Related Experiment Video
Updated: Sep 23, 2025

Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins
Published on: July 8, 2025
Selection of Suitable Protein Structure from Protein Data Bank: An Important Step in Structure-based Drug Design
Prashant R Murumkar1, Mayank Kumar Sharma1, Pradeep Gupta2
1Faculty of Pharmacy, The Maharaja Sayajirao University of Baroda, Vadodara - 390001, India.
Abstract:
The selection of a protein structure is an important step for the success of the drug discovery process using structure-based design. Selection of the right crystal structure is critical as multiple crystal structures are available for the same protein in the Protein Data Bank (PDB). In this communication, we have discussed a systematic approach for selecting the right type of protein structure. Selecting crystal structures of TACE, 11β-HSD1, DprE1, and SARS-CoV-2 Mpro enzymes for some case studies have been discussed for illustration.
Related Concept Videos
Protein Organization
The primary structure of a protein is its amino acid sequence....
Structure-Activity Relationships and Drug Design
SAR studies the intricate relationship between a drug's chemical structure and biological activity. It focuses on understanding how modifications to a drug's structure can influence...
Protein Families
Protein-protein Interfaces
Conserved Binding Sites
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally...
Gene Families
Occasionally these regions can be adapted to take on new roles within the organism, becoming novel genes...

