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3D-footprint: a database for the structural analysis of protein–DNA complexes

Bruno Contreras-Moreira
2009 Nucleic Acids Research  
3D-footprint is a living database, updated and curated on a weekly basis, which provides estimates of binding specificity for all protein-DNA complexes available at the Protein Data Bank.  ...  The relevant content of the database is available for download as flat files and it is also possible to use the 3D-footprint pipeline to analyze protein coordinates input by the user. 3D-footprint is available  ...  for their help, support, suggestions and reviews of 3D-footprint.  ... 
doi:10.1093/nar/gkp781 pmid:19767616 pmcid:PMC2808867 fatcat:5pwlfif6izdpdcojkmbf2c4pkm

Interface Similarity Improves Comparison of DNA-Binding Proteins: The Homeobox Example [chapter]

Álvaro Sebastián, Carlos P. Cantalapiedra, Bruno Contreras-Moreira
2012 Lecture Notes in Computer Science  
The recently published 3D-footprint database contains an up-to-date repository of protein-DNA complexes of known structure that belong to different superfamilies and bind to DNA with distinct specificities  ...  Here we take the complete set of Homeobox proteins from Drosophila melanogaster and their preferred DNA motifs, which would fall in the largest 3D-footprint superfamily and were recently characterized  ...  Introduction 3D-footprint [1] ( is a database that dissects sequence readout in protein-DNA complexes of known structure, extracted from the Protein Data Bank  ... 
doi:10.1007/978-3-642-28062-7_8 fatcat:taow7ed2pvgohg5kmp7gwe534u

NPIDB: nucleic acid—protein interaction database

Dmitry D. Kirsanov, Olga N. Zanegina, Evgeniy A. Aksianov, Sergei A. Spirin, Anna S. Karyagina, Andrei V. Alexeevski
2012 Nucleic Acids Research  
The Nucleic acid-Protein Interaction DataBase ( contains information derived from structures of DNA-protein and RNA-protein complexes extracted from the Protein Data Bank  ...  It provides a web interface and a set of tools for extracting biologically meaningful characteristics of nucleoprotein complexes. The content of the database is updated weekly.  ...  ACKNOWLEDGEMENTS The authors thank Alexey Salnikov for participation in creating the new version of the program CluD, which is used for calculation of hydrophobic interactions between macromolecules, Elena  ... 
doi:10.1093/nar/gks1199 pmid:23193292 pmcid:PMC3531207 fatcat:pxvf4djhcrhppovivekhkok2dm

FootprintDB: Analysis of Plant Cis-Regulatory Elements, Transcription Factors, and Binding Interfaces [chapter]

Bruno Contreras-Moreira, Alvaro Sebastian
2016 Msphere  
It systematically annotates the binding interfaces of the TFs by exploiting protein-DNA complexes deposited in the Protein Data Bank.  ...  This chapter explains step-by-step how to search for DNA motifs and protein sequences in footprintDB and how to focus the search to a particular organism.  ...  This work was funded by grant Euroinvestigación EUI2008-03612 under the framework of the Transnational (Germany, France, Spain) Cooperation within the PLANT-KBBE Initiative.  ... 
doi:10.1007/978-1-4939-6396-6_17 pmid:27557773 fatcat:wnjluag6mfazflewblzgmvosqi

footprintDB: a database of transcription factors with annotated cis elements and binding interfaces

Alvaro Sebastian, Bruno Contreras-Moreira
2013 Computer applications in the biosciences : CABIOS  
A search engine has been designed that drives the prediction of DNA motifs for input TFs, or conversely of TF sequences that might recognize input regulatory sequences, by comparison with database entries  ...  A survey of the included data sources, organisms and TF families was performed together with proprietary database TRANSFAC, finding that footprintDB has a similar coverage of multicellular organisms, while  ...  ACKNOWLEDGEMENTS We thank our colleagues from the STREG project (L.Bülow, R.Hehl, G.Huep, B.Weisshaar, C.Dubos, L.Lepiniec and A.Koller) for their feedback and support while developing this resource.  ... 
doi:10.1093/bioinformatics/btt663 pmid:24234003 fatcat:fmfks636yrb4nm6htdx3r7gfgu

PiDNA: predicting protein–DNA interactions with structural models

Chih-Kang Lin, Chien-Yu Chen
2013 Nucleic Acids Research  
In the past decade, a large number of protein-DNA co-crystallized structures available in the Protein Data Bank have facilitated the understanding of interacting mechanisms between transcription factors  ...  mutated complex structures, and then using the PWM constructed by the structure models with small energy changes to predict the interaction between proteins and DNA sequences.  ...  ACKNOWLEDGEMENTS The authors greatly appreciated the laboratory members of Dr. Huai-Kuang Tsai for providing the program of generating sequence logos as well as the useful comments form Dr. Tony Kuo.  ... 
doi:10.1093/nar/gkt388 pmid:23703214 pmcid:PMC3692134 fatcat:qemsxjnpcfdqdhimwoovrnubva

Molecular Cloning and Expression Analysis of MYB-Related Transcription Factor Gene, ScMYB76 from Sugarcane (Saccharum Hybrid)

Hemalatha Balakrishnan, Prabu Gajjeraman, Yasir Umar Pattiwala
2016 Indian Journal of Science and Technology  
The isolated gene was cloned and sequenced for sequence-structure analysis using various computational tools.  ...  To analyze the sequence-to-structure-to-function paradigm, comparative modeling, docking and validation were performed using I-TASSER, TFmodeller and 3D footprint platforms, respectively.  ...  Conflict of Interest The authors declare that they have no conflict of interest. References  ... 
doi:10.17485/ijst/2016/v9i37/93672 fatcat:mh2jbplyvrgjnbpw3hkwv44ina

TFinDit: transcription factor-DNA interaction data depository

Daniel Turner, RyangGuk Kim, Jun-tao Guo
2012 BMC Bioinformatics  
The database contains annotated transcription factor-DNA complex structures and related data, such as unbound protein structures, thermodynamic data, and binding sequences for the corresponding transcription  ...  Conclusions: TFinDit is a specialized structural database with annotated transcription factor-DNA complex structures and other preprocessed data.  ...  Corona for their help with the project. This work was supported by the National Science Foundation #DBI0844749 to JTG.  ... 
doi:10.1186/1471-2105-13-220 pmid:22943312 pmcid:PMC3483241 fatcat:bsm5ralczbez3mqxqtns6v3sfy

Characterization of Water-Deficit Stress-Responsive R2R3-MYB Transcription Factor Gene, ScMYB50/23 from Sugarcane

Barathkumar Sadasivam, Prabu Gajjeraman
2016 Indian Journal of Science and Technology  
The isolated gene was cloned and sequenced for sequence-structure analysis using various computational tools.  ...  In order to elucidate its sequence-to-structure-to-function paradigm, comparative modeling, docking and validation were performed using I-TASSER, TFmodeller and 3D footprint platforms, respectively.  ...  The work was supported by Science and Engineering Research Board, Department of Science and Technology, Government of India (SR/FT/LS-O5/2011).  ... 
doi:10.17485/ijst/2016/v9i37/93841 fatcat:jzumcuagrbctxghym3h3dj66ve

DNA Readout Viewer (DRV): visualisation of specificity determining patterns of protein binding DNA segments

Krisztian Adam, Zoltan Gyorgypal, Zoltan Hegedus, Arne Elofsson
2019 Bioinformatics  
By applying its intuitive representation concept for various DNA recognition related visualisation tasks, DRV can contribute to unravelling the binding specificity factors of DNA-protein interactions.  ...  DNA Readout Viewer (DRV) aims to provide a novel DNA representation, facilitating in-depth view into these mechanisms by the concurrent visualisation of functional groups and a diverse collection of DNA  ...  complexes of the RCSB database (Burley et al., 2019) .  ... 
doi:10.1093/bioinformatics/btz906 pmid:31793988 pmcid:PMC7141859 fatcat:6igqxkpasnfgjg63wdkgpopvky

The Protein-DNA Interface database

Tomás Norambuena, Francisco Melo
2010 BMC Bioinformatics  
The Protein-DNA Interface database (PDIdb) is a repository containing relevant structural information of Protein-DNA complexes solved by X-ray crystallography and available at the Protein Data Bank.  ...  The current version of the database contains only structures with resolution of 2.5 Å or higher, accounting for a total of 922 entries.  ...  Acknowledgements TN acknowledges a PhD program fellowship from CONICYT Chile. This work was funded by a grant 1080158 from FONDECYT Chile.  ... 
doi:10.1186/1471-2105-11-262 pmid:20482798 pmcid:PMC2885377 fatcat:ma4qy6mo6zc7lowfl2hjhmukbi

DNAproDB: an interactive tool for structural analysis of DNA–protein complexes

Jared M. Sagendorf, Helen M. Berman, Remo Rohs
2017 Nucleic Acids Research  
We processed a large number of DNA-protein complexes retrieved from the Protein Data Bank and created the DNAproDB database to store this data.  ...  Users can search the database by combining features of the DNA, protein or DNAprotein interactions at the interface.  ...  The authors thank Luigi Manna for his assistance in setting up, configuring and maintaining the DNAproDB server at USC and for helpful discussions regarding technical aspects of the project.  ... 
doi:10.1093/nar/gkx272 pmid:28431131 pmcid:PMC5570235 fatcat:nwyx5iwvvrhbzi6jow7qpfv2uu

The twilight zone of cis element alignments

Alvaro Sebastian, Bruno Contreras-Moreira
2012 Nucleic Acids Research  
Our goals are (i) to test TFcompare ( tfcompare), a structural alignment method for protein-DNA complexes; (ii) to benchmark the pairwise alignment of regulatory elements;  ...  Sequence alignment of proteins and nucleic acids is a routine task in bioinformatics.  ...  ACKNOWLEDGEMENTS The authors thank our colleagues from the STREG project and Carlos P. Cantalapiedra, Vladimir Espinosa and Franc¸ois Parcy for their comments on drafts of this article.  ... 
doi:10.1093/nar/gks1301 pmid:23268451 pmcid:PMC3561995 fatcat:oeohciho5ze7vbarqoogqidbfu

DNAproDB: an expanded database and web-based tool for structural analysis of DNA-protein complexes

2019 Nucleic Acids Research  
Our database now contains 95% of all available DNA-protein complexes, making our tools for analysis of these structures accessible to a broad community.  ...  We have updated the structure of our data files to support complex DNA conformations, multiple DNA-protein complexes within a DNAproDB entry and model indexing for analysis of ensemble data.  ...  ACKNOWLEDGEMENTS A collaboration of the authors with Xiaojiang Chen initiated the inclusion of single-stranded DNA-protein com-  ... 
doi:10.1093/nar/gkz889 pmid:31612957 pmcid:PMC7145614 fatcat:qlqhkxjhvndmhpwtouv56jehp4

An affinity-structure database of helix-turn-helix: DNA complexes with a universal coordinate system

Mohammed AlQuraishi, Shengdong Tang, Xide Xia
2015 BMC Bioinformatics  
Furthermore, we present a novel alignment algorithm that structurally aligns the protein-DNA complexes in the database and creates a unified residue-level coordinate system for comparing the physico-chemical  ...  of the corresponding protein-DNA complexes.  ...  To our knowledge none of the databases currently combining structural and binding affinity data, including TFinDit [24] and 3d-footprint [25] , provide such a correspondence.  ... 
doi:10.1186/s12859-015-0819-2 pmid:26586237 pmcid:PMC4653904 fatcat:jfqj2ao5wfgi5khb52ir6ta54y
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