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ANI-1, A data set of 20 million calculated off-equilibrium conformations for organic molecules.

ABSTRACT: One of the grand challenges in modern theoretical chemistry is designing and implementing approximations that expedite ab initio methods without loss of accuracy. Machine learning (ML) methods are emerging as a powerful approach to constructing various forms of transferable atomistic potentials. They have been successfully applied in a variety of applications in chemistry, biology, catalysis, and solid-state physics. However, these models are heavily dependent on the quality and quantity of data used in their fitting. Fitting highly flexible ML potentials, such as neural networks, comes at a cost: a vast amount of reference data is required to properly train these models. We address this need by providing access to a large computational DFT database, which consists of more than 20 M off equilibrium conformations for 57,462 small organic molecules. We believe it will become a new standard benchmark for comparison of current and future methods in the ML potential community.

SUBMITTER: Smith JS

PROVIDER: S-EPMC5735918 | biostudies-literature | 2017 Dec

REPOSITORIES: biostudies-literature

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ANI-1, A data set of 20 million calculated off-equilibrium conformations for organic molecules.

Smith Justin S JS Isayev Olexandr O Roitberg Adrian E AE

Scientific data 20171219

One of the grand challenges in modern theoretical chemistry is designing and implementing approximations that expedite ab initio methods without loss of accuracy. Machine learning (ML) methods are emerging as a powerful approach to constructing various forms of transferable atomistic potentials. They have been successfully applied in a variety of applications in chemistry, biology, catalysis, and solid-state physics. However, these models are heavily dependent on the quality and quantity of data ...[more]

PMID: 29257127

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Project description:In this study, we systematically studied the energy distribution of bioactive conformations of small molecular ligands in their conformational ensembles using ANI-2X, a machine learning potential, in conjunction with one of our recently developed geometry optimization algorithms, known as a conjugate gradient with backtracking line search (CG-BS). We first evaluated the combination of these methods (ANI-2X/CG-BS) using two molecule sets. For the 231-molecule set, ab initio calculations were performed at both the ωB97X/6-31G(d) and B3LYP-D3BJ/DZVP levels for accuracy comparison, while for the 8,992-molecule set, ab initio calculations were carried out at the B3LYP-D3BJ/DZVP level. For each molecule in the two molecular sets, up to 10 conformations were generated, which diminish the influence of individual outliers on the performance evaluation. Encouraged by the performance of ANI-2x/CG-BS in these evaluations, we calculated the energy distributions using ANI-2x/CG-BS for more than 27,000 ligands in the protein data bank (PDB). Each ligand has at least one conformation bound to a biological molecule, and this ligand conformation is labeled as a bound conformation. Besides the bound conformations, up to 200 conformations were generated using OpenEye's Omega2 software (https://docs.eyesopen.com/applications/ omega/) for each conformation. We performed a statistical analysis of how the bound conformation energies are distributed in the ensembles for 17,197 PDB ligands that have their bound conformation energies within the energy ranges of the Omega2-generated conformation ensembles. We found that half of the ligands have their relative conformation energy lower than 2.91 kcal/mol for the bound conformations in comparison with the global conformations, and about 90% of the bound conformations are within 10 kcal/mol above the global conformation energies. This information is useful to guide the construction of libraries for shape-based virtual screening and to improve the docking algorithm to efficiently sample bound conformations.

Dataset Information

ANI-1, A data set of 20 million calculated off-equilibrium conformations for organic molecules.

Publications

ANI-1, A data set of 20 million calculated off-equilibrium conformations for organic molecules.

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