In the post-genomics life sciences, it is crucial to comprehend how proteins interact with small molecules because many crucial proteins require cofactors or small molecule ligands to operate. Additionally, there is a critical need to produce small molecule inhibitors based on the study of protein-ligand interactions for the creation of novel drugs. Analyzing the structures of known protein-ligand complexes in the Protein Data Bank will be the first step towards understanding protein-ligand interactions (PDB). Depending on the ligand conformation, the three-dimensional (3D) ligand-binding structure, and the relative position and orientation of any critical residues at the ligand-binding site, it is frequently necessary to cluster the pertinent ligand-binding structures in the analysis.
Fig 1. Scheme used in the PDB-Ligand database construction. (Shin J-M, et al. 2005)
The size of protein ligand binding structure databases has greatly increased with the advancement of structural genomics. Alfa Chemistry provides specialist services for ligand database projects to help with the creation of distinctive protein ligand binding structure databases that concentrate on the structures of the ligand or ligand binding site. These ligand-binding structures may be even more crucial in a variety of post-genomics applications, such as the creation of small molecule inhibitors for the development of novel medications.
Alfa Chemistry will create a three-dimensional database of ligand binding structures derived from the PDB that enables interactive clustering of ligand binding structures, such as root mean square deviation (RMSD), based on user-specific clustering criteria, such as adaptable combinations of atoms using ligand binding sites. We will demonstrate an online database with PDB ligands in MDL Mol file format. By computing Tanimoto coefficients and 3D superposition, compounds' structural similarity can be determined. Tanimoto coefficients are a method for determining the topological similarity of PDB ligands to recognized medicines. The Ligand Database Project provides very useful information on ligand-protein binding structures and can be easily used to compare or classify ligand binding structures in three dimensions.
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For all ligand binding structures in the PDB, the ligand binding structure database created by the Ligand Database Project may be utilized as an interactive structural analysis and clustering tool. The use of straightforward and adaptable ligand clustering techniques will also make it easier to generate numerous structural comparisons of various related ligand binding structures. This database will be a useful tool for many drug discovery applications in the creation of improved scoring systems and a better understanding of ligand binding structures.
Future Directions and Applications
At least once every four months, the ligand binding structures in our database will be updated. In addition, the speed and ease of ligand-binding structure clustering methodologies and algorithms will be increased. Future developments will also incorporate sub-structural searches between ligand structures. The binding structures of various functional groups in several significant ligands may be examined using this capability. Considering that it offers more thorough details regarding the ligand binding structure, protein sequence and structural data based on clustered ligand binding structures would also be helpful.
Our ligands database project services significantly reduce costs, facilitate further experimentation, and accelerate the drug design process for our global customers. Our personalized, full-service approach will meet your innovative learning needs. If you are interested in our services, please feel free to contact us. We would be happy to work with you and see you succeed!
- Shin J-M, et al. (2005). "PDB-Ligand: A Ligand database based on PDB for The Automated and Customized Classification of Ligand-Binding Structures." Nucleic Acids Res. 33: D238-D241.