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Accurate Prediction of Peptide Binding Sites on Protein Surfaces

Evangelia Petsalaki, Alexander Stark, Eduardo García-Urdiales, Robert B. Russell, Burkhard Rost
2009 PLoS Computational Biology  
To address this gap, we present an approach that can accurately predict peptide binding sites on protein surfaces.  ...  We then scan the surface of a putative binding protein for sites for each of the amino acids present in a peptide partner and search for combinations of high-scoring amino acid sites that satisfy constraints  ...  Acknowledgments The authors would like to thank Olga Kalinina and Matthieu Pichaud for useful discussions regarding the statistics of the method and Toby Gibson for useful comments.  ... 
doi:10.1371/journal.pcbi.1000335 pmid:19325869 pmcid:PMC2653190 fatcat:fjjmiebhfjb5fm4dvdz4ebytd4

Detection of peptide-binding sites on protein surfaces: The first step toward the modeling and targeting of peptide-mediated interactions

Lavi Assaf, Ngan Chi Ho, Movshovitz-Attias Dana, Bohnuud Tanggis, Yueh Christine, Beglov Dmitri, Schueler-Furman Ora, Kozakov Dima
2014 Proteins: Structure, Function, and Bioinformatics  
A number of different protocols have recently been proposed for the accurate modeling of peptide-protein complex structures, given the structure of the protein receptor and the binding site on its surface  ...  Here, we present PeptiMap, a protocol for the accurate mapping of peptide binding sites on protein structures.  ...  (C) Example of accurate PeptiMap prediction of the peptide binding site covering a substantial part of the peptide: Endothiapepsin peptide binding site prediction identifies the peptide binding site of  ... 
doi:10.1002/prot.24579 fatcat:at77tuquajcqnkfoq57nburzge

Detection of peptide-binding sites on protein surfaces: The first step toward the modeling and targeting of peptide-mediated interactions

Assaf Lavi, Chi Ho Ngan, Dana Movshovitz-Attias, Tanggis Bohnuud, Christine Yueh, Dmitri Beglov, Ora Schueler-Furman, Dima Kozakov
2013 Proteins: Structure, Function, and Bioinformatics  
Here we present PeptiMap, a protocol for the accurate mapping of peptide binding sites on protein structures.  ...  When no information about the peptide binding site(s) is a priori available, there is a need for new approaches to locate peptide-binding sites on the protein surface.  ...  Discussion and Conclusion PeptiMap is a new, accurate and robust approach for peptide binding site detection on protein receptor surfaces.  ... 
doi:10.1002/prot.24422 pmid:24123488 pmcid:PMC4183195 fatcat:sngazyztijhofmzluyzu25rwlq

Structural and Dynamic Determinants of Protein-Peptide Recognition

Onur Dagliyan, Elizabeth A. Proctor, Kevin M. D'Auria, Feng Ding, Nikolay V. Dokholyan
2011 Structure  
Protein conformational changes upon binding, an ill-defined peptide binding surface, and the large number of peptide degrees of freedom make the prediction of protein-peptide interactions particularly  ...  We find that, in most cases, we recapitulate the native binding sites and native-like poses of protein-peptide complexes.  ...  Modeling of Protein Side-Chain Flexibility Is Necessary for Accurate Peptide Binding Pose Prediction To investigate the effect of protein conformational dynamics on protein-peptide recognition, we compare  ... 
doi:10.1016/j.str.2011.09.014 pmid:22153506 pmcid:PMC3240807 fatcat:e6o7icbjkvdnfkprfyt3x7yexy

AnchorDock: Blind and Flexible Anchor-Driven Peptide Docking

Avraham Ben-Shimon, Masha Y. Niv
2015 Structure  
Graphical Abstract Highlights d AnchorDock allows flexible and completely blind highresolution docking of peptides d AnchorDock search is directed to the most relevant parts of the conformational space  ...  Miriam Eisenstein for sharing the source code of ANCHORSmap, developed by Ben-Shimon and Eisenstein at the Weizmann Institute of Science. We thank Dr.  ...  James Keck for kindly providing the X-ray coordinates of target T65 after the CAPRI 29 round was concluded, and Dr. Talia  ... 
doi:10.1016/j.str.2015.03.010 pmid:25914054 fatcat:dwxzabg3n5chbf6uug2z7mgjbu

DynaBiS : A Hierarchical Sampling Algorithm to Identify Flexible Binding Sites for Large Ligands and Peptides

Okke Melse, Sabrina Hecht, Iris Antes
2021 Proteins: Structure, Function, and Bioinformatics  
Knowing the ligand or peptide binding site in proteins is highly important to guide drug discovery, but experimental elucidation of the binding site is difficult.  ...  We evaluated DynaBiS and other commonly used binding site identification algorithms against a diverse evaluation set consisting of 26 proteins featuring peptide as well as small ligand binding sites.  ...  . 3.4 | Effect of binding site size and ligand flexibility on binding site identification performance Based on our observation regarding the strong performance of DynaBiS in peptide-binding proteins, we  ... 
doi:10.1002/prot.26182 pmid:34288078 fatcat:2g2dzk47gredfdyykvgs4dp2iu

Predicting Peptide Binding Sites on Protein Surfaces by Clustering Chemical Interactions

Chengfei Yan, Xiaoqin Zou
2015 Biophysical Journal  
We have definitively shown that there is only one Ca 2þ -binding site in HPC2 Cterm, located within its EF-hand domain.  ...  In contrast, the SUPC2 Ccore contains two Ca 2þ -binding sites within its EF-hand domain, which exhibit cooperative Ca 2þ -binding due to internal stabilization.  ...  In the present study, we developed a novel computational approach, referred to as ACCLUSTER, for predicting the peptide binding sites on protein surfaces.  ... 
doi:10.1016/j.bpj.2014.11.1189 fatcat:64tev5jyxbatbcogl6sdgyblki

PepSite: prediction of peptide-binding sites from protein surfaces

L. G. Trabuco, S. Lise, E. Petsalaki, R. B. Russell
2012 Nucleic Acids Research  
For typical cases where a protein-peptide structure of interest is not available, the PepSite web server can be used to predict peptide-binding spots from protein surfaces alone.  ...  An important class of protein-protein interaction corresponds to peptide-mediated interactions, in which a short peptide stretch from one partner interacts with a large protein surface from the other partner  ...  Prediction of hot spots Given a protein structure of interest, preferred sites for amino acid binding ('hot binding spots' or simply 'hot spots') are predicted as follows.  ... 
doi:10.1093/nar/gks398 pmid:22600738 pmcid:PMC3394340 fatcat:i7zx7jlt6fhjxc76nfkcmutkty

Deciphering the Arginine-Binding Preferences at the Substrate-Binding Groove of Ser/Thr Kinases by Computational Surface Mapping

Avraham Ben-Shimon, Masha Y. Niv, Michael Gilson
2011 PLoS Computational Biology  
We applied ANCHORSmap, a new fragment-based computational approach for mapping amino acid side chains on protein surfaces, to predict and characterize the preference of kinases toward Arginine binding.  ...  The method accurately identified all the P22/P25 Arg binding sites previously determined by X-ray crystallography and produced Arg preferences that corresponded to those experimentally found by peptide  ...  Talia Yarnitzky for critical reading of the manuscript. Author Contributions  ... 
doi:10.1371/journal.pcbi.1002288 pmid:22125489 pmcid:PMC3219626 fatcat:4rvveyioqncnxbjhf5ezzdifii

A Comprehensive Review on Current Advances in Peptide Drug Development and Design

Andy Chi-Lung Lee, Janelle Louise Harris, Kum Kum Khanna, Ji-Hong Hong
2019 International Journal of Molecular Sciences  
Despite this, advances in various docking models are only on the merge of making their contribution to peptide drug development.  ...  Deciphering and characterizing peptideprotein recognition mechanisms is thus central for the invention of peptide-based strategies to interfere with endogenous protein interactions, or improvement of  ...  area, mutation hotspots, geometric angles and allosteric effects for calculations of binding free energies to generate more accurate predictions on binding affinities between the interacting proteins  ... 
doi:10.3390/ijms20102383 fatcat:wjv3k734yrbsrncqok2i5lj7ym

Structure-based prediction of protein– peptide binding regions using Random Forest

Ghazaleh Taherzadeh, Yaoqi Zhou, Alan Wee-Chung Liew, Yuedong Yang, Alfonso Valencia
2017 Bioinformatics  
Results: SPRINT-Str achieves robust and consistent results for prediction of protein-peptide binding regions in terms of residues and sites.  ...  The application of SPRINT-Str to protein binding with DNA, RNA, and carbohydrate confirms the method's capability of separating peptide-binding sites from other functional sites.  ...  Conflict of Interest: none declared.  ... 
doi:10.1093/bioinformatics/btx614 pmid:29028926 fatcat:vhfhx4kurbe25bdpvamyzwsvgm

Predicting protein-peptide interaction sites using distant protein complexes as structural templates [article]

Isak Johansson-Åkhe, Claudio Mirabello, Björn Wallner
2018 bioRxiv   pre-print
When tested on its ability to predict binding sites, InterPep successfully pinpointed 255 of 502 (50.7%) binding sites in experimentally determined structures at rank 1 and 348 of 502 (69.3%) among the  ...  predict what region of the protein structure the peptide is most likely to bind.  ...  Another way to tackle the sampling problem is to first predict the peptide binding site on the protein surface [28] [29] [30] [31] [32] .  ... 
doi:10.1101/398768 fatcat:fxsyglirt5dedpt5faautspvty

Identification of diagnostic peptide regions that distinguish Zika virus from related mosquito-borne Flaviviruses

Alexandra J. Lee, Roshni Bhattacharya, Richard H. Scheuermann, Brett E. Pickett, Tian Wang
2017 PLoS ONE  
For ZIKV we identified 104 and 116 15-mer peptides in the E glycoprotein and NS1 non-structural protein, respectively, that contain multiple diagnostic sites and are located in surface-exposed regions  ...  each of 10 Flavivirus species and subtypes from each other by calculating the specificity, sensitivity, and surface exposure of each residue in relevant target proteins.  ...  Diagnostic peptide regions Since one of the primary goals of this study was to identify protein regions that would be predicted to have high sensitivity and specificity for binding by antiviral serum antibodies  ... 
doi:10.1371/journal.pone.0178199 pmid:28562637 pmcid:PMC5451039 fatcat:nq3gy6hkevechc4gnbcv4lvqje

Predicting physiologically relevant SH3 domain mediated protein–protein interactions in yeast

Shobhit Jain, Gary D. Bader
2016 Bioinformatics  
Binding motif patterns can then be used to computationally predict protein interactions mediated by these domains.  ...  these hits using a range of evidence sources related to sequence-based and cellular constraints on protein interactions.  ...  Acknowledgements We thank David Gfeller for help collecting binding peptide data and Mohamed Helmy for critical reading of the manuscript.  ... 
doi:10.1093/bioinformatics/btw045 pmid:26861823 pmcid:PMC4908317 fatcat:sdpvcpymirb3vbxoehrrac2sou

Characterization of PC2 Cterm Calcium-Binding Interaction and its Structural Implications

Yifei Yang, Camille Keeler, Ivana Y. Kuo, Elias J. Lolis, Michael E. Hodsdon, Barbara E. Ehrlich
2015 Biophysical Journal  
We have definitively shown that there is only one Ca 2þ -binding site in HPC2 Cterm, located within its EF-hand domain.  ...  In contrast, the SUPC2 Ccore contains two Ca 2þ -binding sites within its EF-hand domain, which exhibit cooperative Ca 2þ -binding due to internal stabilization.  ...  In the present study, we developed a novel computational approach, referred to as ACCLUSTER, for predicting the peptide binding sites on protein surfaces.  ... 
doi:10.1016/j.bpj.2014.11.1186 fatcat:wtuh5bjyanb7tdyvevyoo3znze
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