Molecular docking: challenges, advances and its use in drug discovery perspective

S Saikia, M Bordoloi - Current drug targets, 2019 - ingentaconnect.com
Molecular docking is a process through which small molecules are docked into the
macromolecular structures for scoring its complementary values at the binding sites. It is a …

[HTML][HTML] Protein–protein interaction prediction with deep learning: A comprehensive review

F Soleymani, E Paquet, H Viktor, W Michalowski… - Computational and …, 2022 - Elsevier
Most proteins perform their biological function by interacting with themselves or other
molecules. Thus, one may obtain biological insights into protein functions, disease …

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 …

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 …

HDOCK: a web server for protein–protein and protein–DNA/RNA docking based on a hybrid strategy

Y Yan, D Zhang, P Zhou, B Li… - Nucleic acids research, 2017 - academic.oup.com
Protein–protein and protein–DNA/RNA interactions play a fundamental role in a variety of
biological processes. Determining the complex structures of these interactions is valuable, in …

HPEPDOCK: a web server for blind peptide–protein docking based on a hierarchical algorithm

P Zhou, B Jin, H Li, SY Huang - Nucleic acids research, 2018 - academic.oup.com
Protein–peptide interactions are crucial in many cellular functions. Therefore, determining
the structure of protein–peptide complexes is important for understanding the molecular …

Molecular mechanism of evolution and human infection with SARS-CoV-2

J He, H Tao, Y Yan, SY Huang, Y Xiao - Viruses, 2020 - mdpi.com
The outbreak of a novel coronavirus, which was later formally named the severe acute
respiratory coronavirus 2 (SARS-CoV-2), has caused a worldwide public health crisis …

Critical assessment of methods for predicting the 3D structure of proteins and protein complexes

SJ Wodak, S Vajda, MF Lensink… - Annual review of …, 2023 - annualreviews.org
Advances in a scientific discipline are often measured by small, incremental steps. In this
review, we report on two intertwined disciplines in the protein structure prediction field …

Molecular docking simulation reveals ACE2 polymorphisms that may increase the affinity of ACE2 with the SARS-CoV-2 Spike protein

M Calcagnile, P Forgez, A Iannelli, C Bucci, M Alifano… - Biochimie, 2021 - Elsevier
There is increasing evidence that ACE2 gene polymorphism can modulate the interaction
between ACE2 and the SARS-CoV-2 spike protein affecting the viral entry into the host cell …

Dual-mechanism glycolipidpeptide with high antimicrobial activity, immunomodulatory activity, and potential application for combined antibacterial therapy

M Niu, X Gu, J Yang, H Cui, X Hou, Y Ma, C Wang… - ACS …, 2023 - ACS Publications
Bacterial drug resistance is becoming increasingly serious, and it is urgent to develop
effective antibacterial drugs. Antimicrobial peptides (AMPs), as potential candidates against …