Computing approximate solutions of the protein structure determination problem using global constraints on discrete crystal lattices.
Crystal lattices are discrete models of the three-dimensional space that have been effectively employed to facilitate the task of determining proteins' natural conformation. This paper investigates alternative global constraints that can be introduced in a constraint solver over discrete crystal lattices. The objective is to enhance the efficiency of lattice solvers in dealing with the construction of approximate solutions of the protein structure determination problem. Some of them (e.g., self-avoiding-walk) have been explicitly or implicitly already used in previous approaches, while others (e.g., the density constraint) are new. The intrinsic complexities of all of them are studied and preliminary experimental results are discussed.
Dal Palù
Alessandro
A
Dipartimento di Matematica, Università di Parma, Viale G.P. Usberti, 53/A-43100 Parma, Italy. alessandro.dalpalu@unipr.it
Dovier
Agostino
A
Pontelli
Enrico
E
D000465:Algorithms; D019295:Computational Biology / Q000379:methods*; D008958:Models, Molecular; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry*
D011506:Proteins