<?xml version="1.0" encoding="UTF-8"?><xml><records><record><source-app name="Biblio" version="6.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Almeida, R. M.</style></author><author><style face="normal" font="default" size="100%">Dell'acqua, S.</style></author><author><style face="normal" font="default" size="100%">Krippahl, L.</style></author><author><style face="normal" font="default" size="100%">Moura, J J</style></author><author><style face="normal" font="default" size="100%">Pauleta, S. R.</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Predicting Protein-Protein Interactions Using BiGGER: Case Studies</style></title><secondary-title><style face="normal" font="default" size="100%">Molecules</style></secondary-title></titles><dates><year><style  face="normal" font="default" size="100%">2016</style></year><pub-dates><date><style  face="normal" font="default" size="100%">Aug 09</style></date></pub-dates></dates><urls><web-urls><url><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/27517887</style></url></web-urls></urls><number><style face="normal" font="default" size="100%">8</style></number><edition><style face="normal" font="default" size="100%">2016/08/16</style></edition><volume><style face="normal" font="default" size="100%">21</style></volume><isbn><style face="normal" font="default" size="100%">1420-3049 (Electronic)1420-3049 (Linking)</style></isbn><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">&lt;p&gt;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.&lt;/p&gt;
</style></abstract><accession-num><style face="normal" font="default" size="100%">27517887</style></accession-num><notes><style face="normal" font="default" size="100%">&lt;p&gt;Almeida, Rui MDell'Acqua, SimoneKrippahl, LudwigMoura, Jose J GPauleta, Sofia RSwitzerlandMolecules (Basel, Switzerland)Molecules. 2016 Aug 9;21(8). pii: E1037. doi: 10.3390/molecules21081037.&lt;/p&gt;
</style></notes><auth-address><style face="normal" font="default" size="100%">UCIBIO, REQUIMTE, Departamento de Quimica, Faculdade de Ciencias e Tecnologia, NOVA, 2829-516 Caparica, Portugal. rui.almeida@fct.unl.pt.Department of Chemistry, University of Pavia, Via Taramelli 12, 27100 Pavia, Italy. simone.dellacqua@unipv.it.CENTRIA, Departamento de Informatica, Faculdade de Ciencias e Tecnologia, NOVA, 2829-516 Caparica, Portugal. a4338@fct.unl.pt.UCIBIO, REQUIMTE, Departamento de Quimica, Faculdade de Ciencias e Tecnologia, NOVA, 2829-516 Caparica, Portugal. jjgm@fct.unl.pt.UCIBIO, REQUIMTE, Departamento de Quimica, Faculdade de Ciencias e Tecnologia, NOVA, 2829-516 Caparica, Portugal. srp@fct.unl.pt.</style></auth-address></record></records></xml>