and-conquer algorithm to find an alignment between a query protein sequence and a protein fold template, which is guaranteed to be globally optimal for its energy function. The threading algorithm presented here significantly improves the computational efficiency of our previously-published algorithm, which makes PROSPECT a practical tool even for large protein threading problems. Mathematically, PROSPECT finds a globally-optimal threading between a query sequence of n residues and a fold template of m residues and M core secondary structures in O(nm + MnN{sup 1.5C{minus}1}) time and O(nm + nN{sup C{minus}1}) space, where C, the topological complexity of the template fold as we term, is a value which characterizes the overall structure of the considered pairwise interactions in the fold; and N represents the maximum number of possible alignments between an individual core of the fold and the query sequence when its neighboring cores are already aligned. PROSPECT allows a user tomore »

- Authors:

- Publication Date:

- Research Org.:
- Oak Ridge National Lab., TN (US)

- Sponsoring Org.:
- USDOE Office of Energy Research (ER) (US)

- OSTI Identifier:
- 3929

- Report Number(s):
- ORNL/CP-101519; KP 11 01 01 0

KP 11 01 01 0; TRN: AH200113%%182

- DOE Contract Number:
- AC05-96OR22464

- Resource Type:
- Conference

- Resource Relation:
- Conference: 7th International Conference on Intelligent Systems for Molecular Biology (ISMB '99), Heidelberg (DE), 08/06/1999; Other Information: PBD: 6 Aug 1999

- Country of Publication:
- United States

- Language:
- English

- Subject:
- 59 BASIC BIOLOGICAL SCIENCES; 60 APPLIED LIFE SCIENCES; 99 GENERAL AND MISCELLANEOUS//MATHEMATICS, COMPUTING, AND INFORMATION SCIENCE; ADDITIVES; ALGORITHMS; ALIGNMENT; COMPUTERS; DISULFIDES; EFFICIENCY; MOLECULAR BIOLOGY; PROTEINS; RESIDUES

### Citation Formats

```
Xu, D., and Xu, Y.
```*PROSPECT: A Computer System for Globally-Optimal Threading*. United States: N. p., 1999.
Web.

```
Xu, D., & Xu, Y.
```*PROSPECT: A Computer System for Globally-Optimal Threading*. United States.

```
Xu, D., and Xu, Y. Fri .
"PROSPECT: A Computer System for Globally-Optimal Threading". United States. https://www.osti.gov/servlets/purl/3929.
```

```
@article{osti_3929,
```

title = {PROSPECT: A Computer System for Globally-Optimal Threading},

author = {Xu, D. and Xu, Y.},

abstractNote = {This paper presents a new computer system, PROSPECT, for protein threading. PROSPECT employs an energy function that consists of three additive terms: (1) a singleton fitness term, (2) a distance-dependent pairwise-interaction preference term, and (3) alignment gap penalty; and currently uses FSSP as its threading template database. PROSPECT uses a divide-and-conquer algorithm to find an alignment between a query protein sequence and a protein fold template, which is guaranteed to be globally optimal for its energy function. The threading algorithm presented here significantly improves the computational efficiency of our previously-published algorithm, which makes PROSPECT a practical tool even for large protein threading problems. Mathematically, PROSPECT finds a globally-optimal threading between a query sequence of n residues and a fold template of m residues and M core secondary structures in O(nm + MnN{sup 1.5C{minus}1}) time and O(nm + nN{sup C{minus}1}) space, where C, the topological complexity of the template fold as we term, is a value which characterizes the overall structure of the considered pairwise interactions in the fold; and N represents the maximum number of possible alignments between an individual core of the fold and the query sequence when its neighboring cores are already aligned. PROSPECT allows a user to incorporate known biological constraints about the query sequence during the threading process. For given constraints, the system finds a globally-optimal threading which satisfies the constraints. Currently PROSPECT can deal with constraints which reflect geometrical relationships among residues of disulfide bonds, active sites, or determined by the NOE constraints of (low-resolution) NMR spectral data.},

doi = {},

journal = {},

number = ,

volume = ,

place = {United States},

year = {1999},

month = {8}

}