pyDockDNA: A new web server for energy-based protein-DNA docking and scoring
Proteins and nucleic acids are essential biological macromolecules for cell life. Indeed, interactions between proteins and DNA regulate many biological processes such as protein synthesis, signal transduction, DNA storage, or DNA replication and repair. Despite their importance, less than 4% of tot...
| Main Authors: | , , , |
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2022-10-01
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| Series: | Frontiers in Molecular Biosciences |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fmolb.2022.988996/full |
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| author | Luis Angel Rodríguez-Lumbreras Luis Angel Rodríguez-Lumbreras Brian Jiménez-García Brian Jiménez-García Silvia Giménez-Santamarina Silvia Giménez-Santamarina Juan Fernández-Recio Juan Fernández-Recio |
| author_facet | Luis Angel Rodríguez-Lumbreras Luis Angel Rodríguez-Lumbreras Brian Jiménez-García Brian Jiménez-García Silvia Giménez-Santamarina Silvia Giménez-Santamarina Juan Fernández-Recio Juan Fernández-Recio |
| author_sort | Luis Angel Rodríguez-Lumbreras |
| collection | DOAJ |
| description | Proteins and nucleic acids are essential biological macromolecules for cell life. Indeed, interactions between proteins and DNA regulate many biological processes such as protein synthesis, signal transduction, DNA storage, or DNA replication and repair. Despite their importance, less than 4% of total structures deposited in the Protein Data Bank (PDB) correspond to protein-DNA complexes, and very few computational methods are available to model their structure. We present here the pyDockDNA web server, which can successfully model a protein-DNA complex with a reasonable predictive success rate (as benchmarked on a standard dataset of protein-DNA complex structures, where DNA is in B-DNA conformation). The server implements the pyDockDNA program, as a module of pyDock suite, thus including third-party programs, modules, and previously developed tools, as well as new modules and parameters to handle the DNA properly. The user is asked to enter Protein Data Bank files for protein and DNA input structures (or suitable models) and select the chains to be docked. The server calculations are mainly divided into three steps: sampling by FTDOCK, scoring with new energy-based parameters and the possibility of applying external restraints. The user can select different options for these steps. The final output screen shows a 3D representation of the top 10 models and a table sorting the model according to the scoring function selected previously. All these output files can be downloaded, including the top 100 models predicted by pyDockDNA. The server can be freely accessed for academic use (https://model3dbio.csic.es/pydockdna). |
| first_indexed | 2024-04-11T10:29:57Z |
| format | Article |
| id | doaj.art-16eae038fc514e338ef924ba7bea44f7 |
| institution | Directory Open Access Journal |
| issn | 2296-889X |
| language | English |
| last_indexed | 2024-04-11T10:29:57Z |
| publishDate | 2022-10-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Molecular Biosciences |
| spelling | doaj.art-16eae038fc514e338ef924ba7bea44f72022-12-22T04:29:28ZengFrontiers Media S.A.Frontiers in Molecular Biosciences2296-889X2022-10-01910.3389/fmolb.2022.988996988996pyDockDNA: A new web server for energy-based protein-DNA docking and scoringLuis Angel Rodríguez-Lumbreras0Luis Angel Rodríguez-Lumbreras1Brian Jiménez-García2Brian Jiménez-García3Silvia Giménez-Santamarina4Silvia Giménez-Santamarina5Juan Fernández-Recio6Juan Fernández-Recio7Barcelona Supercomputing Center, Barcelona, SpainInstituto de Ciencias de la Vid y del Vino (ICVV), Logroño, SpainBarcelona Supercomputing Center, Barcelona, SpainZymvol Biomodeling SL, Barcelona, SpainBarcelona Supercomputing Center, Barcelona, SpainICMol, Universitat de València, Paterna, SpainBarcelona Supercomputing Center, Barcelona, SpainInstituto de Ciencias de la Vid y del Vino (ICVV), Logroño, SpainProteins and nucleic acids are essential biological macromolecules for cell life. Indeed, interactions between proteins and DNA regulate many biological processes such as protein synthesis, signal transduction, DNA storage, or DNA replication and repair. Despite their importance, less than 4% of total structures deposited in the Protein Data Bank (PDB) correspond to protein-DNA complexes, and very few computational methods are available to model their structure. We present here the pyDockDNA web server, which can successfully model a protein-DNA complex with a reasonable predictive success rate (as benchmarked on a standard dataset of protein-DNA complex structures, where DNA is in B-DNA conformation). The server implements the pyDockDNA program, as a module of pyDock suite, thus including third-party programs, modules, and previously developed tools, as well as new modules and parameters to handle the DNA properly. The user is asked to enter Protein Data Bank files for protein and DNA input structures (or suitable models) and select the chains to be docked. The server calculations are mainly divided into three steps: sampling by FTDOCK, scoring with new energy-based parameters and the possibility of applying external restraints. The user can select different options for these steps. The final output screen shows a 3D representation of the top 10 models and a table sorting the model according to the scoring function selected previously. All these output files can be downloaded, including the top 100 models predicted by pyDockDNA. The server can be freely accessed for academic use (https://model3dbio.csic.es/pydockdna).https://www.frontiersin.org/articles/10.3389/fmolb.2022.988996/fullstructural modelingAb initio dockingprotein-DNA interactionscoring functiondocking benchmarknucleotide parameters |
| spellingShingle | Luis Angel Rodríguez-Lumbreras Luis Angel Rodríguez-Lumbreras Brian Jiménez-García Brian Jiménez-García Silvia Giménez-Santamarina Silvia Giménez-Santamarina Juan Fernández-Recio Juan Fernández-Recio pyDockDNA: A new web server for energy-based protein-DNA docking and scoring Frontiers in Molecular Biosciences structural modeling Ab initio docking protein-DNA interaction scoring function docking benchmark nucleotide parameters |
| title | pyDockDNA: A new web server for energy-based protein-DNA docking and scoring |
| title_full | pyDockDNA: A new web server for energy-based protein-DNA docking and scoring |
| title_fullStr | pyDockDNA: A new web server for energy-based protein-DNA docking and scoring |
| title_full_unstemmed | pyDockDNA: A new web server for energy-based protein-DNA docking and scoring |
| title_short | pyDockDNA: A new web server for energy-based protein-DNA docking and scoring |
| title_sort | pydockdna a new web server for energy based protein dna docking and scoring |
| topic | structural modeling Ab initio docking protein-DNA interaction scoring function docking benchmark nucleotide parameters |
| url | https://www.frontiersin.org/articles/10.3389/fmolb.2022.988996/full |
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