Web Servers/Open Source Tools/Program Suites

  • Protein Barcode

    Protein Barcode is a reductionist approach by reducing the three dimensional structure of a given protein to a barcode format. The barcode representation can be used to compare and contrast different proteins based on their structure.

    Reference: Structure Based Barcoding of Proteins Rahul Metri, Gaurav Jerath, Govind Kailas, Nitin Gachhe , Adityabarna Pal & Vibin Ramakrishnan (2014) Protein Science 23:117–120

    URL: http://iitg.ac.in/probar/

  • Basic Protein Engineering Toolkit (bPE Toolkit)

    PbPE Toolkit is a basic protein engineering toolkit consisting of six independent programs, that can be incorporated in a pipeline of various protein structure files. The users can create their own computational workflow by the use of this toolkit. All programs are fully downloadable.

    Reference: bPE toolkit:Toolkit for Computational Protein Engineering Gaurav Jerath, Prakash K. Hazam and Vibin Ramakrishnan. Systems and Synthetic Biology. (2014) 8:337–341.

    URL: http://iitg.ac.in/bpetoolkit/

  • Geofold: Prediction of Protein Unfolding Pathways

    Geofold is a tool to map protein unfolding. Developed in Bystroff lab in RPI, Troy New York. Reference: Developing a detailed mechanistic model for protein unfolding.

    Reference:Vibin Ramakrishnan, Saeed Salem; Saipraveen Srinivasan, Mohammed Zaki, Suzanne Mathews, Wilfredo Colon and Christopher Bystroff. Proteins: Structure Function & Bioinformatics (2012), 80, 920-934.

    URL: http://www.bioinfo.rpi.edu/geofold/server.php/


    Tool for sequence optimization, developed and calibrated against a set of small to medium sized proteins. Developed in IIT Bombay in Durani Lab.

    Reference: Automated design tool for heterochiral protein folds. Ranjiit Ranbhor, Anil Kumar, Abhijit Tendulkar, Kirti Patel, Vibin Ramakrishnan & Sucheel Durani IEE ACM Transactions (under Review)