[HTML][HTML] A guide to in silico drug design

Y Chang, BA Hawkins, JJ Du, PW Groundwater… - Pharmaceutics, 2023 - mdpi.com
The drug discovery process is a rocky path that is full of challenges, with the result that very
few candidates progress from hit compound to a commercially available product, often due …

Computational approaches to predict protein–protein interactions in crowded cellular environments

G Grassmann, M Miotto, F Desantis… - Chemical …, 2024 - ACS Publications
Investigating protein–protein interactions is crucial for understanding cellular biological
processes because proteins often function within molecular complexes rather than in …

gmx_MMPBSA: a new tool to perform end-state free energy calculations with GROMACS

MS Valdés-Tresanco… - Journal of chemical …, 2021 - ACS Publications
Molecular mechanics/Poisson–Boltzmann (Generalized-Born) surface area is one of the
most popular methods to estimate binding free energies. This method has been proven to …

Nucleic acid delivery for therapeutic applications

A Gupta, JL Andresen, RS Manan, R Langer - Advanced drug delivery …, 2021 - Elsevier
Recent medical advances have exploited the ability to address a given disease at the
underlying level of transcription and translation. These treatment paradigms utilize nucleic …

Molecular dynamics simulations in drug discovery and pharmaceutical development

OMH Salo-Ahen, I Alanko, R Bhadane, AMJJ Bonvin… - Processes, 2020 - mdpi.com
Molecular dynamics (MD) simulations have become increasingly useful in the modern drug
development process. In this review, we give a broad overview of the current application …

End-point binding free energy calculation with MM/PBSA and MM/GBSA: strategies and applications in drug design

E Wang, H Sun, J Wang, Z Wang, H Liu… - Chemical …, 2019 - ACS Publications
Molecular mechanics Poisson–Boltzmann surface area (MM/PBSA) and molecular
mechanics generalized Born surface area (MM/GBSA) are arguably very popular methods …

Terahertz photons improve cognitive functions in posttraumatic stress disorder

Y Yu, K Wu, X Yang, J Long, C Chang - Research, 2023 - spj.science.org
Posttraumatic stress disorder (PTSD) is a serious psychosis leading to cognitive impairment.
To restore cognitive functions for patients, the main treatments are based on medication or …

What is the current value of MM/PBSA and MM/GBSA methods in drug discovery?

T Tuccinardi - Expert opinion on drug discovery, 2021 - Taylor & Francis
The computer-aided drug design field is constituted by a wide range of different approaches
that can be roughly classified as either ligand-or receptor-based techniques. In order to …

Accurate determination of protein: ligand standard binding free energies from molecular dynamics simulations

H Fu, H Chen, M Blazhynska… - Nature protocols, 2022 - nature.com
Designing a reliable computational methodology to calculate protein: ligand standard
binding free energies is extremely challenging. The large change in configurational enthalpy …

Nelfinavir was predicted to be a potential inhibitor of 2019-nCov main protease by an integrative approach combining homology modelling, molecular docking and …

Z Xu, C Peng, Y Shi, Z Zhu, K Mu, X Wang, W Zhu - BioRxiv, 2020 - biorxiv.org
nCov has caused more than 80 deaths as of 27 January 2020 in China, and infection cases
have been reported in more than 10 countries. However, there is no approved drug to treat …