Related Experiment Video
Updated: Mar 15, 2026
10:29
Quantitative Structure-Activity Relationship, Activity Prediction, and Molecular Dynamics of Non-nucleotide Reverse Transcriptase Inhibitors
Published on: May 9, 2025
2.6K
Ligand-based virtual screening interface between PyMOL and LiSiCA.
Athira Dilip1, Samo Lešnik1, Tanja Štular2
1National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia.
Journal of Cheminformatics
|September 9, 2016
Summary
Ligand-based virtual screening using PyMOL and LiSiCA aids drug discovery. This interface helps identify novel bioactive molecules by screening large chemical databases efficiently.
Area of Science:
- Computational chemistry
- Drug discovery
- cheminformatics
Background:
- Ligand-based virtual screening (LBVS) is crucial for early-stage drug development.
- LBVS utilizes the similarity principle to reduce large chemical databases for experimental testing.
- It can identify novel bioactive molecules with diverse scaffolds, enhancing structural variability.
Purpose of the Study:
- To present an interface between PyMOL and LiSiCA for LBVS.
- To demonstrate the utility of this interface in drug discovery.
Main Methods:
- Development of an interface between PyMOL and LiSiCA software.
- Application of the interface for ligand-based virtual screening.
Main Results:
- Successful integration of PyMOL and LiSiCA.
- Demonstration of the interface's capability in early drug discovery stages.
Conclusions:
- The PyMOL-LiSiCA interface streamlines LBVS.
- This tool facilitates efficient identification of potential drug candidates.
Related Concept Videos
02:40Ligand Binding Sites
9.0K
9.0K
02:40Ligand Binding Sites
15.6K
Proteins are dynamic macromolecules that carry out a wide variety of essential processes; however, the activities of most proteins depend on their interactions with other molecules or ions, known as ligands.
Protein-ligand interactions are quite specific; even though numerous potential ligands surround a cellular protein at any given time, only a particular ligand can bind to that protein. Moreover, a ligand binds only to a dedicated area on the surface of the protein, known as the...
Protein-ligand interactions are quite specific; even though numerous potential ligands surround a cellular protein at any given time, only a particular ligand can bind to that protein. Moreover, a ligand binds only to a dedicated area on the surface of the protein, known as the...
15.6K
00:49Ligand Binding and Linkage
5.9K
Allosteric proteins have more than one ligand binding site; the binding of a ligand to any of these sites influences the binding of ligands to the other sites. When a protein is allosteric, its binding sites are called coupled or linked. In the case of enzymes, the site that binds to the substrate is known as the active site and the other site is known as the regulatory site. When a ligand binds to the regulatory site, this leads to conformational changes in the protein that can influence...
5.9K
00:49Ligand Binding and Linkage
4.2K
4.2K
02:00Molecular Models
45.1K
Physical models representing molecular architectures of chemical compounds play essential roles in understanding chemistry. The use of molecular models makes it easier to visualize the structures and shapes of atoms and molecules.
45.1K
02:04Protein-protein Interfaces
14.9K
Many proteins form complexes to carry out their functions, making protein-protein interactions (PPIs) essential for an organism's survival. Most PPIs are stabilized by numerous weak noncovalent chemical forces. The physical shape of the interfaces determines the way two proteins interact. Many globular proteins have closely-matching shapes on their surfaces, which form a large number of weak bonds. Additionally, many PPIs occur between two helices or between a surface cleft and a...
14.9K