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10.1016/j.csbj.2020.11.029 http://scihub22266oqcxt.onion/10.1016/j.csbj.2020.11.029 33250973!7679229!33250973     free     free     free Deprecated: Implicit conversion from float 209.6 to int loses precision in C:\Inetpub\vhosts\kidney.de\httpdocs\pget.php on line 534 Deprecated: Implicit conversion from float 209.6 to int loses precision in C:\Inetpub\vhosts\kidney.de\httpdocs\pget.php on line 534 Deprecated: Implicit conversion from float 209.6 to int loses precision in C:\Inetpub\vhosts\kidney.de\httpdocs\pget.php on line 534 Deprecated: Implicit conversion from float 209.6 to int loses precision in C:\Inetpub\vhosts\kidney.de\httpdocs\pget.php on line 534 Deprecated: Implicit conversion from float 209.6 to int loses precision in C:\Inetpub\vhosts\kidney.de\httpdocs\pget.php on line 534       Comput+Struct+Biotechnol+J 2020 ; 18 (ä): 3750-3761 Nephropedia Template TP {{tp|p=33250973|t=2020. Docking-based identification of small-molecule binding sites at protein-protein interfaces |pdf=|usr=}}{{33250973}} gab.com Text Docking-based identification of small-molecule binding sites at protein-protein interfaces JO: Comput Struct Biotechnol J http://www.kidney.de/pget.php?&tw=1&pmid=33250973 #FOAvip Protein-protein interactions play an essential role in many biological processes, and their perturbation is a major cause of disease. The use of small molecules to modulate them is attracting increased attention, but protein interfaces generally do not have clear cavities for binding small compounds. A proposed strategy is to target interface hot-spot residues, but their identification through computational approaches usually require the complex structure, which is not often available. In this context, pyDock energy-based docking and scoring can predict hot-spots on the unbound proteins, thus not requiring the complex structure. Here, we have devised a new strategy to detect protein-protein inhibitor binding sites, based on the integration of molecular dynamics for the generation of transient cavities, and docking-based interface hot-spot prediction for the selection of the suitable cavities. This integrative approach has been validated on a test set formed by protein-protein complexes with known inhibitors for which complete structural data of unbound molecules and complexes is available. The results show that local conformational sampling with short molecular dynamics can generate transient cavities similar to the known inhibitor binding sites, and that docking simulations can identify the best cavities with similar predictive accuracy as when knowing the real interface. In a few cases, these predicted pockets are shown to be suitable for protein-ligand docking. The proposed strategy will be useful for many protein-protein complexes for which there is no available structure, as long as the the unbound proteins do not deviate dramatically from the bound conformations. Twit Text FOAVip Docking-based identification of small-molecule binding sites at protein-protein interfaces ????Comput Struct Biotechnol J http://www.kidney.de/pget.php?&tw=1&pmid=33250973 #FOAvip Twit Text # Free Paper on # # # # # LINK http://www.kidney.de/pget.php?&tw=1&pmid=33250973 #FOAvip English Wikipedia <ref>{{Cite pmid|33250973}}</ref> Docking-based identification of small-molecule binding sites at protein-protein interfaces #MMPMID33250973 Rosell M; Fernandez-Recio J Comput Struct Biotechnol J 2020[]; 18 (ä): 3750-3761 PMID33250973show ga Protein-protein interactions play an essential role in many biological processes, and their perturbation is a major cause of disease. The use of small molecules to modulate them is attracting increased attention, but protein interfaces generally do not have clear cavities for binding small compounds. A proposed strategy is to target interface hot-spot residues, but their identification through computational approaches usually require the complex structure, which is not often available. In this context, pyDock energy-based docking and scoring can predict hot-spots on the unbound proteins, thus not requiring the complex structure. Here, we have devised a new strategy to detect protein-protein inhibitor binding sites, based on the integration of molecular dynamics for the generation of transient cavities, and docking-based interface hot-spot prediction for the selection of the suitable cavities. This integrative approach has been validated on a test set formed by protein-protein complexes with known inhibitors for which complete structural data of unbound molecules and complexes is available. The results show that local conformational sampling with short molecular dynamics can generate transient cavities similar to the known inhibitor binding sites, and that docking simulations can identify the best cavities with similar predictive accuracy as when knowing the real interface. In a few cases, these predicted pockets are shown to be suitable for protein-ligand docking. The proposed strategy will be useful for many protein-protein complexes for which there is no available structure, as long as the the unbound proteins do not deviate dramatically from the bound conformations. äDocking-based identification of small-molecule binding sites at protei(epmc).pdf DeepDyve Pubget Overpricing