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BAP

A dynamical view of binding affinity

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EC-Contrib. €

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Partnership

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Project "BAP" data sheet

The following table provides information about the project.

Coordinator
UNIVERSITEIT UTRECHT 

Organization address
address: HEIDELBERGLAAN 8
city: UTRECHT
postcode: 3584 CS
website: www.uu.nl

contact info
title: n.a.
name: n.a.
surname: n.a.
function: n.a.
email: n.a.
telephone: n.a.
fax: n.a.

 Coordinator Country Netherlands [NL]
 Project website https://www.uu.nl/medewerkers/AVangone
 Total cost 165˙598 €
 EC max contribution 165˙598 € (100%)
 Programme 1. H2020-EU.1.3.2. (Nurturing excellence by means of cross-border and cross-sector mobility)
 Code Call H2020-MSCA-IF-2014
 Funding Scheme MSCA-IF-EF-ST
 Starting year 2015
 Duration (year-month-day) from 2015-10-01   to  2017-09-30

 Partnership

Take a look of project's partnership.

# participants  country  role  EC contrib. [€] 
1    UNIVERSITEIT UTRECHT NL (UTRECHT) coordinator 165˙598.00

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 Project objective

Almost all critical functions in the cell rely on specific protein-protein interactions (PPIs). Understanding interactions is therefore a crucial step in the investigation of biological systems and in drug design. Despite all the research efforts that have been devoted to unravel principles of PPIs in the past decades, we still lack a thorough understanding of the energetics of proteins association, which is limiting our ability to consistently predict protein complexes, engineer high-affinity interactions and design new drugs. An improved understanding of protein binding affinity holds the key for resolving some of the most important problems in molecular biology, with wide implications in related fields. In this project I propose a novel approach to reliably predict the binding affinity by adding the so-far neglected dynamical dimension to the problem. Unlike traditional methods like empirical energy-based scoring, I will assess the conservation of interface contacts in protein complexes during dynamics trajectories. By correlating such properties to experimental binding affinities, a new predictor will be developed. Preliminary results on limited set of complexes already indicate that this approach has a great potential, outperforming any predictor proposed to date. Moreover, I will expand this novel approach and assess its applicability to other critical research fields related to biomolecular interactions, such as docking and proteins and interactions engineering. This project will allow me to reinforce and further expand my skills and expertise, create new collaborations and reinforce my position as researcher in Europe, which will enable me to reach full independency in the future.

 Publications

year authors and title journal last update
List of publications.
2015 Anna Vangone, Alexandre MJJ Bonvin
Contacts-based prediction of binding affinity in protein–protein complexes
published pages: , ISSN: 2050-084X, DOI: 10.7554/eLife.07454
eLife 4 2019-06-17
2016 Li C. Xue, João Pglm Rodrigues, Panagiotis L. Kastritis, Alexandre Mjj Bonvin, Anna Vangone
PRODIGY: a web server for predicting the binding affinity of protein–protein complexes
published pages: btw514, ISSN: 1367-4803, DOI: 10.1093/bioinformatics/btw514
Bioinformatics 2019-06-17
2016 Renée C. G. de Bruin, Anita G. M. Stam, Anna Vangone, Paul M. P. van Bergen en Henegouwen, Henk M. W. Verheul, Zsolt Sebestyén, Jürgen Kuball, Alexandre M. J. J. Bonvin, Tanja D. de Gruijl, Hans J. van der Vliet
Prevention of Vγ9Vδ2 T Cell Activation by a Vγ9Vδ2 TCR Nanobody
published pages: 308-317, ISSN: 0022-1767, DOI: 10.4049/jimmunol.1600948
The Journal of Immunology 198/1 2019-06-17
2015 Thom Vreven, Iain H. Moal, Anna Vangone, Brian G. Pierce, Panagiotis L. Kastritis, Mieczyslaw Torchala, Raphael Chaleil, Brian Jiménez-García, Paul A. Bates, Juan Fernandez-Recio, Alexandre M.J.J. Bonvin, Zhiping Weng
Updates to the Integrated Protein–Protein Interaction Benchmarks: Docking Benchmark Version 5 and Affinity Benchmark Version 2
published pages: 3031-3041, ISSN: 0022-2836, DOI: 10.1016/j.jmb.2015.07.016
Journal of Molecular Biology 427/19 2019-06-17
2017 Anna Vangone, Alexandre Bonvin
PRODIGY: A Contact-based Predictor of Binding Affinity in Protein-protein Complexes
published pages: , ISSN: 2331-8325, DOI: 10.21769/BioProtoc.2124
BIO-PROTOCOL 7/3 2019-06-17
2016 Cunliang Geng, Anna Vangone, Alexandre M.J.J. Bonvin
Exploring the interplay between experimental methods and the performance of predictors of binding affinity change upon mutations in protein complexes
published pages: 291-299, ISSN: 1741-0126, DOI: 10.1093/protein/gzw020
Protein Engineering Design and Selection 29/8 2019-06-17

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