In silico methods and tools for drug discovery

B Shaker, S Ahmad, J Lee, C Jung, D Na - Computers in biology and …, 2021 - Elsevier
In the past, conventional drug discovery strategies have been successfully employed to
develop new drugs, but the process from lead identification to clinical trials takes more than …

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 …

Protein structure prediction with in-cell photo-crosslinking mass spectrometry and deep learning

K Stahl, A Graziadei, T Dau, O Brock… - Nature …, 2023 - nature.com
While AlphaFold2 can predict accurate protein structures from the primary sequence,
challenges remain for proteins that undergo conformational changes or for which few …

Benchmarking AlphaFold for protein complex modeling reveals accuracy determinants

R Yin, BY Feng, A Varshney, BG Pierce - Protein Science, 2022 - Wiley Online Library
High‐resolution experimental structural determination of protein–protein interactions has led
to valuable mechanistic insights, yet due to the massive number of interactions and …

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 …

The HDOCK server for integrated protein–protein docking

Y Yan, H Tao, J He, SY Huang - Nature protocols, 2020 - nature.com
Abstract The HDOCK server (http://hdock. phys. hust. edu. cn/) is a highly integrated suite of
homology search, template-based modeling, structure prediction, macromolecular docking …

Comparative host-coronavirus protein interaction networks reveal pan-viral disease mechanisms

DE Gordon, J Hiatt, M Bouhaddou, VV Rezelj, S Ulferts… - Science, 2020 - science.org
INTRODUCTION The emergence of three lethal coronaviruses in< 20 years and the urgency
of the COVID-19 pandemic have prompted efforts to develop new therapeutic strategies …

Macromolecular modeling and design in Rosetta: recent methods and frameworks

JK Leman, BD Weitzner, SM Lewis, J Adolf-Bryfogle… - Nature …, 2020 - nature.com
The Rosetta software for macromolecular modeling, docking and design is extensively used
in laboratories worldwide. During two decades of development by a community of …

Progress in molecular docking

J Fan, A Fu, L Zhang - Quantitative Biology, 2019 - Springer
Background In recent years, since the molecular docking technique can greatly improve the
efficiency and reduce the research cost, it has become a key tool in computer-assisted drug …

Role of changes in SARS-CoV-2 spike protein in the interaction with the human ACE2 receptor: An in silico analysis

JT Ortega, ML Serrano, FH Pujol, HR Rangel - EXCLI journal, 2020 - pmc.ncbi.nlm.nih.gov
Many human viral diseases are a consequence of a zoonotic event. Some of the diseases
caused by these zoonotic events have affected millions of people around the world, some of …