ArticleJournal of chemical theory and computation2014
A Comparative Study of Transferable Aspherical Pseudoatom Databank and Classical Force Fields for Predicting Electrostatic Interactions in Molecular Dimers.
Article in Journal of chemical theory and computation, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed, 30 citations in OpenAlex.
- Article
- Aspherical atom refinements on X-ray data of diverse structures including disordered and covalent organic framework systems: a time-accuracy trade-off.Journal of applied crystallography · 2023Article
- An Imbalance in the Force: The Need for Standardized Benchmarks for Molecular Simulation.Journal of chemical information and modeling · 2023Review
- The Role of Electrostatic Interactions in IFIT5-RNA Complexes Predicted by the UBDB+EPMM Method.The journal of physical chemistry. B · 2022Article
- Multipolar Atom Types from Theory and Statistical Clustering (MATTS) Data Bank: Restructurization and Extension of UBDB.Journal of chemical information and modeling · 2022Article
- Multipolar Atom Types from Theory and Statistical Clustering (MATTS) Data Bank: Impact of Surrounding Atoms on Electron Density from Cluster Analysis.Journal of chemical information and modeling · 2022Article
- Electron density is not spherical: the many applications of the transferable aspherical atom model.Computational and structural biotechnology journal · 2022Review
- A Quantum Chemical Topology Picture of Intermolecular Electrostatic Interactions and Charge Penetration Energy.Journal of chemical theory and computation · 2021Article
- Combining Molecular Dynamic Information and an Aspherical-Atom Data Bank in the Evaluation of the Electrostatic Interaction Energy in Multimeric Protein-Ligand Complex: A Case Study for HIV-1 Protease.Molecules (Basel, Switzerland) · 2021Article
- Refinement of organic crystal structures with multipolar electron scattering factors.Acta crystallographica. Section A, Foundations and advances · 2020Article
- Transferable aspherical atom model refinement of protein and DNA structures against ultrahigh-resolution X-ray data.Acta crystallographica. Section D, Structural biology · 2016Article
- Electrostatic interactions in aminoglycoside-RNA complexes.Biophysical journal · 2015Article
Corrections and comments
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Authors and funding
7 authors at 2 institutions in 2 countries.
Funding
Abstract
Accurate and fast evaluation of electrostatic interactions in molecular systems is one of the most challenging tasks in the rapidly advancing field of macromolecular chemistry and drug design. Electrostatic interactions are of crucial importance in biological systems. They are well represented by quantum mechanical methods; however, such calculations are computationally expensive. In this study, we have evaluated the University of Buffalo Pseudoatom Databank (UBDB)1,2 approach for approximation of electrostatic properties of macromolecules and their complexes. We selected the S663 and JSCH-20054 data sets (208 molecular complexes in total) for this study. These complexes represent a wide range of chemical and biological systems for which hydrogen bonding, electrostatic, and van der Waals interactions play important roles. Reference electrostatic energies were obtained directly from wave functions at the B3LYP/aug-cc-pVTZ level of theory using the SAPT (Symmetry-Adapted Perturbation Theory) scheme for calculation of electrostatic contributions to total intermolecular interaction energies. Electrostatic energies calculated on the basis of the UBDB were compared with corresponding reference results. Results were also compared with energies computed using a point charge model from popular force fields (AM1-BCC and RESP used in AMBER and CGenFF from CHARMM family). The energy trends are quite consistent (
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