Web Servers/Open Source Tools/Program Suites
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
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.
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.
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)