Use of molecular docking computational tools in drug discovery

F Stanzione, I Giangreco, JC Cole - Progress in medicinal chemistry, 2021 - Elsevier
Molecular docking has become an important component of the drug discovery process.
Since first being developed in the 1980s, advancements in the power of computer hardware …

Structure and dynamics of molecular networks: a novel paradigm of drug discovery: a comprehensive review

P Csermely, T Korcsmáros, HJM Kiss, G London… - Pharmacology & …, 2013 - Elsevier
Despite considerable progress in genome-and proteome-based high-throughput screening
methods and in rational drug design, the increase in approved drugs in the past decade did …

Molecular docking-based computational platform for high-throughput virtual screening

B Zhang, H Li, K Yu, Z Jin - CCF Transactions on High Performance …, 2022 - Springer
Abstract Structure-based virtual screening is a key, routine computational method in
computer-aided drug design. Such screening can be used to identify potentially highly active …

De novo molecule design through the molecular generative model conditioned by 3D information of protein binding sites

M Xu, T Ran, H Chen - Journal of Chemical Information and …, 2021 - ACS Publications
De novo molecule design through the molecular generative model has gained increasing
attention in recent years. Here, a novel generative model was proposed by integrating the …

Structure-based druggability assessment—identifying suitable targets for small molecule therapeutics

EB Fauman, BK Rai, ES Huang - Current opinion in chemical biology, 2011 - Elsevier
A target is druggable if it can be modulated in vivo by a drug-like molecule. The general
properties of oral drugs are summarized by the 'rule of 5'which specifies parameters related …

An enumerative algorithm for de novo design of proteins with diverse pocket structures

B Basanta, MJ Bick, AK Bera, C Norn… - Proceedings of the …, 2020 - National Acad Sciences
To create new enzymes and biosensors from scratch, precise control over the structure of
small-molecule binding sites is of paramount importance, but systematically designing …

Study and design of stability in GH5 cellulases

S Badieyan, DR Bevan, C Zhang - Biotechnology and …, 2012 - Wiley Online Library
Thermostable enzymes that hydrolyze lignocellulosic materials provide potential
advantages in process configuration and enhancement of production efficiency over their …

Mechanistically guided workflow for relating complex reactive site topologies to catalyst performance in C–H functionalization reactions

RC Cammarota, W Liu, J Bacsa… - Journal of the …, 2022 - ACS Publications
Leveraging congested catalyst scaffolds has emerged as a key strategy for altering innate
substrate site-selectivity profiles in C–H functionalization reactions. Similar to enzyme active …

istar: A web platform for large-scale protein-ligand docking

H Li, KS Leung, PJ Ballester, MH Wong - PLoS One, 2014 - journals.plos.org
Protein-ligand docking is a key computational method in the design of starting points for the
drug discovery process. We are motivated by the desire to automate large-scale docking …

Structural and free energy landscape of novel mutations in ribosomal protein S1 (rpsA) associated with pyrazinamide resistance

MT Khan, A Khan, AU Rehman, Y Wang, K Akhtar… - Scientific Reports, 2019 - nature.com
Resistance to key first-line drugs is a major hurdle to achieve the global end tuberculosis
(TB) targets. A prodrug, pyrazinamide (PZA) is the only drug, effective in latent TB …