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 …

[HTML][HTML] Long non-coding RNA and RNA-binding protein interactions in cancer: experimental and machine learning approaches

H Shaath, R Vishnubalaji, R Elango… - Seminars in cancer …, 2022 - Elsevier
Understanding the complex and specific roles played by non-coding RNAs (ncRNAs), which
comprise the bulk of the genome, is important for understanding virtually every hallmark of …

Omicron and Delta variant of SARS‐CoV‐2: a comparative computational study of spike protein

S Kumar, TS Thambiraja, K Karuppanan… - Journal of medical …, 2022 - Wiley Online Library
Emerging severe acute respiratory syndrome coronavirus type 2 (SARS‐CoV‐2) variants,
especially those of concern, may have an impact on the virus's transmissibility and …

Omicron (BA. 1) and sub‐variants (BA. 1.1, BA. 2, and BA. 3) of SARS‐CoV‐2 spike infectivity and pathogenicity: A comparative sequence and structural‐based …

S Kumar, K Karuppanan… - Journal of medical …, 2022 - Wiley Online Library
The Omicron variant of the severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2)
has now spread throughout the world. We used computational tools to assess the spike …

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 …

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 …

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 …

Structure of fish Toll-like receptors (TLR) and NOD-like receptors (NLR)

BR Sahoo - International journal of biological macromolecules, 2020 - Elsevier
Innate immunity driven by pattern recognition receptor (PRR) protects the host from invading
pathogens. Aquatic animals like fish where the adaptive immunity is poorly developed …

A nuclease that mediates cell death induced by DNA damage and poly (ADP-ribose) polymerase-1

Y Wang, R An, GK Umanah, H Park, K Nambiar… - Science, 2016 - science.org
INTRODUCTION Poly (ADP-ribose)(PAR) polymerase-1 (PARP-1) is a nuclear enzyme
responding to oxidative stress and DNA damage. Excessive activation of PARP-1 causes an …

How good is automated protein docking?

D Kozakov, D Beglov, T Bohnuud… - Proteins: Structure …, 2013 - Wiley Online Library
The protein docking server ClusPro has been participating in critical assessment of
prediction of interactions (CAPRI) since its introduction in 2004. This article evaluates the …