Worldwide Protein Data Bank (wwPDB): A virtual treasure for research in biotechnology

P Behzadi, M Gajdács - European Journal of Microbiology and …, 2022 - akjournals.com
Abstract The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RSCB
PDB) provides a wide range of digital data regarding biology and biomedicine. This huge …

Navigating transcriptomic connectivity map** workflows to link chemicals with bioactivities

I Shah, J Bundy, B Chambers, LJ Everett… - Chemical research in …, 2022 - ACS Publications
Screening new compounds for potential bioactivities against cellular targets is vital for drug
discovery and chemical safety. Transcriptomics offers an efficient approach for assessing …

In silico Prediction, Characterization, Molecular Docking, and Dynamic Studies on Fungal SDRs as Novel Targets for Searching Potential Fungicides Against …

M Aamir, VK Singh, MK Dubey, M Meena… - Frontiers in …, 2018 - frontiersin.org
Vascular wilt of tomato caused by Fusarium oxysporum f. sp. lycopersici (FOL) is one of the
most devastating diseases, that delimits the tomato production worldwide. Fungal short …

Spectroscopic and quantum/classical mechanics based computational studies to compare the ability of andrographolide and its derivative to inhibit nitric oxide …

BG AS, JC Prasana, S Muthu, CS Abraham… - Spectrochimica Acta Part …, 2019 - Elsevier
The inhibition of the enzyme Nitric Oxide Synthase by a bioactive compounds results in it
possessing anti-inflammatory property. The ability of Andrographolide and its derivative …

No dance, no partner! A tale of receptor flexibility in docking and virtual screening

A Basciu, L Callea, S Motta, AMJJ Bonvin… - Annual Reports in …, 2022 - Elsevier
Modern drug design relies on a detailed understanding of the molecular recognition process
by which biological partners such as a protein and a drug interact and bind to each other …

Fragment-to-lead tailored in silico design

M Rachman, S Piticchio, M Majewski, X Barril - Drug Discovery Today …, 2021 - Elsevier
Fragment-based drug discovery (FBDD) emerged as a disruptive technology and became
established during the last two decades. Its rationality and low entry costs make it appealing …

Novel combinations of experimental and computational analysis tested on the binding of metalloprotoporphyrins to albumin

J Hu, EH Soraiz, CN Johnson, B Demeler… - International journal of …, 2019 - Elsevier
Abstract The evidence that Human Serum Albumin (HSA) binds metal ions and
organometallic compounds has generated interest in its physiological role as a …

[HTML][HTML] A community proposal to integrate structural bioinformatics activities in ELIXIR (3D-Bioinfo Community)

C Orengo, S Velankar, S Wodak, V Zoete… - …, 2020 - ncbi.nlm.nih.gov
Structural bioinformatics provides the scientific methods and tools to analyse, archive,
validate, and present the biomolecular structure data generated by the structural biology …

Graph Representation Learning for Interactive Biomolecule Systems

X **ong, B Zhou, YG Wang - arxiv preprint arxiv:2304.02656, 2023 - arxiv.org
Advances in deep learning models have revolutionized the study of biomolecule systems
and their mechanisms. Graph representation learning, in particular, is important for …

On identifying collective displacements in apo-proteins that reveal eventual binding pathways

D Dube, N Ahalawat, H Khandelia… - PLoS computational …, 2019 - journals.plos.org
Binding of small molecules to proteins often involves large conformational changes in the
latter, which open up pathways to the binding site. Observing and pinpointing these rare …