Analyzing the motion of flexible protein loops is becoming increasingly important in understanding the various roles that proteins play in human body. LoopTK is a C++ based object-oriented toolkit which models the kinematics of a protein chain and provides methods to explore its motion space. In LoopTK, a protein chain is modeled as a robot manipulator with bonds acting as arms and the dihedral degree of freedoms acting as joints.
LoopTK is designed specifically to model the kinematics of protein loops, but it can be used to analyze the motion of any part of the protein chain. LoopTK provides methods for sampling the conformation space of protein loops as well as the self motion space of a loop. Example applications for LoopTK include x-ray crystallography, homology modeling, and drug design.
LoopTK was developed in close collaboration with the Joint Center for Structural Genomics (JCSG) at the Stanford Linear Accelerator Center. Now a part of the JCSG's protein structure determination process, loopTK models missing protein fragments into experimental data (http://smb.slac.stanford.edu/XpleoServer/Xpleo.jsp
This material is based upon work supported by the National Science Foundation under Grant No. 0443939. Any opinions, findings, and conclusions or recommendations expressed in the above material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation.
Purpose/Synopsis: Provide an easy to use API to model, manipulate, and analyze proteins and their loops. Integrate existing models and algorithms into a single modeling framework - for example, rotamers, PDB files, inverse kinematic algorithms, etc.
Audience: Biomedical and computational researchers interested in protein loop kinematics.
Long Term Goals and Related Uses: Integrate the toolkit with other modeling software.
Allow researchers to quickly and easily develop analyses on proteins.
Become an integral part of automating the generation of protein models from x-ray crystallographic data.
Ontology Classification: Protein_Interaction_Modeling
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Keywords: protein 3d structure, protein chain, protein kinematics, protein loop, protein modeling
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