HOME Protein Structure Prediction MUFOLD-LOOP MUFOLD-DB Clustering Members
X-ray crystallography is the main method for determining 3D protein structures. In many cases, however, flexible loop regions of proteins cannot be resolved by this approach. This leads to incomplete structures in the protein data bank, preventing further computational study and analysis of these proteins. For instance, all-atom molecular dynamics (MD) simulation studies of structure-function relationship require complete protein structures. To address this shortcoming, we have developed and implemented an efficient computational method for building missing protein loops. We have implemented the method as a simple stand-alone program MUFOLD-LOOP, which can also be used as a plugin in existing molecular modeling software, e.g., VMD. The quality and stability of the generated structures are assessed and tested via energy scoring functions and by equilibrium MD simulations. The proposed method can also be used in template-based protein structure prediction.
If you have any questions, please contact: jzxt9@missouri.edu
Files Specification
MUFOLD-LOOP Written in python. Tools for protein structure loop modeling
Example Example of loop modeling of Myosin VI using MUFOLD-LOOP
Readme The help information
Please Cite:
Jiong Zhang, Son Nguyen, Dong Xu, Yi Shang, Ioan Kosztin:
MUFOLD-LOOP: a new loop modeling tool for protein structures.