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MSc Thesis Defense Announcement of Lokesh Gupta:"Molecular Distance Geometry Approach for solving Alpha Carbon Trace Problem"

Tuesday, May 19, 2020 - 10:00 to 12:00


The School of Computer Science is pleased to present…

MSc Thesis Defense by: Lokesh Gupta

Date: Tuesday May 19, 2020
Time: 10:00 am – 12:00 pm


The alpha-carbon trace problem is to determine the 3 -D coordinates of the main chain atoms (C, N, and O) from just the alpha carbon coordinates. This thesis presents a novel approach to solving the alpha carbon trace problem. The current approach uses the algorithms which are used to solve the Molecular Distance Geometry Problem in order to find the coordinates of the atoms in the peptide plane of a given protein. Once, the coordinates of the atoms (alpha carbon, C, N, and O) in the single peptide plane are computed, the two alpha carbon atoms are aligned with the first two alpha carbon atoms in the alpha carbon trace by finding the appropriate rotation and translation. The same rotations and translations are applied to all the other atoms in the peptide plane (C, N, and O). The process is then repeated for the entire trace and the coordinates of all the atoms in the Main Chain of the protein are retrieved. In order to predict the Side Chain atoms from the Main Chain, SCWRL4.0 is used. The output generated by SCWRL4.0 is then subjected to LBFGS energy minimizer using a tool called MESHI. The key advantage of using our approach is that eliminates the building and searching of a huge protein fragment library. Experiments show that our approach is highly comparable to other approaches such as BBQ, PD2Main, and PULCHRA for solving the alpha carbon trace problem. 
Keywords:Molecular Distance Geometry Problem, Alpha Carbon Trace Problem, Protein Structure Prediction

Thesis Committee:

Internal Reader: Dr. Dan Wu      
External Reader: Dr. Myron Hlynka         
Advisor: Dr. Asish Mukhopadhyay
Chair: Dr. Christie Ezeife

MSc Thesis Defense Announcement

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