TY - GEN
T1 - A filtering technique for fragment assembly- based proteins loop modeling with constraints
AU - Campeotto, Federico
AU - Dal Palù, Alessandro
AU - Dovier, Agostino
AU - Fioretto, Ferdinando
AU - Pontelli, Enrico
PY - 2012
Y1 - 2012
N2 - Methods to predict the structure of a protein often rely on the knowledge of macro sub-structures and their exact or approximated relative positions in space. The parts connecting these sub-structures are called loops and, in general, they are characterized by a high degree of freedom. The modeling of loops is a critical problem in predicting protein conformations that are biologically realistic. This paper introduces a class of constraints that models a general multi-body system; we present a proof of NP-completeness and provide filtering techniques, inspired by inverse kinematics, that can drastically reduce the search space of potential conformations. The paper shows the application of the constraint in solving the protein loop modeling problem, based on fragments assembly.
AB - Methods to predict the structure of a protein often rely on the knowledge of macro sub-structures and their exact or approximated relative positions in space. The parts connecting these sub-structures are called loops and, in general, they are characterized by a high degree of freedom. The modeling of loops is a critical problem in predicting protein conformations that are biologically realistic. This paper introduces a class of constraints that models a general multi-body system; we present a proof of NP-completeness and provide filtering techniques, inspired by inverse kinematics, that can drastically reduce the search space of potential conformations. The paper shows the application of the constraint in solving the protein loop modeling problem, based on fragments assembly.
UR - http://www.scopus.com/inward/record.url?scp=84868277188&partnerID=8YFLogxK
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U2 - 10.1007/978-3-642-33558-7_61
DO - 10.1007/978-3-642-33558-7_61
M3 - Conference contribution
AN - SCOPUS:84868277188
SN - 9783642335570
T3 - Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
SP - 850
EP - 866
BT - Principles and Practice of Constraint Programming - 18th International Conference, CP 2012, Proceedings
T2 - 18th International Conference on Principles and Practice of Constraint Programming, CP 2012
Y2 - 8 October 2012 through 12 October 2012
ER -