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PCRPi - DB: a database of computationally annotated hot spots in protein interfaces

Joan Segura, Narcis Fernandez-Fuentes
2010 Nucleic Acids Research  
Presaging Critical Residues in Protein Interfaces Database (PCRPi-DB) is a public repository that archives computationally annotated hot spots in protein complexes for which the 3D structure is known.  ...  There is a clear interest in identifying hot spots because of its application in drug discovery and protein design.  ...  CONCLUSION A database of computationally annotated hot spots in protein interfaces, PCRPi-DB, is presented.  ... 
doi:10.1093/nar/gkq1068 pmid:21097468 pmcid:PMC3013674 fatcat:a6gyg2ucw5fsbn4jpxyhkmw364

Hot-spot analysis for drug discovery targeting protein-protein interactions

Mireia Rosell, Juan Fernández-Recio
2018 Expert Opinion on Drug Discovery  
Areas covered In this review, the authors cover a variety of computational methods that have been reported for the energetic analysis of protein-protein interfaces in search of hot-spots, and the structural  ...  Computational analysis and docking can help to locate the interface, molecular dynamics can be used to find suitable cavities, and hot-spot predictions can focus the search for inhibitors of protein-protein  ...  In this context, it is interesting to mention the PCRPi database (PCRPi-DB), which contains computationally annotated hot-spot residues in all protein-protein complexes for which a high-resolution 3D structure  ... 
doi:10.1080/17460441.2018.1430763 pmid:29376444 fatcat:ysr5fpq5wzexlkjgxfgzadve4q

Computational Prediction of Protein Hot Spot Residues

John Kenneth Morrow, Shuxing Zhang
2012 Current pharmaceutical design  
Design of therapeutic agents that interact with hot spot residues has proven to be a valid methodology in disrupting unwanted protein-protein interactions.  ...  Here we review the state of knowledge around protein-protein interactions, hot spots, and give an overview of multiple in silico prediction techniques of hot spot residues.  ...  Acknowledgments This work was supported in part by the US Department of Defense Concept Awards (BC085871), Grant # IRG-08-061-01 from the American Cancer Society and MDACC-UT Austin CTT-TI3D grants.  ... 
doi:10.2174/138161212799436412 pmid:22316154 pmcid:PMC3807665 fatcat:glhmapaayrdd3ojdnquzfuzbja

Computational Tools and Databases for the Study and Characterization of Protein Interactions [chapter]

Joan Segura, Jose Ramon Blas Pastor, Narcis Fernandez-Fuentes
2012 Protein-Protein Interactions - Computational and Experimental Tools  
Moreover, PCPRi is a central part of a database that compiles and annotates hot spot in protein interfaces: PCRPI-DB .  ...  Prediction and charting of hot spots in protein interfaces The final part of the chapter describes the current state in computational prediction of hot spots in protein interfaces.  ... 
doi:10.5772/37268 fatcat:sd5xvcmfara7thw7goulplbwlq

Structural Prediction of Protein–Protein Interactions by Docking: Application to Biomedical Problems [chapter]

Didier Barradas-Bautista, Mireia Rosell, Chiara Pallara, Juan Fernández-Recio
2018 Advances in Protein Chemistry and Structural Biology  
In addition, prediction of interface and hot-spot residues is very useful in order to guide and interpret mutagenesis experiments, as well as to understand functional and mechanistic aspects of the interaction  ...  PROTEIN-PROTEIN DOCKING IN BIOMEDICINE 3 Keywords: Protein-protein interactions, complex structure, computational docking, interface prediction, hot-spot residues, drug discovery, edgetic effect, pathological  ...  Interface and hot-spot prediction The use of new approaches continues to enable the study of protein interactions from different perspectives.  ... 
doi:10.1016/bs.apcsb.2017.06.003 pmid:29412997 fatcat:6dsojxsybrfrthdz3yhlqmplxu