Complex macrocycle exploration: parallel, heuristic, and constraint-based conformer generation using ForceGen.

ABSTRACT: ForceGen is a template-free, non-stochastic approach for 2D to 3D structure generation and conformational elaboration for small molecules, including both non-macrocycles and macrocycles. For conformational search of non-macrocycles, ForceGen is both faster and more accurate than the best of all tested methods on a very large, independently curated benchmark of 2859 PDB ligands. In this study, the primary results are on macrocycles, including results for 431 unique examples from four separate benchmarks. These include complex peptide and peptide-like cases that can form networks of internal hydrogen bonds. By making use of new physical movements ("flips" of near-linear sub-cycles and explicit formation of hydrogen bonds), ForceGen exhibited statistically significantly better performance for

SUBMITTER: Jain AN 

PROVIDER: S-EPMC6554267 | biostudies-literature | 2019 Jun

REPOSITORIES: biostudies-literature