The multi-structural approximation with torsional anharmonicity (MS-T) method and its variants have been widely used for calculating conformational-rovibrational partition functions of large molecules. The present work aimed to propose a systematic method to assess and explain the performance of various variants of the MS-T method. First, we proposed the simplest variant MS-T(2NN) (two nearest neighborhood torsions are coupled) and systematically validated it for large alkanes -CH ( = 6-10) and their transition states of hydrogen abstraction reactions. Second, we proposed a metric-based method to explain the underlying reason for the good performance of MS-T(2NN)─it includes the torsional conformers that have dominant contributions to the partition function calculations. These conformers are closer to the lowest-energy conformer in the space of dihedral and energy metrics. Third, the same observation and explanation apply to the other two variants, MS-2DT (any two torsions are coupled) and MS-3DT (any three torsional are coupled), which contain increasingly more torsional conformers than MS-T(2NN) but are subsets of the complete set of torsional conformers considered by the MS-T method. Overall, the present method provides a mathematically rigorous and computationally effective diagnosis tool to assess various MS-T methods dealing with the torsional anharmonicity of large molecules in the partition function calculation.
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http://dx.doi.org/10.1021/acs.jpca.2c04724 | DOI Listing |
Chem Sci
December 2024
ByteDance Research Bellevue Washington 98004 USA
A force field is a critical component in molecular dynamics simulations for computational drug discovery. It must achieve high accuracy within the constraints of molecular mechanics' (MM) limited functional forms, which offers high computational efficiency. With the rapid expansion of synthetically accessible chemical space, traditional look-up table approaches face significant challenges.
View Article and Find Full Text PDFBioinformatics
January 2025
Department of Molecular Genetics, University of Toronto, Ontario, M5S 3K3, Canada.
Motivation: Accurate prediction of protein side-chain conformations is necessary to understand protein folding, protein-protein interactions and facilitate de novo protein design.
Results: Here we apply torsional flow matching and equivariant graph attention to develop FlowPacker, a fast and performant model to predict protein side-chain conformations conditioned on the protein sequence and backbone. We show that FlowPacker outperforms previous state-of-the-art baselines across most metrics with improved runtime.
Brief Bioinform
November 2024
School of Information Science and Technology, Northeast Normal University, 130117 Changchun, China.
Acta Crystallogr E Crystallogr Commun
October 2024
Department of PG Studies and Research in Physics Albert Einstein Block UCS Tumkur University, Tumkur Karnataka-572103 India.
In the title compound, CHNO, the torsion angle associated with the phenyl benzoate group is -173.7 (2)° and that for the benz-yloxy group is -174.8 (2)° establishing an -type conformation.
View Article and Find Full Text PDFArch Biochem Biophys
December 2024
Department of Pharmaceutical Sciences, School of Health Sciences and Technology, UPES, Dehradun, 248007, Uttarakhand, India. Electronic address:
KRAS (Kirsten rat sarcoma viral oncogene homologue), the most common mutated protein in human cancers, is the leading cause of morbidity and mortality. Before Sotorasib (AMG-510) was approved for non-small cell lung cancer treatment in 2020, the oncogenic KRAS mutations were believed to be non-druggable. High-resolution X-ray crystal structures of GDP-bound KRAS mutants with and without inhibitor are resolved and deposited in the Protein Data Bank (PDB).
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