Next Article in Journal
Synthesis and Structure-Activity Relationship of Some New Thiophene-Based Heterocycles as Potential Antimicrobial Agents
Next Article in Special Issue
Molecular Modeling Studies of 11β-Hydroxysteroid Dehydrogenase Type 1 Inhibitors through Receptor-Based 3D-QSAR and Molecular Dynamics Simulations
Previous Article in Journal
Chemo-Enzymatic Synthesis of Oligoglycerol Derivatives
Previous Article in Special Issue
Bioactive Molecule Prediction Using Extreme Gradient Boosting
Open AccessArticle

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
*
Authors to whom correspondence should be addressed.
These authors contributed equally to this manuscript.
Academic Editor: Leif A. Eriksson
Molecules 2016, 21(8), 1037; https://doi.org/10.3390/molecules21081037
Received: 10 June 2016 / Revised: 3 August 2016 / Accepted: 4 August 2016 / Published: 9 August 2016
(This article belongs to the Collection Molecular Docking)
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
Show Figures

Graphical abstract

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.

Show more citation formats Show less citations formats
Note that from the first issue of 2016, MDPI journals use article numbers instead of page numbers. See further details here.

Article Access Map by Country/Region

1
Back to TopTop