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DBAASP v3: database of antimicrobial/cytotoxic activity and structure of peptides as a resource for development of new therapeutics

Malak Pirtskhalava, Anthony A Amstrong, Maia Grigolava, Mindia Chubinidze, Evgenia Alimbarashvili, Boris Vishnepolsky, Andrei Gabrielian, Alex Rosenthal, Darrell E Hurt, Michael Tartakovsky
2020 Nucleic Acids Research  
The Database of Antimicrobial Activity and Structure of Peptides (DBAASP) is an open-access, comprehensive database containing information on amino acid sequences, chemical modifications, 3D structures  ...  Furthermore, DBAASP has implemented a structure modelling pipeline that automates the setup, execution and upload of molecular dynamics (MD) simulations of database peptides.  ...  These and many other properties of the database make it a comprehensive resource to perform structure-activity relationship studies and to develop models for the de novo design of peptides with desired  ... 
doi:10.1093/nar/gkaa991 pmid:33151284 fatcat:6m6nixrjr5gqxj3dmptxftkmne

ENNAVIA is an innovative new method which employs neural networks for antiviral and anti-coronavirus activity prediction for therapeutic peptides [article]

Patrick Brendan Timmons, Chandralal M Hewage
2021 bioRxiv   pre-print
As the quantity of sequencing data grows annually, the development of an accurate in silico method for the prediction of peptide antiviral activities is important.  ...  Antiviral peptides often possess excellent biological activity and a favourable toxicity profile, and therefore represent a promising field of novel antiviral drugs.  ...  Acknowledgements The authors would also like to thank University College Dublin for the Research Scholarship granted to P.B.T.  ... 
doi:10.1101/2021.03.25.436982 fatcat:cakycirycjac7efsxpz4bhusda

Mechanistic Understanding from Molecular Dynamics in Pharmaceutical Research 2: Lipid Membrane in Drug Design

Tomasz Róg, Mykhailo Girych, Alex Bunker
2021 Pharmaceuticals  
In the standard "lock and key" paradigm, only the interaction between the drug and a specific active site of a specific protein is considered; the environment in which the drug acts is, from a biophysical  ...  interested in exploring how the tool of MD simulation can be applied to their research and computational scientists interested in exploring the possibility of a pharmaceutical context for their research  ...  Author Contributions: All authors have read and agreed to the published version of the manuscript. Funding: This research received no external funding.  ... 
doi:10.3390/ph14101062 pmid:34681286 pmcid:PMC8537670 fatcat:2ybd7h6hafarfhmh7jf7kahokq