Development and application of bioinformatics tools for protein loop modelling

Martín Hernández, Iván (2019). Development and application of bioinformatics tools for protein loop modelling. Thesis (Master thesis), E.T.S. de Ingeniería Agronómica, Alimentaria y de Biosistemas (UPM). https://doi.org/10.5281/zenodo.3665304.

Description

Title: Development and application of bioinformatics tools for protein loop modelling
Author/s:
  • Martín Hernández, Iván
Contributor/s:
  • Chacón Montes, Pablo
  • Fernández Pacios, Luis
Item Type: Thesis (Master thesis)
Masters title: Biología Computacional
Date: June 2019
Subjects:
Faculty: E.T.S. de Ingeniería Agronómica, Alimentaria y de Biosistemas (UPM)
Department: Biotecnología - Biología Vegetal
Creative Commons Licenses: Recognition - Share

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Abstract

Prediction of protein loop structures is crucial for protein structure modelling, structural refinement, antibody design, or ion channels modelling. Here we propose several methodological improvements to our loop modelling online service: Random Coordinate Descent (RCD+ http://rcd.chaconlab.org/). This server combines an ab initio loop closure algorithm with a full-atom refinement in Rosetta. We propose to include a novel knowledge-based pairwise potential (KORP) which takes into account information of the relative position and orientation per residue. The inclusion of KORP, a Ramachandran potential correction, and an extensive parameter optimization significantly improve the prediction accuracy of the loop modelling procedure. Moreover, superior efficiency has been achieved by drastically reducing the number of loop candidates to be further refined. The approach has been successfully validated with several standard loop benchmarks. Interestingly, promising results were obtained even in one of the most challenging applications scenarios: the H3 loops prediction of the antibody complementary determining regions.

More information

Item ID: 58160
DC Identifier: http://oa.upm.es/58160/
OAI Identifier: oai:oa.upm.es:58160
DOI: 10.5281/zenodo.3665304
Deposited by: Iván Martín Hernández
Deposited on: 24 Feb 2020 07:48
Last Modified: 24 Feb 2020 07:48
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