TY - GEN
T1 - Reducing the computational load of energy evaluations for protein folding
AU - Santos, Eunice E.
AU - Santos, Eugene
PY - 2004/9/24
Y1 - 2004/9/24
N2 - Predicting the native conformation using computational protein models requires a large number of energy evaluations even with simplified models such as hydrophobic-hydrophilic (HP) models. Clearly, energy evaluations constitute a significant portion of computational time. We hypothesize that given the structured nature of algorithms that search for candidate conformations such as stochastic methods, energy evaluation computations can be cached and reused, thus saving computational time and effort. In this paper, we present a caching approach and apply it to the triangular 2D-HP lattice model. We provide theoretical analysis and prediction of the expected savings from caching as applied this model. We conduct experiments using a sophisticated evolutionary algorithm that contains elements of local search, memetic algorithms, diversity replacement, etc. in order to verify our hypothesis and demonstrate a significant level of savings in computational effort and time that caching can provide.
AB - Predicting the native conformation using computational protein models requires a large number of energy evaluations even with simplified models such as hydrophobic-hydrophilic (HP) models. Clearly, energy evaluations constitute a significant portion of computational time. We hypothesize that given the structured nature of algorithms that search for candidate conformations such as stochastic methods, energy evaluation computations can be cached and reused, thus saving computational time and effort. In this paper, we present a caching approach and apply it to the triangular 2D-HP lattice model. We provide theoretical analysis and prediction of the expected savings from caching as applied this model. We conduct experiments using a sophisticated evolutionary algorithm that contains elements of local search, memetic algorithms, diversity replacement, etc. in order to verify our hypothesis and demonstrate a significant level of savings in computational effort and time that caching can provide.
UR - http://www.scopus.com/inward/record.url?scp=4544347767&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=4544347767&partnerID=8YFLogxK
U2 - 10.1109/BIBE.2004.1317328
DO - 10.1109/BIBE.2004.1317328
M3 - Conference contribution
AN - SCOPUS:4544347767
SN - 0769521738
SN - 9780769521732
T3 - Proceedings - Fourth IEEE Symposium on Bioinformatics and Bioengineering, BIBE 2004
SP - 79
EP - 86
BT - Proceedings - Fourth IEEE Symposium on Bioinformatics and Bioengineering, BIBE 2004
T2 - Proceedings - Fourth IEEE Symposium on Bioinformatics and Bioengineering, BIBE 2004
Y2 - 19 May 2004 through 21 May 2004
ER -