А зачем мы считали? Налаштування

[tyoma]

После 2007 года - я не вижу ни привета ни отчета по этому проэкту. Сайт в полудауне. В общем логичный вопрос - нас кинули? И второй вопрос - а где написано, что нас опять не кидают/будут кидать в подобных проэктах? В ФАДе как бы говорилось про открытость результатов, так где они? Ну или раскажите про тяжелую судьбу создателей ФАДа, хоть какую то, кто то знает?

[Alien]

не работает картинка
кстати, в инглиш версии больше список публикаций http://folding.stanford.edu/English/Papers#ntoc8 есть даже за 2010 год

Нашел интересную для себя информацию

ABSTRACT. Multiple variants of the AMBER all-atom force field were quantitatively evaluated with respect to their ability to accurately characterize helix-coil equilibria in explicit solvent simulations. Using a global distributed computing network, absolute conformational convergence was achieved for large ensembles of the capped A21 and Fs helical peptides. Further assessment of these AMBER variants was conducted via simulations of a flexible 164-residue five-helix-bundle protein, apolipophorin-III, on the 100 ns timescale. Of the contemporary potentials that had not been assessed previously, the AMBER-99SB force field showed significant helix-destabilizing tendencies, with beta bridge formation occurring in helical peptides, and unfolding of apolipophorin-III occurring on the tens of nanoseconds timescale. The AMBER-03 force field, while showing adequate helical propensities for both peptides and stabilizing apolipophorin-III, (i) predicts an unexpected decrease in helicity with ALA to ARG+ substitution, (ii) lacks experimentally observed 3-10 helical content, and (iii) deviates strongly from average apolipophorin-III NMR structural properties. As is observed for AMBER-99SB, AMBER-03 significantly overweighs the contribution of extended and polyproline backbone configurations to the conformational equilibrium. In contrast, the AMBER-99phi force field, which was previously shown to best reproduce experimental measurements of the helix-coil transition in model helical peptides, adequately stabilizes apolipophorin-III and yields both an average gyration radius and polar solvent exposed surface area that are in excellent agreement with the NMR ensemble.

как я и говорил тут сразу виден методологический характер исследований.
при построении белково-нуклеиновых комплексов в 2011 году, мне понадобится эта информация ибо я хотел использовать силовое поле AMBER-03 и думал над тем почему остальные используют AMBER-99.
http://www.plosone.org/article/info:doi/10...al.pone.0010056

почитал чуть дальше

Simulations were then run in parallel on a local computing cluster using the AMBER-94, AMBER-99w, AMBER-99SB, and AMBER-03 force fields with 12 A ° cutoffs imposed on non-bonded interactions to accurately account for tertiary contacts within the helical bundle. Eight 100 ns simulations per force field were conducted, yielding a total apoLp-III sampling time of 3.2 ms. Each 100 ns simulation of this system, composed of 40,118 atoms in all, required approximately 6 months of wall-clock time on a single 2.5 GHz Xeon processing core.

еще писали сэнки волонтерам ФАХ