Skip to main content

Table 4 Results for biological and designed sequences

From: A replica exchange Monte Carlo algorithm for protein folding in the HP model

ID E* PERM t 1 MathType@MTEF@5@5@+=feaafiart1ev1aaatCvAUfKttLearuWrP9MDH5MBPbIqV92AaeXatLxBI9gBaebbnrfifHhDYfgasaacH8akY=wiFfYdH8Gipec8Eeeu0xXdbba9frFj0=OqFfea0dXdd9vqai=hGuQ8kuc9pgc9s8qqaq=dirpe0xb9q8qiLsFr0=vr0=vr0dc8meaabaqaciaacaGaaeqabaqabeGadaaakeaacqqGqbaucqqGfbqrcqqGsbGucqqGnbqtdaWgaaWcbaGaemiDaq3aaSbaaWqaaiabigdaXaqabaaaleqaaaaa@33F5@ PERM t 2 MathType@MTEF@5@5@+=feaafiart1ev1aaatCvAUfKttLearuWrP9MDH5MBPbIqV92AaeXatLxBI9gBaebbnrfifHhDYfgasaacH8akY=wiFfYdH8Gipec8Eeeu0xXdbba9frFj0=OqFfea0dXdd9vqai=hGuQ8kuc9pgc9s8qqaq=dirpe0xb9q8qiLsFr0=vr0=vr0dc8meaabaqaciaacaGaaeqabaqabeGadaaakeaacqqGqbaucqqGfbqrcqqGsbGucqqGnbqtdaWgaaWcbaGaemiDaq3aaSbaaWqaaiabikdaYaqabaaaleqaaaaa@33F7@ PERM t e x p MathType@MTEF@5@5@+=feaafiart1ev1aaatCvAUfKttLearuWrP9MDH5MBPbIqV92AaeXatLxBI9gBaebbnrfifHhDYfgasaacH8akY=wiFfYdH8Gipec8Eeeu0xXdbba9frFj0=OqFfea0dXdd9vqai=hGuQ8kuc9pgc9s8qqaq=dirpe0xb9q8qiLsFr0=vr0=vr0dc8meaabaqaciaacaGaaeqabaqabeGadaaakeaacqqGqbaucqqGfbqrcqqGsbGucqqGnbqtdaWgaaWcbaGaemiDaq3aaSbaaWqaaiabdwgaLjabdIha4jabdchaWbqabaaaleqaaaaa@373A@ ACO-HPPFP-3 REMC pm REMC m
B50-5 -22 5 sec 118 sec 9 sec 820 sec 6 sec 5 sec
B50-7 -17 271 sec 299 sec 284 sec 130 sec 1 sec 2 sec
D-1 -19 3 795 sec 1 sec 2 sec 236 sec 1 sec 1 sec
D-2 -17 9 257 sec 19 356 sec 12 524 sec 951 sec 44 sec 41 sec
  1. Results for PERM and ACO-HPPFP-3 are reproduced from [9]. In all instances, REMC finds optimal conformations relatively easily compared with the other algorithms. REMC does not demonstrate an inherit difficulty folding sequences when conformations involve hydrophobic cores confined to one end of the sequence or the case involving both ends. For every instance, 100 independent runs were conducted of 1 CPU hour each. In cases where not every run reached the same energy value after 1 hour, the expected run-time to reach the energy value shown in the table was calculated using the equation detailed by Parkes and Walser [54].