Dielectric continuum methods for quantum chemistry

JM Herbert - Wiley Interdisciplinary Reviews: Computational …, 2021‏ - Wiley Online Library
This review describes the theory and implementation of implicit solvation models based on
continuum electrostatics. Within quantum chemistry this formalism is sometimes …

Deep learning for advancing peptide drug development: Tools and methods in structure prediction and design

X Wu, H Lin, R Bai, H Duan - European Journal of Medicinal Chemistry, 2024‏ - Elsevier
Peptides can bind challenging disease targets with high affinity and specificity, offering
enormous opportunities for addressing unmet medical needs. However, peptides' unique …

Fast identification of possible drug treatment of coronavirus disease-19 (COVID-19) through computational drug repurposing study

J Wang - Journal of chemical information and modeling, 2020‏ - ACS Publications
The recent outbreak of novel coronavirus disease-19 (COVID-19) calls for and welcomes
possible treatment strategies using drugs on the market. It is very efficient to apply computer …

Integrated unsupervised–supervised modeling and prediction of protein–peptide affinities at structural level

P Zhou, L Wen, J Lin, L Mei, Q Liu… - Briefings in …, 2022‏ - academic.oup.com
Cell signal networks are orchestrated directly or indirectly by various peptide-mediated
protein–protein interactions, which are normally weak and transient and thus ideal for …

Assessing the performance of MM/PBSA and MM/GBSA methods. 10. Prediction reliability of binding affinities and binding poses for RNA–ligand complexes

D Jiang, H Du, H Zhao, Y Deng, Z Wu… - Physical Chemistry …, 2024‏ - pubs.rsc.org
Ribonucleic acid (RNA)–ligand interactions play a pivotal role in a wide spectrum of
biological processes, ranging from protein biosynthesis to cellular reproduction. This …

Multi-epitope peptide vaccines targeting dengue virus serotype 2 created via immunoinformatic analysis

RN Morgan, NSM Ismail, MY Alshahrani… - Scientific Reports, 2024‏ - nature.com
Abstract The Middle East has witnessed a greater spread of infectious Dengue viruses, with
serotype 2 (DENV-2) being the most prevalent form. Through this work, multi-epitope …

Predicting the mutation effects of protein–ligand interactions via end-point binding free energy calculations: strategies and analyses

Y Yu, Z Wang, L Wang, S Tian, T Hou, H Sun - Journal of Cheminformatics, 2022‏ - Springer
Protein mutations occur frequently in biological systems, which may impact, for example, the
binding of drugs to their targets through impairing the critical H-bonds, changing the …

Uncovering the kinetic characteristics and degradation preference of PROTAC systems with advanced theoretical analyses

R Tang, Z Wang, S **ang, L Wang, Y Yu, Q Wang… - JACS Au, 2023‏ - ACS Publications
Proteolysis-targeting chimeras (PROTACs), which can selectively induce the degradation of
target proteins, represent an attractive technology in drug discovery. A large number of …

Characterizing the cooperative effect of PROTAC systems with end-point binding free energy calculation

K Xu, Z Wang, S **ang, R Tang, Q Deng… - Journal of Chemical …, 2024‏ - ACS Publications
Proteolytic targeting chimeras (PROTACs), as an emerging type of drug, function by
proximity-based modalities that narrow the distance between a target protein and the E3 …

Rational prediction of PROTAC-compatible protein–protein interfaces by molecular docking

GP Pereira, B Jiménez-García, R Pellarin… - Journal of Chemical …, 2023‏ - ACS Publications
Proteolysis targeting chimeras (PROTACs) are heterobifunctional ligands that mediate the
interaction between a protein target and an E3 ligase, resulting in a ternary complex, whose …