The dead-end elimination theorem and its use in protein side-chain positioning Export

@article{desmet:92, abstract = {THE prediction of a protein's tertiary structure is still a considerable problem because the huge amount of possible conformational space1 makes it computationally difficult. With regard to side-chain modelling, a solution has been attempted by the grouping of side-chain conformations into representative sets of rotamers2–5. Nonetheless, an exhaustive combinatorial search is still limited to carefully identified packing units5,6containing a limited number of residues. For larger systems other strategies had to be develop-ped, such as the Monte Carlo Procedure6,7 and the genetic algorithm and clustering approach8. Here we present a theorem, referred to as the 'dead-end elimination' theorem, which imposes a suitable condition to identify rotamers that cannot be members of the global minimum energy conformation. Application of this theorem effectively controls the computational explosion of the rotamer combinatorial problem, thereby allowing the determination of the global minimum energy conformation of a large collection of side chains.}, author = {Desmet, Johan and Maeyer, Marc D. and Hazes, Bart and Lasters, Ignace}, citeulike-article-id = {579510}, citeulike-linkout-0 = {http://dx.doi.org/10.1038/356539a0}, citeulike-linkout-1 = {http://dx.doi.org/10.1038/356539a0}, doi = {10.1038/356539a0}, journal = {Nature}, keywords = {design, packing, protein}, month = {April}, number = {6369}, pages = {539--542}, posted-at = {2009-01-08 22:13:57}, priority = {0}, title = {The dead-end elimination theorem and its use in protein side-chain positioning}, url = {http://dx.doi.org/10.1038/356539a0}, volume = {356}, year = {1992} }

TY - JOUR ID - desmet:92 L3 - citeulike-article-id:579510 N2 - THE prediction of a protein's tertiary structure is still a considerable problem because the huge amount of possible conformational space1 makes it computationally difficult. With regard to side-chain modelling, a solution has been attempted by the grouping of side-chain conformations into representative sets of rotamers2–5. Nonetheless, an exhaustive combinatorial search is still limited to carefully identified packing units5,6containing a limited number of residues. For larger systems other strategies had to be develop-ped, such as the Monte Carlo Procedure6,7 and the genetic algorithm and clustering approach8. Here we present a theorem, referred to as the 'dead-end elimination' theorem, which imposes a suitable condition to identify rotamers that cannot be members of the global minimum energy conformation. Application of this theorem effectively controls the computational explosion of the rotamer combinatorial problem, thereby allowing the determination of the global minimum energy conformation of a large collection of side chains. IS - 6369 JF - Nature EP - 542 TI - The dead-end elimination theorem and its use in protein side-chain positioning VL - 356 SP - 539 KW - design KW - packing KW - protein AU - Desmet, Johan AU - Maeyer, Marc AU - Hazes, Bart AU - Lasters, Ignace PY - 1992/04// UR - http://dx.doi.org/10.1038/356539a0 ER -