Geomol: Torsional geometric generation of molecular 3d conformer ensembles

O Ganea, L Pattanaik, C Coley… - Advances in …, 2021 - proceedings.neurips.cc
Prediction of a molecule's 3D conformer ensemble from the molecular graph holds a key
role in areas of cheminformatics and drug discovery. Existing generative models have …

[HTML][HTML] Computational methods in drug discovery

SP Leelananda, S Lindert - Beilstein journal of organic …, 2016 - beilstein-journals.org
The process for drug discovery and development is challenging, time consuming and
expensive. Computer-aided drug discovery (CADD) tools can act as a virtual shortcut …

Efficient exploration of chemical space with docking and deep learning

Y Yang, K Yao, MP Repasky, K Leswing… - Journal of Chemical …, 2021 - ACS Publications
With the advent of make-on-demand commercial libraries, the number of purchasable
compounds available for virtual screening and assay has grown explosively in recent years …

Chemical space docking enables large-scale structure-based virtual screening to discover ROCK1 kinase inhibitors

P Beroza, JJ Crawford, O Ganichkin… - Nature …, 2022 - nature.com
With the ever-increasing number of synthesis-on-demand compounds for drug lead
discovery, there is a great need for efficient search technologies. We present the successful …

DOCK 6: Impact of new features and current docking performance

WJ Allen, TE Balius, S Mukherjee… - Journal of …, 2015 - Wiley Online Library
This manuscript presents the latest algorithmic and methodological developments to the
structure‐based design program DOCK 6.7 focused on an updated internal energy function …

[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 …

Merging ligand-based and structure-based methods in drug discovery: An overview of combined virtual screening approaches

J Vázquez, M López, E Gibert, E Herrero, FJ Luque - Molecules, 2020 - mdpi.com
Virtual screening (VS) is an outstanding cornerstone in the drug discovery pipeline. A variety
of computational approaches, which are generally classified as ligand-based (LB) and …

Beware of docking!

YC Chen - Trends in pharmacological sciences, 2015 - cell.com
Docking is now routine in virtual screening or lead optimization for drug screening and
design. The number of papers related to docking has dramatically increased over the past …

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 …

Amyloid β protein and Alzheimer's disease: When computer simulations complement experimental studies

J Nasica-Labouze, PH Nguyen, F Sterpone… - Chemical …, 2015 - ACS Publications
Alzheimer's disease (AD) challenges our society with an annual estimated cost of $1.08
trillion in the United States alone by 2050. 1 AD is a progressive irreversible neurological …