Quality assessment of docked protein interfaces using 3D convolution

Proteins play a vital role in most biological processes, most of which occur through interactions between proteins. When proteins interact they form a complex, whose functionality is different from the individual proteins in the complex. Therefore understanding protein interactions and their interfaces is an important problem. Experimental methods for this task are expensive and time consuming, which has led to the development of docking methods for predicting the structures of protein complexes. These methods produce a large number of potential solutions, and the energy functions used in these methods are not good enough to find solutions that are close to the native state of the complex. Deep learning and its ability to model complex problems has opened up the opportunity to model protein complexes and learn from scratch how to rank docking solutions. As a part of this work, we have developed a 3D convolutional network approach that uses raw atomic densities to address this problem. Our method achieves performance which is on par with state-of-art methods. We have evaluated our model on docked protein structures simulated from four docking tools namely ZDOCK, HADDOCK, FRODOCK and ClusPro on targets from Docking Benchmark Data version 5 (DBD5).

Name thesis:degree_name

Master of Science (M.S.)

Level thesis:degree_level

Masters

Discipline thesis:degree_discipline

Computer Science

Grantor dc:publisher

Colorado State University. Libraries

Year dc:date.issued

2021

Authors dc:creator

• Bontha, Mridula, author
• Ben-Hur, Asa, advisor
• Beveridge, J. Ross, committee member
• King, Emily J., committee member

Statement dc:rights

• Copyright and other restrictions may apply. User is responsible for compliance with all applicable laws. For information about copyright law, please see https://libguides.colostate.edu/copyright.

Language dc:language.iso

eng, English

Identifier URI

https://doi.org/10.25675/3.02505

OAI identifier oai:identifier

oai:mountainscholar.org:10217/232476