Unknown

Dataset Information

0

ASTRO-FOLD 2.0: an Enhanced Framework for Protein Structure Prediction.


ABSTRACT: The three-dimensional (3-D) structure prediction of proteins, given their amino acid sequence, is addressed using the first principles-based approach ASTRO-FOLD 2.0. The key features presented are: (1) Secondary structure prediction using a novel optimization-based consensus approach, (2) ?-sheet topology prediction using mixed-integer linear optimization (MILP), (3) Residue-to-residue contact prediction using a high-resolution distance-dependent force field and MILP formulation, (4) Tight dihedral angle and distance bound generation for loop residues using dihedral angle clustering and non-linear optimization (NLP), (5) 3-D structure prediction using deterministic global optimization, stochastic conformational space annealing, and the full-atomistic ECEPP/3 potential, (6) Near-native structure selection using a traveling salesman problem-based clustering approach, ICON, and (7) Improved bound generation using chemical shifts of subsets of heavy atoms, generated by SPARTA and CS23D. Computational results of ASTRO-FOLD 2.0 on 47 blind targets of the recently concluded CASP9 experiment are presented.

SUBMITTER: Subramani A 

PROVIDER: S-EPMC3462460 | biostudies-literature | 2012 May

REPOSITORIES: biostudies-literature

altmetric image

Publications

ASTRO-FOLD 2.0: an Enhanced Framework for Protein Structure Prediction.

Subramani A A   Wei Y Y   Floudas C A CA  

AIChE journal. American Institute of Chemical Engineers 20110531 5


The three-dimensional (3-D) structure prediction of proteins, given their amino acid sequence, is addressed using the first principles-based approach ASTRO-FOLD 2.0. The key features presented are: (1) Secondary structure prediction using a novel optimization-based consensus approach, (2) β-sheet topology prediction using mixed-integer linear optimization (MILP), (3) Residue-to-residue contact prediction using a high-resolution distance-dependent force field and MILP formulation, (4) Tight dihed  ...[more]

Similar Datasets

| S-EPMC1303441 | biostudies-literature
| S-EPMC2858251 | biostudies-literature
| S-EPMC5064833 | biostudies-literature
| S-EPMC2144327 | biostudies-other
| S-EPMC4150472 | biostudies-literature
| S-EPMC9252784 | biostudies-literature
| S-EPMC2866277 | biostudies-literature
| S-EPMC5570192 | biostudies-literature
| S-EPMC4821492 | biostudies-literature
| S-EPMC3667494 | biostudies-literature