Computational Tools/Web servers
1. Protein Barcode
Description: Tool structure based barcoding of proteins (MID IITG)
Reference: Structure Based Barcoding of Proteins Rahul Metri, Gaurav Jerath, Govind Kailas, Nitin Gachhe , Adityabarna Pal & Vibin Ramakrishnan (2014) Protein Science 23:117–120
2. Basic Protein Engineering Toolkit (bPE Toolkit, MID IITG)
Description: Consists of six useful protein modeling tools
Reference: bPE toolkit:Toolkit for Computational Protein Engineering Gaurav Jerath, Prakash K. Hazam and Vibin Ramakrishnan. Systems and Synthetic Biology. (2014) 8:337–341.
3. Geofold: Protein Unfolding Pathway prediction server (Bystroff Lab)
Description: Tool for predicting protein unfolding pathways
Reference: Vibin Ramakrishnan, Saeed Salem; Saipraveen Srinivasan, Mohammed Zaki, Suzanne Mathews, Wilfredo Colon and Christopher Bystroff. Proteins: Structure Function & Bioinformatics (2012), 80, 920-934.
4. IDEAS (Durani Lab)
Description: Software for protein inverse design
Reference: Ranbhor Ranjit, Anil Kumar, Abhijit Tendulkar, Kirti Patel, Vibin Ramakrishnan*, and Susheel Durani. IDeAS: Automated Design Tool for Hetero-chiral Protein Folds. Physical biology. (2018), doi::10.1088/1478-3975/aacdc3
5. Time Piece model for Virtual Activity Profiling of Drug molecules (IBAB)
Description: Tool virtual activity profiling of drugs.
Reference: Aimy Sebastian, Andreas Bender and Vibin Ramakrishnan*; Virtual Activity Profiling of Bioactive Molecules by 1D Fingerprinting. Molecular Informatics (2010) 29, 773-779.