Structural basis of potential inhibitors targeting SARS-CoV-2 main protease

HM Mengist, T Dilnessa, T Jin - Frontiers in Chemistry, 2021 - frontiersin.org
The Coronavirus disease-19 (COVID-19) pandemic is still devastating the world causing
significant social, economic, and political chaos. Corresponding to the absence of globally …

[HTML][HTML] Integrating structure-based approaches in generative molecular design

M Thomas, A Bender, C de Graaf - Current Opinion in Structural Biology, 2023 - Elsevier
Generative molecular design for drug discovery and development has seen a recent
resurgence promising to improve the efficiency of the design-make-test-analyse cycle; by …

Automated topology builder version 3.0: Prediction of solvation free enthalpies in water and hexane

M Stroet, B Caron, KM Visscher… - Journal of chemical …, 2018 - ACS Publications
The ability of atomic interaction parameters generated using the Automated Topology
Builder and Repository version 3.0 (ATB3. 0) to predict experimental hydration free …

Testing and validation of the Automated Topology Builder (ATB) version 2.0: prediction of hydration free enthalpies

KB Koziara, M Stroet, AK Malde, AE Mark - Journal of computer-aided …, 2014 - Springer
To test and validate the Automated force field Topology Builder and Repository (ATB;
http://compbio. biosci. uq. edu. au/atb/) the hydration free enthalpies for a set of 214 drug-like …

Learning subpocket prototypes for generalizable structure-based drug design

Z Zhang, Q Liu - International Conference on Machine …, 2023 - proceedings.mlr.press
Generating molecules with high binding affinities to target proteins (aka structure-based
drug design) is a fundamental and challenging task in drug discovery. Recently, deep …

[PDF][PDF] The art and practice of structure‐based drug design: a molecular modeling perspective

RS Bohacek, C McMartin, WC Guida - Medicinal research reviews, 1996 - azevedolab.net
The conceptual basis for structure-based drug design was formulated 100 years ago by Emil
Fischer. 1 His" lock and key" hypothesis is a constantly recurring leitmotif in modern drug …

Drug repurposing for viral cancers: A paradigm of machine learning, deep learning, and virtual screening‐based approaches

F Ahmed, IS Kang, KH Kim, A Asif… - Journal of Medical …, 2023 - Wiley Online Library
Cancer management is major concern of health organizations and viral cancers account for
approximately 15.4% of all known human cancers. Due to large number of patients, efficient …

The process of structure-based drug design

AC Anderson - Chemistry & biology, 2003 - cell.com
The field of structure-based drug design is a rapidly growing area in which many successes
have occurred in recent years. The explosion of genomic, proteomic, and structural …

Further development and validation of empirical scoring functions for structure-based binding affinity prediction

R Wang, L Lai, S Wang - Journal of computer-aided molecular design, 2002 - Springer
New empirical scoring functions have been developed to estimate the binding affinity of a
given protein-ligand complex with known three-dimensional structure. These scoring …

The PDBbind database: methodologies and updates

R Wang, X Fang, Y Lu, CY Yang… - Journal of medicinal …, 2005 - ACS Publications
We have developed the PDBbind database to provide a comprehensive collection of
binding affinities for the protein− ligand complexes in the Protein Data Bank (PDB). This …