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TFmodeller: comparative modelling of protein–DNA complexes

Bruno Contreras-Moreira, Pierre-Alain Branger, Julio Collado-Vides
2007 Computer applications in the biosciences : CABIOS  
This data is derived from 442 superposed protein-DNA complexes, that were also analyzed to generate Table 3 , that shows how accurately different H-bonding residues are modelled by SCWRL.  ...  Accuracy is measured in terms of RMSD and in terms of coincident DNA contacts (REL). footprint benchmark and TFmodeller web server ( Fig1 Fig2  ... 
doi:10.1093/bioinformatics/btm148 pmid:17459960 fatcat:dzs5lj3nkzcg7bckpsmbvgh3gm

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  
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.  ...  Comparative modeling and docking of ScMYB76 with MYBCORE cis-motif was generated and evaluated by structure quality assessment parameters.  ...  Conflict of Interest The authors declare that they have no conflict of interest. References  ... 
doi:10.17485/ijst/2016/v9i37/93672 fatcat:mh2jbplyvrgjnbpw3hkwv44ina

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  
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.  ...  Comparative modeling and docking of ScMYB50/23 with MYBCORE cis-motif was generated and evaluated by structure quality assessment parameters.  ...  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

Integrative computational protocol for the discovery of inhibitors of the Helicobacter pylori nickel response regulator (NikR)

Aldo Segura-Cabrera, Xianwu Guo, Arturo Rojo-Domínguez, Mario A. Rodríguez-Pérez
2011 Journal of Molecular Modeling  
These compounds target the DNA-binding sites of HpNikR so that HpNikR-compound binding could be able to mimic key interactions in the DNA-protein recognition process.  ...  HpNikR inhibitors with promising potential against H. pylori could also act against other human bacterial pathogens due to the conservation of targeting motif of NikR involved in DNA-protein interaction  ...  TFmodeller compiles information about protein-DNA interfaces deposited in the Protein Data Bank and uses it to model similar interfaces and produce a list of residues interacting with DNA related by homology  ... 
doi:10.1007/s00894-011-0962-2 pmid:21360181 fatcat:5ezve2bqivczhdizguemzqdqna

2‐oxoglutarate modulates the affinity of FurA for the ntcA promoter in Anabaena sp. PCC 7120

Jorge Guío, Cristina Sarasa‐Buisan, Adrián Velázquez‐Campoy, María Teresa Bes, María F. Fillat, María Luisa Peleato, Emma Sevilla
2019 FEBS Letters  
This study provides evidence of a new additional control point in the complex network controlled by the NtcA and FurA proteins.  ...  Both of them show a complex intertwined regulatory circuit to achieve a suitable regulation of nitrogen fixation.  ...  As FurA is a DNA-binding protein, a new model was constructed in complex with DNA using the TFmodeller server (Fig. 1D ).  ... 
doi:10.1002/1873-3468.13610 pmid:31538336 fatcat:3nkiu3fkxndongnu5k55imyn4i

Prediction of TF target sites based on atomistic models of protein-DNA complexes

Vladimir Angarica, Abel Pérez, Ana T Vasconcelos, Julio Collado-Vides, Bruno Contreras-Moreira
2008 BMC Bioinformatics  
Results: Here we describe a structure-based methodology for predicting sequence motifs starting from the coordinates of a TF-DNA complex.  ...  Thirdly, the algorithm is compared with a reference structural method based on contact counts, obtaining comparable predictions for the experimental complexes and more accurate sequence motifs for the  ...  This paper is dedicated to the memory of Juan Antonio Contreras Beorlegui.  ... 
doi:10.1186/1471-2105-9-436 pmid:18922190 pmcid:PMC2585596 fatcat:whh22rtiyrgdvftreshfpmzfpq

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 web interface allows the user to: (i) browse DNA-binding proteins by keyword; (ii) find proteins that recognize a similar DNA motif and (iii) BLAST similar DNA-binding proteins, highlighting interface  ...  Vladimir Espinosa Angarica, Carlos Rodrı´guez Penagos, Alberto Santos Zavaleta, Osvaldo Gran˜a, Jacques Van Helden, Heladia Salgado and Julio Collado-Vides for their help, support, suggestions and reviews of  ... 
doi:10.1093/nar/gkp781 pmid:19767616 pmcid:PMC2808867 fatcat:5pwlfif6izdpdcojkmbf2c4pkm

An effective approach for generating a three-Cys2His2 zinc-finger-DNA complex model by docking

Chun-Chi Chou, M Rajasekaran, Chinpan Chen
2010 BMC Bioinformatics  
However, a protein-DNA complex model whereby the protein wraps around DNA has not been reported.  ...  This approach is efficient for generating a zinc-finger protein-DNA complex model for unknown complex structures in which the protein wraps around DNA.  ...  Homology modeling is an alternative approach to obtain a protein-DNA complex model. Programs such as TFmodeller can model the complex according to homologous complex structure [2] .  ... 
doi:10.1186/1471-2105-11-334 pmid:20565873 pmcid:PMC2905368 fatcat:muz4yxojknakbjjt4t2xdffbmi

Dissection of FixK 2 protein‐DNA interaction unveils new insights into Bradyrhizobium diazoefficiens lifestyles control

Juan J. Cabrera, Andrea Jiménez‐Leiva, Laura Tomás‐Gallardo, Sergio Parejo, Sara Casado, María J. Torres, Eulogio J. Bedmar, María J. Delgado, Socorro Mesa
2021 Environmental Microbiology  
While R200 was essential for DNA binding and activity of FixK2 , L195 was involved in protein-DNA complex stability.  ...  The FixK2 protein plays a pivotal role in a complex regulatory network, which controls genes for microoxic, denitrifying, and symbiotic nitrogen-fixing lifestyles in Bradyrhizobium diazoefficiens.  ...  All authors read and approved the final version of the manuscript.  ... 
doi:10.1111/1462-2920.15661 pmid:34227211 fatcat:etap5pdsojbj3nomqinkwn5u6m

Algoritmos en bioinformática estructural

Bruno Contreras-Moreira
Apéndices 7.1 Abreviaturas CM Comparative Modelling DSSP Define Secondary Structure of Proteins FR Fold Recognition NMR Nuclear Magnetic Resonance NN Nearest Neighbor PCR Polymerase Chain  ...  -Obtain the probability of obtaining the given proportion of aligned residues (with respect to the shortest protein model) by chance.  ... 
doi:10.20350/digitalcsic/8544 fatcat:q5jbsipewnhtflwxokvhpmlcee