Cheminformatics in natural product‐based drug discovery

Y Chen, J Kirchmair - Molecular Informatics, 2020 - Wiley Online Library
This review seeks to provide a timely survey of the scope and limitations of cheminformatics
methods in natural product‐based drug discovery. Following an overview of data resources …

Automated exploration of the low-energy chemical space with fast quantum chemical methods

P Pracht, F Bohle, S Grimme - Physical Chemistry Chemical Physics, 2020 - pubs.rsc.org
We propose and discuss an efficient scheme for the in silico sampling for parts of the
molecular chemical space by semiempirical tight-binding methods combined with a meta …

ProteinsPlus: a comprehensive collection of web-based molecular modeling tools

K Schöning-Stierand, K Diedrich, C Ehrt… - Nucleic Acids …, 2022 - academic.oup.com
Upon the ever-increasing number of publicly available experimentally determined and
predicted protein and nucleic acid structures, the demand for easy-to-use tools to investigate …

[HTML][HTML] Challenges in natural product-based drug discovery assisted with in silico-based methods

CV Simoben, SB Babiaka, AFA Moumbock… - Rsc Advances, 2023 - pubs.rsc.org
The application of traditional medicine by humans for the treatment of ailments as well as
improving the quality of life far outdates recorded history. To date, a significant percentage of …

Improving conformer generation for small rings and macrocycles based on distance geometry and experimental torsional-angle preferences

S Wang, J Witek, GA Landrum… - Journal of chemical …, 2020 - ACS Publications
The conformer generator ETKDG is a stochastic search method that utilizes distance
geometry together with knowledge derived from experimental crystal structures. It has been …

[HTML][HTML] Autonomous reaction network exploration in homogeneous and heterogeneous catalysis

M Steiner, M Reiher - Topics in Catalysis, 2022 - Springer
Autonomous computations that rely on automated reaction network elucidation algorithms
may pave the way to make computational catalysis on a par with experimental research in …

[HTML][HTML] A human-machine interface for automatic exploration of chemical reaction networks

M Steiner, M Reiher - Nature Communications, 2024 - nature.com
Autonomous reaction network exploration algorithms offer a systematic approach to explore
mechanisms of complex chemical processes. However, the resulting reaction networks are …

[HTML][HTML] TorsiFlex: an automatic generator of torsional conformers. Application to the twenty proteinogenic amino acids

D Ferro-Costas, I Mosquera-Lois… - Journal of …, 2021 - Springer
In this work, we introduce TorsiFlex, a user-friendly software written in Python 3 and
designed to find all the torsional conformers of flexible acyclic molecules in an automatic …

[HTML][HTML] Fast, efficient fragment-based coordinate generation for Open Babel

N Yoshikawa, GR Hutchison - Journal of cheminformatics, 2019 - Springer
Rapidly predicting an accurate three dimensional geometry of a molecule is a crucial task for
cheminformatics and across a wide range of molecular modeling. Consequently, developing …

A computational protocol for vibrational circular dichroism spectra of cyclic oligopeptides

KDR Eikås, MTP Beerepoot… - The Journal of Physical …, 2022 - ACS Publications
Cyclic peptides are a promising class of compounds for next-generation antibiotics as they
may provide new ways of limiting antibiotic resistance development. Although their cyclic …