Improvements, trends, and new ideas in molecular docking: 2012–2013 in review

E Yuriev, J Holien, PA Ramsland - Journal of Molecular …, 2015 - Wiley Online Library
Molecular docking is a computational method for predicting the placement of ligands in the
binding sites of their receptor (s). In this review, we discuss the methodological …

Defining and exploring chemical spaces

CW Coley - Trends in Chemistry, 2021 - cell.com
Designing functional molecules with desirable properties is often a challenging, multi-
objective optimization. For decades, there have been computational approaches to facilitate …

Identification of inhibitors of SARS-CoV-2 3CL-pro enzymatic activity using a small molecule in vitro repurposing screen

M Kuzikov, E Costanzi, J Reinshagen… - ACS pharmacology & …, 2021 - ACS Publications
Compound repurposing is an important strategy for the identification of effective treatment
options against SARS-CoV-2 infection and COVID-19 disease. In this regard, SARS-CoV-2 …

A review on parallel virtual screening softwares for high-performance computers

NA Murugan, A Podobas, D Gadioli, E Vitali… - Pharmaceuticals, 2022 - mdpi.com
Drug discovery is the most expensive, time-demanding, and challenging project in
biopharmaceutical companies which aims at the identification and optimization of lead …

Mashup: making serverless computing useful for hpc workflows via hybrid execution

RB Roy, T Patel, V Gadepally, D Tiwari - Proceedings of the 27th ACM …, 2022 - dl.acm.org
This work introduces Mashup, a novel strategy to leverage serverless computing model for
executing scientific workflows in a hybrid fashion by taking advantage of both the traditional …

CReM: chemically reasonable mutations framework for structure generation

P Polishchuk - Journal of Cheminformatics, 2020 - Springer
Abstract Structure generators are widely used in de novo design studies and their
performance substantially influences an outcome. Approaches based on the deep learning …

Rational design of allosteric modulators: Challenges and successes

A Chatzigoulas, Z Cournia - Wiley Interdisciplinary Reviews …, 2021 - Wiley Online Library
Recent advances in structural biology and computational techniques have revealed
allosteric mechanisms for an abundance of targets leading to the establishment of rational …

Cytopathic SARS-CoV-2 screening on VERO-E6 cells in a large-scale repurposing effort

A Zaliani, L Vangeel, J Reinshagen, D Iaconis… - Scientific data, 2022 - nature.com
Worldwide, there are intensive efforts to identify repurposed drugs as potential therapies
against SARS-CoV-2 infection and the associated COVID-19 disease. To date, the anti …

Modern tools and techniques in computer-aided drug design

T Anwar, P Kumar, AU Khan - Molecular docking for computer-aided drug …, 2021 - Elsevier
Computer-aided drug design (CADD) has become an effective tool for the development of
therapeutics. CADD approaches parallelly assist the main drug discovery pipeline in many …

Chemistry‐driven hit‐to‐lead optimization guided by structure‐based approaches

L Hoffer, C Muller, P Roche, X Morelli - Molecular Informatics, 2018 - Wiley Online Library
For several decades, hit identification for drug discovery has been facilitated by
developments in both fragment‐based and high‐throughput screening technologies …