New contact measures for the protein docking problem

Conference · Mon Dec 01 00:00:00 EST 1997

OSTI ID:549012

Lenhof, H P ^[1]

---

1. Max-Planck-Institut fuer Informatik, Saabruecken (Germany)

We have developed and implemented a parallel distributed algorithm for the rigid-body protein docking problem. The algorithm is based on a new fitness function for evaluating the surface matching of a given conformation. The fitness function is defined as the weighted sum of two contact measures, the geometric contact measure and the chemical contact measure. The geometric contact measure measures the {open_quotes}size{close_quotes} of the contact area of two molecules. It is a potential function that counts the {open_quotes}van der Waals contacts{close_quotes} between the atoms of the two molecules (the algorithm does not compute the Lennard-Jones potential). The chemical contact measure is also based on the {open_quotes}van der Waals contacts{close_quotes} principle: We consider all atoms pairs that have a {open_quotes}van der Waals{close_quotes} contact, but instead of adding a constant for each pair (a, b), we add a {open_quotes}chemical weight{close_quotes} that depends on the atom pair (a, b). We tested our docking algorithm with a test set that contains the test examples of Norel et al. and Fischer et al. and compared the results of our docking algorithm with the results of Norel et al., Fischer et al. and Meyer et al. In 32 of 35 test examples the best conformation with respect to the fitness function was an approximation of the real conformation. 37 refs., 6 figs., 4 tabs.

• Research Organization: Association for Computing Machinery, New York, NY (United States); Sloan (Alfred P.) Foundation, New York, NY (United States)
• OSTI ID: 549012
• Report Number(s): CONF-970137-; TRN: 97:005298-0024
• Resource Relation: Conference: RECOMB `97: 1. annual conference on research in computational molecular biology, Santa Fe, NM (United States), 20-22 Jan 1997; Other Information: PBD: 1997; Related Information: Is Part Of RECOMB 97. Proceedings of the first annual international conference on computational molecular biology; PB: 370 p.
• Country of Publication: United States
• Language: English

Related Subjects

55 BIOLOGY AND MEDICINE
BASIC STUDIES
99 MATHEMATICS
COMPUTERS
INFORMATION SCIENCE
MANAGEMENT
LAW
MISCELLANEOUS
ATOMS
LENNARD-JONES POTENTIAL
VAN DER WAALS FORCES
PROTEINS
STRUCTURE-ACTIVITY RELATIONSHIPS
PROTEIN STRUCTURE
SHAPE
BIOCHEMISTRY
CONFORMAL MAPPING
ALGORITHMS
PARALLEL PROCESSING
COMPUTER CODES
CONFORMATIONAL CHANGES
MOLECULAR BIOLOGY
MOLECULES
RECEPTORS