Stochastic protein folding simulation in the three-dimensional HP-model

We present results from three-dimensional protein folding simulations in the HP-model on ten benchmark problems. The simulations are executed by a simulated annealing-based algorithm with a time-dependent cooling schedule. The neighbourhood relation is determined by the pull-move set. The results provide experimental evidence that the maximum depth D of local minima of the underlying energy landscape can be upper bounded by D < n(2/3). The local search procedure employs the stopping criterion (In/delta)(D/gamma) where m is an estimation of the average number of neighbouring conformations, gamma relates to the mean of non-zero differences of the objective function for neighbouring conformations, and 1-delta is the confidence that a minimum conformation has been found. The bound complies with the results obtained for the ten benchmark problems. (c) 2008 Elsevier Ltd. All rights reserved.

Simulação computacional do enovelamento de proteínas utilizando o Modelo HP

Pós-graduação em Ciência e Tecnologia de Materiais - FC

Algoritmos evolutivos e modelo HP para predição de estruturas de proteínas

Predição de estruturas de proteínas (PSP) é um problema computacionalmente complexo. Modelos simplificados da molécula proteica (como o Modelo HP) e o uso de Algoritmos Evolutivos (AEs) estão entre as principais técnicas investigadas para PSP. Entretanto, a avaliação de uma estrutura representada pelo Modelo HP considera apenas o número de contatos hidrofóbicos, não possibilitando distinguir entre estruturas com o mesmo número de contatos hidrofóbicos. Neste trabalho, é apresentada uma nova formulação multiobjetivo para PSP em Modelo HP. Duas métricas são avaliadas: o número de contatos hidrofóbicos e a distância entre os aminoácidos hidrofóbicos, as quais são tratados pelo AE Multiobjetivo em Tabelas (AEMT). O algoritmo mostrou-se rápido e robusto.

Integer Programming Approach to HP Folding

One of the most widely studied protein structure prediction models is the hydrophobic-hydrophilic (HP) model, which explains the hydrophobic interaction and tries to maximize the number of contacts among hydrophobic amino-acids. In order to find a lower bound for the number of contacts, a number of heuristics have been proposed, but finding the optimal solution is still a challenge. In this research, we focus on creating a new integer programming model which is capable to provide tractable input for mixed-integer programming solvers, is general enough and allows relaxation with provable good upper bounds. Computational experiments using benchmark problems show that our formulation achieves these goals.

Teste de raios x na avaliação da qualidade de sementes de abóbora

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Termodinâmica do enovelamento de cadeias heteropoliméricas através do algoritmo de Wang-Landau

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Organizational, intermediate (field), (direct and general support), and depot maintenance repair parts and special tools list : engine, gasoline, 6 HP, military standard models, DOD model 4A032-1, 4A032-2, NSN 2805-00-776-0483, 2805-00-068-7512.

"April 1977."

Operator's and organizational maintenance manual : water purification unit, van-type, body mounted, electric driven, AC, 115, 208 V, single- and 3-phase, 60 hertz, 1/20 to 2 hp, 3000 gph (MET-PRO model 3000V), NSN 4610-00-168-1799.

"18 June 1980."

Operators, organizational, direct support, and general support maintenance manual : water purification unit, 420 gallons per hour, electric driven, 115V, single phase, 60 hertz 1/20 to 1 1/4 hp (Litton Systems, Inc. model LPU 420-1), FSN 4610-012-5490.

"1 October 1969"--P. i.

Operator and organizational maintenance manual (including repair parts and special tools list) : cleaner, steam pressure, jet, trailer mounted, kerosene or light diesel oil fired, electric motor, 1 hp, 115 V, AC/DC, 60 C, SGLE-PH (Geranco Manufacturing Corporation, model GS-400) (4940-865-4738).

"June 1967."

Field and depot maintenance manual : propelling unit, marine outboard, diesel driven, 165 hp, design 9002 (Murray & Tregurtha Harbormaster model OA6(TC)) serial numbers 216 thru 305, FSN 2010-278-0793.

"February 1962."