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Sense and simplicity in HADDOCK scoring: Lessons from CASP‐CAPRI round 1
Our information‐driven docking approach HADDOCK is a consistent top predictor and scorer since the start of its participation in the CAPRI community‐wide experiment. This sustained performance is due, in part, to its ability to integrate experimental data and/or bioinformatics information into the m...
Autores principales: | , , , , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
John Wiley and Sons Inc.
2016
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5324763/ https://www.ncbi.nlm.nih.gov/pubmed/27802573 http://dx.doi.org/10.1002/prot.25198 |
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author | Vangone, A. Rodrigues, J. P. G. L. M. Xue, L. C. van Zundert, G. C. P. Geng, C. Kurkcuoglu, Z. Nellen, M. Narasimhan, S. Karaca, E. van Dijk, M. Melquiond, A. S. J. Visscher, K. M. Trellet, M. Kastritis, P. L. Bonvin, A. M. J. J. |
author_facet | Vangone, A. Rodrigues, J. P. G. L. M. Xue, L. C. van Zundert, G. C. P. Geng, C. Kurkcuoglu, Z. Nellen, M. Narasimhan, S. Karaca, E. van Dijk, M. Melquiond, A. S. J. Visscher, K. M. Trellet, M. Kastritis, P. L. Bonvin, A. M. J. J. |
author_sort | Vangone, A. |
collection | PubMed |
description | Our information‐driven docking approach HADDOCK is a consistent top predictor and scorer since the start of its participation in the CAPRI community‐wide experiment. This sustained performance is due, in part, to its ability to integrate experimental data and/or bioinformatics information into the modelling process, and also to the overall robustness of the scoring function used to assess and rank the predictions. In the CASP‐CAPRI Round 1 scoring experiment we successfully selected acceptable/medium quality models for 18/14 of the 25 targets – a top‐ranking performance among all scorers. Considering that for only 20 targets acceptable models were generated by the community, our effective success rate reaches as high as 90% (18/20). This was achieved using the standard HADDOCK scoring function, which, thirteen years after its original publication, still consists of a simple linear combination of intermolecular van der Waals and Coulomb electrostatics energies and an empirically derived desolvation energy term. Despite its simplicity, this scoring function makes sense from a physico‐chemical perspective, encoding key aspects of biomolecular recognition. In addition to its success in the scoring experiment, the HADDOCK server takes the first place in the server prediction category, with 16 successful predictions. Much like our scoring protocol, because of the limited time per target, the predictions relied mainly on either an ab initio center‐of‐mass and symmetry restrained protocol, or on a template‐based approach whenever applicable. These results underline the success of our simple but sensible prediction and scoring scheme. Proteins 2017; 85:417–423. © 2016 Wiley Periodicals, Inc. |
format | Online Article Text |
id | pubmed-5324763 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2016 |
publisher | John Wiley and Sons Inc. |
record_format | MEDLINE/PubMed |
spelling | pubmed-53247632017-03-14 Sense and simplicity in HADDOCK scoring: Lessons from CASP‐CAPRI round 1 Vangone, A. Rodrigues, J. P. G. L. M. Xue, L. C. van Zundert, G. C. P. Geng, C. Kurkcuoglu, Z. Nellen, M. Narasimhan, S. Karaca, E. van Dijk, M. Melquiond, A. S. J. Visscher, K. M. Trellet, M. Kastritis, P. L. Bonvin, A. M. J. J. Proteins Articles Our information‐driven docking approach HADDOCK is a consistent top predictor and scorer since the start of its participation in the CAPRI community‐wide experiment. This sustained performance is due, in part, to its ability to integrate experimental data and/or bioinformatics information into the modelling process, and also to the overall robustness of the scoring function used to assess and rank the predictions. In the CASP‐CAPRI Round 1 scoring experiment we successfully selected acceptable/medium quality models for 18/14 of the 25 targets – a top‐ranking performance among all scorers. Considering that for only 20 targets acceptable models were generated by the community, our effective success rate reaches as high as 90% (18/20). This was achieved using the standard HADDOCK scoring function, which, thirteen years after its original publication, still consists of a simple linear combination of intermolecular van der Waals and Coulomb electrostatics energies and an empirically derived desolvation energy term. Despite its simplicity, this scoring function makes sense from a physico‐chemical perspective, encoding key aspects of biomolecular recognition. In addition to its success in the scoring experiment, the HADDOCK server takes the first place in the server prediction category, with 16 successful predictions. Much like our scoring protocol, because of the limited time per target, the predictions relied mainly on either an ab initio center‐of‐mass and symmetry restrained protocol, or on a template‐based approach whenever applicable. These results underline the success of our simple but sensible prediction and scoring scheme. Proteins 2017; 85:417–423. © 2016 Wiley Periodicals, Inc. John Wiley and Sons Inc. 2016-11-24 2017-03 /pmc/articles/PMC5324763/ /pubmed/27802573 http://dx.doi.org/10.1002/prot.25198 Text en © 2016 The Authors Proteins: Structure, Function, and Bioinformatics Published by Wiley Periodicals, Inc. This is an open access article under the terms of the Creative Commons Attribution‐NonCommercial (http://creativecommons.org/licenses/by-nc/4.0/) License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited and is not used for commercial purposes. |
spellingShingle | Articles Vangone, A. Rodrigues, J. P. G. L. M. Xue, L. C. van Zundert, G. C. P. Geng, C. Kurkcuoglu, Z. Nellen, M. Narasimhan, S. Karaca, E. van Dijk, M. Melquiond, A. S. J. Visscher, K. M. Trellet, M. Kastritis, P. L. Bonvin, A. M. J. J. Sense and simplicity in HADDOCK scoring: Lessons from CASP‐CAPRI round 1 |
title | Sense and simplicity in HADDOCK scoring: Lessons from CASP‐CAPRI round 1 |
title_full | Sense and simplicity in HADDOCK scoring: Lessons from CASP‐CAPRI round 1 |
title_fullStr | Sense and simplicity in HADDOCK scoring: Lessons from CASP‐CAPRI round 1 |
title_full_unstemmed | Sense and simplicity in HADDOCK scoring: Lessons from CASP‐CAPRI round 1 |
title_short | Sense and simplicity in HADDOCK scoring: Lessons from CASP‐CAPRI round 1 |
title_sort | sense and simplicity in haddock scoring: lessons from casp‐capri round 1 |
topic | Articles |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5324763/ https://www.ncbi.nlm.nih.gov/pubmed/27802573 http://dx.doi.org/10.1002/prot.25198 |
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