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Molecules 2016, 21(8), 1037; doi:10.3390/molecules21081037

Predicting Protein-Protein Interactions Using BiGGER: Case Studies

1
UCIBIO, REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, NOVA, 2829-516 Caparica, Portugal
2
Department of Chemistry, University of Pavia, Via Taramelli 12, 27100 Pavia, Italy
3
CENTRIA, Departamento de Informática, Faculdade de Ciências e Tecnologia, NOVA, 2829-516 Caparica, Portugal
These authors contributed equally to this manuscript.
*
Authors to whom correspondence should be addressed.
Academic Editor: Leif A. Eriksson
Received: 10 June 2016 / Revised: 3 August 2016 / Accepted: 4 August 2016 / Published: 9 August 2016
(This article belongs to the Collection Molecular Docking)
View Full-Text   |   Download PDF [3467 KB, uploaded 9 August 2016]   |  

Abstract

The importance of understanding interactomes makes preeminent the study of protein interactions and protein complexes. Traditionally, protein interactions have been elucidated by experimental methods or, with lower impact, by simulation with protein docking algorithms. This article describes features and applications of the BiGGER docking algorithm, which stands at the interface of these two approaches. BiGGER is a user-friendly docking algorithm that was specifically designed to incorporate experimental data at different stages of the simulation, to either guide the search for correct structures or help evaluate the results, in order to combine the reliability of hard data with the convenience of simulations. Herein, the applications of BiGGER are described by illustrative applications divided in three Case Studies: (Case Study A) in which no specific contact data is available; (Case Study B) when different experimental data (e.g., site-directed mutagenesis, properties of the complex, NMR chemical shift perturbation mapping, electron tunneling) on one of the partners is available; and (Case Study C) when experimental data are available for both interacting surfaces, which are used during the search and/or evaluation stage of the docking. This algorithm has been extensively used, evidencing its usefulness in a wide range of different biological research fields. View Full-Text
Keywords: protein-protein interactions; BiGGER; docking; electron transfer complexes; molecular recognition; NMR protein-protein interactions; BiGGER; docking; electron transfer complexes; molecular recognition; NMR
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This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. (CC BY 4.0).

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MDPI and ACS Style

Almeida, R.M.; Dell’Acqua, S.; Krippahl, L.; Moura, J.J.G.; Pauleta, S.R. Predicting Protein-Protein Interactions Using BiGGER: Case Studies. Molecules 2016, 21, 1037.

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