Sense and simplicity in HADDOCK scoring: Lessons from CASP-CAPRI round 1

A Vangone, J P G L M Rodrigues, L C Xue, G C P van Zundert, C. Geng, Z Kurkcuoglu, M Nellen, S Narasimhan, E Karaca, M van Dijk, A S J Melquiond, K M Visscher, M Trellet, P L Kastritis, A M J J Bonvin

Research output: Contribution to journalArticle

Abstract

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.

LanguageEnglish
Pages417-423
Number of pages7
JournalProteins
Volume85
Issue number3
DOIs
StatePublished - Mar 2017

Cite this

Vangone, A., Rodrigues, J. P. G. L. M., Xue, L. C., van Zundert, G. C. P., Geng, C., Kurkcuoglu, Z., ... Bonvin, A. M. J. J. (2017). Sense and simplicity in HADDOCK scoring: Lessons from CASP-CAPRI round 1. Proteins, 85(3), 417-423. DOI: 10.1002/prot.25198
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. In: Proteins. 2017 ; Vol. 85, No. 3. pp. 417-423
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Vangone, A, Rodrigues, JPGLM, Xue, LC, van Zundert, GCP, Geng, C, Kurkcuoglu, Z, Nellen, M, Narasimhan, S, Karaca, E, van Dijk, M, Melquiond, ASJ, Visscher, KM, Trellet, M, Kastritis, PL & Bonvin, AMJJ 2017, 'Sense and simplicity in HADDOCK scoring: Lessons from CASP-CAPRI round 1' Proteins, vol 85, no. 3, pp. 417-423. DOI: 10.1002/prot.25198

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.

In: Proteins, Vol. 85, No. 3, 03.2017, p. 417-423.

Research output: Contribution to journalArticle

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AU - Rodrigues,J P G L M

AU - Xue,L C

AU - van Zundert,G C P

AU - Geng,C.

AU - Kurkcuoglu,Z

AU - Nellen,M

AU - Narasimhan,S

AU - Karaca,E

AU - van Dijk,M

AU - Melquiond,A S J

AU - Visscher,K M

AU - Trellet,M

AU - Kastritis,P L

AU - Bonvin,A M J J

N1 - © 2016 The Authors Proteins: Structure, Function, and Bioinformatics Published by Wiley Periodicals, Inc.

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N2 - 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.

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Vangone A, Rodrigues JPGLM, Xue LC, van Zundert GCP, Geng C, Kurkcuoglu Z et al. Sense and simplicity in HADDOCK scoring: Lessons from CASP-CAPRI round 1. Proteins. 2017 Mar;85(3):417-423. Available from, DOI: 10.1002/prot.25198