Computer Physics Communications 41(1986)169—177 169 North-Holland, Amsterdam ASSOCIATION OF PROTEINS: ADAPTATION AND COUPLING OF TWO AVAILABLE PROGRAMS Luis SEIJO, Brant COGHLAN and Serafin FRAGA Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada T6G 2G2 Received 13 November 1985; in revised form 22 January 1986 ADAPTATION SUMMARY Title of adaptation: AGAB Nature of the physical problem Determination of the optimal spatial conformations and rela- Adaptation number: oooi tive positions of two proteins from their amino acid sequence. Programs obtainable from: CPC Program Library, Queen’s Method of solution University of Belfast, N. Ireland (see application form in this In a cycle, the internal structure of each protein is optimized in issue) the presence of the other protein, then their relative position is changed. Optimization of a single protein is performed, under Reference to original programs: an energy criterion, by rotation around the bonds C,,—C’, Cat, no. Title Ref in CPC C’—N, N—Ce, and C,,—Cp [1]. Translation and rotation of one ACEO AMYR 29 (1983) 351 protein with respect to the other is governed by the gradient of AABU POETA 36 (1985) 391 the interaction energy between them [2]. Restrictions on the complexity of the problem Program added to complete the system of programs: COUPLER The ones in the original programs. Authors of original programs: Serafin Fraga; Brant Coghlan Typical running time and Serafin Fraga Dependent on the size of the proteins. CPU times for the three test cases are 49, 275 and 201 s. Computer: Amdhal 580/5860 and IBM-type computers; Instal- lation: University of Alberta Computing Services Unusual features of the system of programs Operating system: MTS It can also be used to optimize the structure of a single protein in the presence of an other molecule which is not a protein. Programming language used in the adapted programs: Fortran IV. The ordered run of the programs is controlled by a set of References orders written in MTS Macro Processor language [1] B. Coghlan and S. Fraga, Comput. Phys. Commun. 36 (1985) 391. No. of bits in a word: 32 [2] S. Fraga, Comput. Phys. Commun. 29 (1983) 351. OO1O-4655/86/$0150 © Elsevier Science Publishers BV. (North-Holland Physics Publishing Division)