Summary: LigDig is a web server designed to answer questions that previously required several independent queries to diverse data sources. It also performs basic manipulations and analyses of the structures of protein–ligand complexes. The LigDig webserver is modular...
Protein-protein interaction is important in molecular and cellular biology for catalysis, regulation, immune response, and inhibition. Therefore, it is of interest to decipher PPI for the understanding of molecular biology events. Experimental methods such as yeast two-hybrid and biophysical (X-ray, ...
Comparative Study of Molecular Interaction of Quercetin and Imatinib with BCR-ABL Fusion Protein In-Silico for the Selective Anti-CML Activity of Quercetin The non-covalent protein ligand interactions were detected using protein鈥搇igand interaction profiler (PLIP) webserver. Results: The mean binding...
Protein-Ligand Interaction Profiler (PLIP) Analyze noncovalent protein-ligand interactions in 3D structures with ease. Use CaseWeb ServerDockerSingularityPython Module "I want to analyze my protein-ligand complex!"✔️✔️🟡❌ "I want to analyzea billionprotein-ligand complexes!"❌🟡✔...
A Web server, DNAbinder, has been set up for discrimination, which has the options to select the discrimination method for DNA-binding domains or DNA-binding proteins. It is available at http://www.imtech.res.in/ raghava/dnabinder/. Figure 7.13 shows the prediction procedure using DNAbinder...
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 ...
Protein Interactions Calculator (PIC) server (http://pic.mbu.iisc.ernet.in) and LigPlot+ were used for protein-ligand interaction analysis. This program is applicable for depicting schematic diagrams of hydrogen and hydrophobic contact in protein-ligand complex41,42. Molecular dynamics (MD) ...
While the binding of retinol to apo CRBP-I is modulated by changes in the protein dynamics around the portal region that are induced by an initial nonspecific interaction of the ligand with the protein surface (27), experiments in progress indicate that retinol binding to CRBP-II does not ...
(Fig.3c, e). In our quantitative analysis, only seven proteins from the test set, represented in 79 PDB structures, were found to adopt both DFG-in and DFG-out conformations, as annotated by the Kinase–Ligand Interaction Fingerprints and Structures (KLIFS) web server39. Figure3f and g ...
ProLIF (Protein-Ligand Interaction Fingerprints) is a tool designed to generate interaction fingerprints for complexes made of ligands, protein, DNA or RNA molecules extracted from molecular dynamics trajectories, docking simulations and experimental structures. ...