Development of Biological Database for Protein-Ligand Interaction from Natural Resources Using Molecular Modelling Software TechniquesEbolatobacconeemturmerichibiscusdockingdatabaseEbola virus is single-stranded, negative RNA linear genome that encodes for seven proteins. The Ebola virus causes hemorrhagic fever...
, BindingDB (http://www.bindingdb.org;Liu et al. 2007), protein–ligand interaction database, PLID (http://203.199.182.73/gnsmmg/databases/plid/;Reddy et al. 2008), and so on. View chapter Explore book Exploring the binding potential of carbon nanotubes and fullerene towards major drug...
Mutated sequences were generated from the original sequences based on the mutations denoted in each database. We used the alpha-carbon 3D coordinates of each amino acid as the coordinates of that amino acid from the protein’s Protein Data Bank (PDB) file. The receptor–ligand index was ...
DrugBank is a bioinformatics/cheminformatics resource that combines detailed drug data with comprehensive drug target information [12]. A number of ligand-protein interaction databases have also emerged including LigBase [13], PDBsite [14], SitesBase [15], MSDsite [16], PDB-Ligand [17] and ...
All bait-prey pairs (75 baits × 78 preys) were considered for the RRS, and 88 were selected that had the lowest chances of interaction, using the following criteria: (1) absence from the PRS; (2) absence from the Integrated Interactions Database ver. 2018-11 (ref.49), thereby en...
For example, PSEA using the proteome-unique sets, such as protein-protein interaction database, could provide biological insights that are distinguished from those by genome-based annotations. Furthermore, inclusion of all differentially abundant proteins or genes with PSEA will avoid missing possible...
2024. “PLINDER: The Protein-Ligand Interactions Dataset and Evaluation Resource.” bioRxiv ICML'24 ML4LMS Please see the citation file for details. About Protein Ligand INteraction Dataset and Evaluation Resource plinder.sh Resources Readme License Apache-2.0 license Citation Cite this ...
With the growth of protein structure data, the analysis of molecular interactions between ligands and their target molecules is gaining importance. PLIP, the protein–ligand interaction profiler, detects and visualises these interactions and provides data in formats suitable for further processing. PLIP ...
We collaborate with one such group, led by Marc Vidal, whose aim is the construction of a protein-protein interaction map for C. elegans. In this paper we first describe WISTdb, a database designed to store the interaction data generated in Marc Vidal’s laboratory. We then describe...
Protein-protein interaction and quaternary structure. Q. Rev. Biophys. 41, 133–180 (2008). Article CAS PubMed Google Scholar Thorn, K. S. & Bogan, A. A. ASEdb: a database of alanine mutations and their effects on the free energy of binding in protein interactions. Bioinformatics 17,...