Software for molecular docking: a review

NS Pagadala, K Syed, J Tuszynski - Biophysical reviews, 2017 - Springer
Molecular docking methodology explores the behavior of small molecules in the binding site
of a target protein. As more protein structures are determined experimentally using X-ray …

Recent structural insights into cytochrome P450 function

FP Guengerich, MR Waterman, M Egli - Trends in pharmacological …, 2016 - cell.com
Cytochrome P450 (P450) enzymes are important in the metabolism of drugs, steroids, fat-
soluble vitamins, carcinogens, pesticides, and many other types of chemicals. Their catalytic …

Structural biology in the clouds: the WeNMR-EOSC ecosystem

RV Honorato, PI Koukos, B Jiménez-García… - Frontiers in molecular …, 2021 - frontiersin.org
Structural biology aims at characterizing the structural and dynamic properties of biological
macromolecules at atomic details. Gaining insight into three dimensional structures of …

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 …

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 …

COVID-19 spike-host cell receptor GRP78 binding site prediction

IM Ibrahim, DH Abdelmalek, ME Elshahat, AA Elfiky - Journal of infection, 2020 - Elsevier
Objectives Understanding the novel coronavirus (COVID-19) mode of host cell recognition
may help to fight the disease and save lives. The spike protein of coronaviruses is the main …

[HTML][HTML] ATG9A and ATG2A form a heteromeric complex essential for autophagosome formation

AR van Vliet, GN Chiduza, SL Maslen, VE Pye, D Joshi… - Molecular cell, 2022 - cell.com
Summary ATG9A and ATG2A are essential core members of the autophagy machinery.
ATG9A is a lipid scramblase that allows equilibration of lipids across a membrane bilayer …

Independent se (3)-equivariant models for end-to-end rigid protein docking

OE Ganea, X Huang, C Bunne, Y Bian… - arXiv preprint arXiv …, 2021 - arxiv.org
Protein complex formation is a central problem in biology, being involved in most of the cell's
processes, and essential for applications, eg drug design or protein engineering. We tackle …

HawkDock: a web server to predict and analyze the protein–protein complex based on computational docking and MM/GBSA

G Weng, E Wang, Z Wang, H Liu, F Zhu… - Nucleic acids …, 2019 - academic.oup.com
Protein–protein interactions (PPIs) play an important role in the different functions of cells,
but accurate prediction of the three-dimensional structures for PPIs is still a notoriously …

The ClusPro web server for protein–protein docking

D Kozakov, DR Hall, B Xia, KA Porter, D Padhorny… - Nature protocols, 2017 - nature.com
Abstract The ClusPro server (https://cluspro. org) is a widely used tool for protein–protein
docking. The server provides a simple home page for basic use, requiring only two files in …