Nativelike topology assembly of small proteins using predicted restraints in Monte Carlo folding simulations
نویسندگان
چکیده
منابع مشابه
Nativelike topology assembly of small proteins using predicted restraints in Monte Carlo folding simulations.
By incorporating predicted secondary and tertiary restraints derived from multiple sequence alignments into ab initio folding simulations, it has been possible to assemble native-like tertiary structures for a test set of 19 nonhomologous proteins ranging from 29 to 100 residues in length and representing all secondary structural classes. Secondary structural restraints are provided by the PHD ...
متن کاملFold assembly of small proteins using monte carlo simulations driven by restraints derived from multiple sequence alignments.
The feasibility of predicting the global fold of small proteins by incorporating predicted secondary and tertiary restraints into ab initio folding simulations has been demonstrated on a test set comprised of 20 non-homologous proteins, of which one was a blind prediction of target 42 in the recent CASP2 contest. These proteins contain from 37 to 100 residues and represent all secondary structu...
متن کاملFolding and Aggregation of Proteins with Monte Carlo Simulations
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We demonstrate that evolutionary Monte Carlo ~EMC! can be applied successfully to simulations of protein folding on simple lattice models, and to finding the ground state of a protein. In all cases, EMC is faster than the genetic algorithm and the conventional Metropolis Monte Carlo, and in several cases it finds new lower energy states. We also propose one method for the use of secondary struc...
متن کاملFolding simulations of small proteins.
Understanding how a protein folds is a long-standing challenge in modern science. We have used an optimized atomistic model (united-residue force field) to simulate folding of small proteins of various structures: HP-36 (alpha protein), protein A (beta), 1fsd (alpha+beta), and betanova (beta). Extensive Monte Carlo folding simulations (ten independent runs with 10(9) Monte Carlo steps at a temp...
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ژورنال
عنوان ژورنال: Proceedings of the National Academy of Sciences
سال: 1998
ISSN: 0027-8424,1091-6490
DOI: 10.1073/pnas.95.3.1020