title: Predicting Protein-Protein Interactions Using BiGGER: Case Studies.
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.
authors: UCIBIO, REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, NOVA, 2829-516 Caparica, Portugal. rui.almeida@fct.unl.pt.
authors: Rui M
authors: RM
authors: Almeida
authors: Department of Chemistry, University of Pavia, Via Taramelli 12, 27100 Pavia, Italy. simone.dellacqua@unipv.it.
authors: Simone
authors: S
authors: Dell'Acqua
authors: CENTRIA, Departamento de Informática, Faculdade de Ciências e Tecnologia, NOVA, 2829-516 Caparica, Portugal. a4338@fct.unl.pt.
authors: Ludwig
authors: L
authors: Krippahl
authors: UCIBIO, REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, NOVA, 2829-516 Caparica, Portugal. jjgm@fct.unl.pt.
authors: José J G
authors: JJ
authors: Moura
authors: UCIBIO, REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, NOVA, 2829-516 Caparica, Portugal. srp@fct.unl.pt.
authors: Sofia R
authors: SR
authors: Pauleta
mesh_terms: D000465:Algorithms; D062105:Molecular Docking Simulation; D011506:Proteins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*
chemical_list: D011506:Proteins
keywords: BiGGER; NMR; docking; electron transfer complexes; molecular recognition; protein-protein interactions