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PepX: a structural database of non-redundant protein–peptide complexes

Peter Vanhee, Joke Reumers, Francois Stricher, Lies Baeten, Luis Serrano, Joost Schymkowitz, Frederic Rousseau
2009 Nucleic Acids Research  
In addition, these complexes have been clustered based on their binding interfaces rather than sequence homology, providing a set of structurally diverse protein-peptide interactions.  ...  In PepX (http://pepx.switchlab.org), we have designed an unbiased and exhaustive data set of all protein-peptide complexes available in the Protein Data Bank with peptide lengths up to 35 residues.  ...  DATABASE CONTENTS Construction of a nonredundant dataset of protein-peptide complexes We have filtered the Brookhaven Protein Data Bank (PDB) (18) for protein-peptide complexes requiring X-ray structures  ... 
doi:10.1093/nar/gkp893 pmid:19880386 pmcid:PMC2808939 fatcat:j2equyek7jhuvdashxxxk5nxj4

PepBind: A Comprehensive Database and Computational Tool for Analysis of Protein–peptide Interactions

Arindam Atanu Das, Om Prakash Sharma, Muthuvel Suresh Kumar, Ramadas Krishna, Premendu P. Mathur
2013 Genomics, Proteomics & Bioinformatics  
The Peptide Binding Protein Database (Pep-Bind) is a curated and searchable repository of the structures, sequences and experimental observations of 3100 protein-peptide complexes.  ...  This initial database release focuses on providing protein-peptide interface information along with structure and sequence information for protein-peptide complexes deposited in the Protein Data Bank (  ...  While pep-tiDB is a set of 103 curated PDB files for non-redundant protein-peptide complexes, PepX contains 1431 non-redundant X-ray structures clustered based on their binding interfaces and backbone  ... 
doi:10.1016/j.gpb.2013.03.002 pmid:23896518 pmcid:PMC4357787 fatcat:anmth4vr6vfi3gkfrnnyaqc77y

YAPP-CD: Yet another protein-peptide complex database [article]

Joon-Sang Park
2021 bioRxiv   pre-print
To obtain reliable results with a template-based docking method, the template database must be comprehensive enough; that is, there must be similar templates of protein-peptide complexes to the protein  ...  Among various protein-peptide docking algorithms, template-based approaches, which utilize known protein-peptide complexes or templates to predict a new one, have been shown to yield more reliable results  ...  Pepx: a structural database of non-redundant protein-peptide complexes. Nucleic Acids Res. 2010;38(suppl-1):545-51. 25. Frappier, V.; Duran, M.; Keating, AE.  ... 
doi:10.1101/2021.06.16.448765 fatcat:omgkay24ovbnfd6uadwpgs7aei

Propedia: a database for protein–peptide identification based on a hybrid clustering algorithm

Pedro M. Martins, Lucianna H. Santos, Diego Mariano, Felippe C. Queiroz, Luana L. Bastos, Isabela de S. Gomes, Pedro H. C. Fischer, Rafael E. O. Rocha, Sabrina A. Silveira, Leonardo H. F. de Lima, Mariana T. Q. de Magalhães, Maria G. A. Oliveira (+1 others)
2021 BMC Bioinformatics  
The main advantage of Propedia over other peptide databases is that it allows a more comprehensive analysis of similarity and redundancy.  ...  Conclusions Propedia is a database and tool to support structure-based rational design of peptides for special purposes.  ...  Altogether, 535 clusters were formed, plus 1356 singletons, for a total of 1891 non redundant protein-peptide interfaces.  ... 
doi:10.1186/s12859-020-03881-z pmid:33388027 fatcat:4hklg6cuajhp5o2nddpby46ylm

Learning a peptide-protein binding affinity predictor with kernel ridge regression

Sébastien Giguère, Mario Marchand, François Laviolette, Alexandre Drouin, Jacques Corbeil
2013 BMC Bioinformatics  
For the first time, a machine learning predictor is capable of accurately predicting the binding affinity of any peptide to any protein.  ...  Combined with kernel ridge regression and SupCK, a novel binding pocket kernel, the proposed kernel yields biologically relevant and good prediction accuracy on the PepX database.  ...  Data PepX database The PepX database [31] contains 1431 high-quality peptide-protein complexes along with their protein and peptide sequences, high quality crystal structures, and binding energies  ... 
doi:10.1186/1471-2105-14-82 pmid:23497081 pmcid:PMC3651388 fatcat:eq3lure3anfmbp5btgjjkjezpy

Improved Modeling of Peptide-Protein Binding through Global Docking and Accelerated Molecular Dynamics Simulations [article]

jinan Wang, Andrey Alekseenko, Dima Kozakov, Yinglong Miao
2019 bioRxiv   pre-print
GaMD simulations refined the peptide-protein complex structures with significantly reduced peptide backbone RMSDs of 0.6 - 2.7 angstroms, yielding two high quality (sub-angstrom) and one medium quality  ...  Peptides mediate up to 40% of known protein-protein interactions in higher eukaryotes and play a key role in cellular signaling, protein trafficking, immunology and oncology.  ...  Acknowledgements This work was supported in part by the National Institutes of Health (R01GM132572), National Supplementary Material The Supplementary Material for this article can be found online at  ... 
doi:10.1101/743773 fatcat:evkjyso4i5ajjdreeq7r7ehxv4

Improved Modeling of Peptide-Protein Binding Through Global Docking and Accelerated Molecular Dynamics Simulations

Jinan Wang, Andrey Alekseenko, Dima Kozakov, Yinglong Miao
2019 Frontiers in Molecular Biosciences  
GaMD simulations refined the peptide-protein complex structures with significantly reduced peptide backbone RMSDs of 0.6-2.7 Å, yielding two high quality (sub-angstrom) and one medium quality models.  ...  Peptides mediate up to 40% of known protein-protein interactions in higher eukaryotes and play a key role in cellular signaling, protein trafficking, immunology, and oncology.  ...  System Setup Three model peptides were selected from the PeptiDB database of non-redundant peptide-protein complex structures (London et al., 2010) .  ... 
doi:10.3389/fmolb.2019.00112 pmid:31737642 pmcid:PMC6835073 fatcat:ry7kpp3iqbblthtq45z3pop3zu

BioLiP: a semi-manually curated database for biologically relevant ligand–protein interactions

Jianyi Yang, Ambrish Roy, Yang Zhang
2012 Nucleic Acids Research  
In addition, to facilitate the use of BioLiP for function annotation of uncharacterized proteins, a new consensus-based algorithm COACH is developed to predict ligand-binding sites from protein sequence  ...  BioLiP (http://zhanglab.ccmb.med.umich.edu/ BioLiP/) is a semi-manually curated database for biologically relevant ligand-protein interactions.  ...  sites, ProtChemSI (12) (http://pcidb.russelllab.org/) for the network of proteinchemical structural interactions, PepX (13) (http://pepx .switchlab.org/) for protein-peptide interactions and RsiteDB (  ... 
doi:10.1093/nar/gks966 pmid:23087378 pmcid:PMC3531193 fatcat:oxdg7gtdljdc3i7whmo4bwlzge

Modeling peptide-protein complexes: docking, simulations, and machine learning

Arup Mondal, Liwei Chang, Alberto Perez
2022 QRB Discovery  
However, predicting peptide-protein complexes remains more challenging than protein-protein or protein-small molecule interactions, in part due to the high flexibility peptides have.  ...  Peptides mediate up to 40% of protein interactions, their high specificity and ability to bind in places where small molecules cannot make them potential drug candidates.  ...  Acknowledgement The authors thank XSEDE resources through Conflict of interest The authors declare no conflicts of interest. Author contributions  ... 
doi:10.1017/qrd.2022.14 fatcat:mvekc2tug5dfpevxm7euqtgluu

PeptiSite: A structural database of peptide binding sites in 4D

Chayan Acharya, Irina Kufareva, Andrey V. Ilatovskiy, Ruben Abagyan
2014 Biochemical and Biophysical Research Communications - BBRC  
We developed PeptiSite, a comprehensive and reliable database of biologically and structurally characterized peptide-binding sites, in which each site is represented by an ensemble of its complexes with  ...  This structural database for protein-peptide interactions enables understanding of structural principles of these interactions and may assist the development of an efficient peptide docking benchmark.  ...  of crystal structures of various receptors interacting with peptide ligands that are reported in the Protein Data Bank (PDB) as of May 2013. [62] A 3D structure of a single complex gives only a limited  ... 
doi:10.1016/j.bbrc.2013.12.132 pmid:24406170 pmcid:PMC3975830 fatcat:ofopqw4hzfd3pbdz7mrzg5f6qe

Computer-aided design of amino acid-based therapeutics: a review

Tayebeh Farhadi, Seyed MohammadReza Hashemian
2018 Drug Design, Development and Therapy  
complex structures from the PDB. 89 PeptidDB is a curated database of 103 protein-peptide complexes. 90 The abundance of the structural information specifically on monomeric proteins could be gathered  ...  PepX, 88 PepBind 89 and peptidDB were generated. 90 The PepX database, derived from the PDB, comprises unique protein-peptide interface collections. 88 The PepBind database contains 4,986 proteinpeptide  ... 
doi:10.2147/dddt.s159767 pmid:29795978 pmcid:PMC5958949 fatcat:mkd3acifezhb3cq2pfdo2ngxb4

BriX: a database of protein building blocks for structural analysis, modeling and design

Peter Vanhee, Erik Verschueren, Lies Baeten, Francois Stricher, Luis Serrano, Frederic Rousseau, Joost Schymkowitz
2010 Nucleic Acids Research  
Since the availability of sufficient protein structures to tackle complex problems such as modeling backbone moves or docking remains a problem, alternative approaches using small, recurrent protein fragments  ...  To overcome the lack of loops classified in BriX, we constructed the Loop BriX database of non-regular structure elements, clustered according to end-to-end distance between the regular residues flanking  ...  ACKNOWLEDGEMENTS The authors thank Almer M. van der Sloot and Joke Reumers for critical reading of the manuscript.  ... 
doi:10.1093/nar/gkq972 pmid:20972210 pmcid:PMC3013806 fatcat:ajmnm3rbxndavlcncjvbdwwqgu

Pocketome: an encyclopedia of small-molecule binding sites in 4D

Irina Kufareva, Andrey V. Ilatovskiy, Ruben Abagyan
2011 Nucleic Acids Research  
To assist in understanding the flexible protein-ligand interactions, we constructed the Pocketome, an encyclopedia of about one thousand experimentally solved conformational ensembles of druggable binding  ...  The core of the Pocketome is derived regularly and automatically from the current releases of the Protein Data Bank and the Uniprot Knowledgebase; this core is complemented by entries built from manually  ...  The files in the online version of the database are simplified to include only non-redundant set of pocket compositions (i.e. distinct ligands in combinations with distinct point mutants only).  ... 
doi:10.1093/nar/gkr825 pmid:22080553 pmcid:PMC3245087 fatcat:k4oncvpplbhsjfh3zg5ifgy354

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  
Importantly, a variety of computation-aided rational designs for peptide therapeutics have been developed, which aim to deliver comprehensive docking for peptideprotein interaction interfaces.  ...  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  ...  Another database PepX is comprised of more than 500 experimentally studied peptide interactions with high-resolution structures and allows simple inputs of user-defined peptide templates [83] .  ... 
doi:10.3390/ijms20102383 fatcat:wjv3k734yrbsrncqok2i5lj7ym

BactPepDB: a database of predicted peptides from a exhaustive survey of complete prokaryote genomes

J. Rey, P. Deschavanne, P. Tuffery
2014 Database: The Journal of Biological Databases and Curation  
BactPepDB: a database of predicted peptides from a exhaustive survey of complete prokaryote genomes.  ...  Additional information is related to homologs within order, predicted signal sequence, transmembrane segments, disulfide bonds, secondary structure, and the existence of a related 3D structure in the Protein  ...  Conflict of interest: None declared.  ... 
doi:10.1093/database/bau106 pmid:25377257 pmcid:PMC4221844 fatcat:3tf6pquwuzdmpm52t6ol57vi7m
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