AI in computational chemistry through the lens of a decade-long journey

Dral, Pavlo O.

doi:10.1039/d4cc00010b

Cited by 2 publications

References 173 publications

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Quantum chemical package Jaguar: A survey of recent developments and unique features

Cao,

Balduf,

Beachy

et al. 2024

The Journal of Chemical Physics

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This paper is dedicated to the quantum chemical package Jaguar, which is commercial software developed and distributed by Schrödinger, Inc. We discuss Jaguar’s scientific features that are relevant to chemical research as well as describe those aspects of the program that are pertinent to the user interface, the organization of the computer code, and its maintenance and testing. Among the scientific topics that feature prominently in this paper are the quantum chemical methods grounded in the pseudospectral approach. A number of multistep workflows dependent on Jaguar are covered: prediction of protonation equilibria in aqueous solutions (particularly calculations of tautomeric stability and pKa), reactivity predictions based on automated transition state search, assembly of Boltzmann-averaged spectra such as vibrational and electronic circular dichroism, as well as nuclear magnetic resonance. Discussed also are quantum chemical calculations that are oriented toward materials science applications, in particular, prediction of properties of optoelectronic materials and organic semiconductors, and molecular catalyst design. The topic of treatment of conformations inevitably comes up in real world research projects and is considered as part of all the workflows mentioned above. In addition, we examine the role of machine learning methods in quantum chemical calculations performed by Jaguar, from auxiliary functions that return the approximate calculation runtime in a user interface, to prediction of actual molecular properties. The current work is second in a series of reviews of Jaguar, the first having been published more than ten years ago. Thus, this paper serves as a rare milestone on the path that is being traversed by Jaguar’s development in more than thirty years of its existence.

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Quantum chemical package Jaguar: A survey of recent developments and unique features

Cao,

Balduf,

Beachy

et al. 2024

The Journal of Chemical Physics

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Elucidating Electronic Structure Variations in Nucleic Acid-Protein Complexes Involved in Transcription Regulation Using a Tight-Binding Approach

Du,

Liu

2024

Preprint

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Transcription factor (TF) are proteins that regulates the transcription of genetic information from DNA to messenger RNA by binding to a specific DNA sequence. Nucleic acid-protein interactions are crucial in regulating transcription in biological systems. This work presents a quick and convenient method for constructing tight-binding models and offers physical insights into the electronic structure properties of transcription factor complexes and DNA motifs. The tight binding Hamiltonian parameters are generated using the random forest regression algorithm, which reproduces the given ab-initio level calculations with reasonable accuracy. We present a library of residue-level parameters derived from extensive electronic structure calculations over various possible combinations of nucleobases and amino acid side chains from high-quality DNA-protein complex structures. As an example, our approach can reasonably generate the subtle electronic structure details for the orthologous transcription factors human AP-1 and Epstein-Barr virus Zta within a few seconds on a laptop. This method potentially enhances our understanding of the electronic structure variations of gene-protein interaction complexes, even those involving dozens of proteins and genes. We hope this study offers a powerful tool for analyzing transcription regulation mechanisms at an electronic structural level.

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AI in computational chemistry through the lens of a decade-long journey

Abstract: This article gives a perspective on the progress of AI tools in computational chemistry through the lens of the author’s decade-long contributions put in the wider context of the trends...

Cited by 2 publications

References 173 publications

Quantum chemical package Jaguar: A survey of recent developments and unique features

Quantum chemical package Jaguar: A survey of recent developments and unique features

Elucidating Electronic Structure Variations in Nucleic Acid-Protein Complexes Involved in Transcription Regulation Using a Tight-Binding Approach

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