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 …

Protein–protein docking: Past, present, and future

S Sunny, PB Jayaraj - The protein journal, 2022 - Springer
The biological significance of proteins attracted the scientific community in exploring their
characteristics. The studies shed light on the interaction patterns and functions of proteins in …

Computational enzyme engineering pipelines for optimized production of renewable chemicals

M Scherer, SJ Fleishman, PR Jones… - … in bioengineering and …, 2021 - frontiersin.org
To enable a sustainable supply of chemicals, novel biotechnological solutions are required
that replace the reliance on fossil resources. One potential solution is to utilize tailored …

Native ion mobility-mass spectrometry reveals the formation of β-barrel shaped amyloid-β hexamers in a membrane-mimicking environment

N Österlund, R Moons, LL Ilag, F Sobott… - Journal of the …, 2019 - ACS Publications
The mechanisms behind the Amyloid-β (Aβ) peptide neurotoxicity in Alzheimer's disease are
intensely studied and under debate. One suggested mechanism is that the peptides …

GalaxyRefine2: simultaneous refinement of inaccurate local regions and overall protein structure

GR Lee, J Won, L Heo, C Seok - Nucleic acids research, 2019 - academic.oup.com
The 3D structure of a protein can be predicted from its amino acid sequence with high
accuracy for a large fraction of cases because of the availability of large quantities of …

Building structural models of a whole mycoplasma cell

M Maritan, L Autin, J Karr, MW Covert, AJ Olson… - Journal of molecular …, 2022 - Elsevier
Building structural models of entire cells has been a long-standing cross-discipline
challenge for the research community, as it requires an unprecedented level of integration …

Gene products and processes contributing to lanthanide homeostasis and methanol metabolism in Methylorubrum extorquens AM1

P Roszczenko-Jasińska, HN Vu, GA Subuyuj… - Scientific Reports, 2020 - nature.com
Lanthanide elements have been recently recognized as “new life metals” yet much remains
unknown regarding lanthanide acquisition and homeostasis. In Methylorubrum extorquens …

In silico identification of Tretinoin as a SARS-CoV-2 envelope (E) protein ion channel inhibitor

D Dey, S Borkotoky, M Banerjee - Computers in biology and medicine, 2020 - Elsevier
Viroporins are oligomeric, pore forming, viral proteins that play critical roles in the life cycle
of pathogenic viruses. Viroporins like HIV-1 Vpu, Alphavirus 6 K, Influenza M2, HCV p7, and …

[HTML][HTML] Enhancing the hydrolytic activity of a lipase towards larger triglycerides through lid domain engineering

L Fernandez-Lopez, S Roda, A Robles-Martín… - International Journal of …, 2023 - mdpi.com
Lipases have valuable potential for industrial use, particularly those mostly active against
water-insoluble substrates, such as triglycerides composed of long-carbon chain fatty acids …

Viral rhodopsins 1 are an unique family of light-gated cation channels

D Zabelskii, A Alekseev, K Kovalev, V Rankovic… - Nature …, 2020 - nature.com
Phytoplankton is the base of the marine food chain as well as oxygen and carbon cycles and
thus plays a global role in climate and ecology. Nucleocytoplasmic Large DNA Viruses that …