addenda and errata\(\def\hfill{\hskip 5em}\def\hfil{\hskip 3em}\def\eqno#1{\hfil {#1}}\)

Journal logoSTRUCTURAL
BIOLOGY
ISSN: 2059-7983

PRISM-EM: template interface-based modelling of multi-protein complexes guided by cryo-electron microscopy density maps. Corrigendum

aCenter for Computational Biology and Bioinformatics and College of Engineering, Koc University, 34450 Istanbul, Turkey, bChemical and Biological Engineering, College of Engineering, Koc University, 34450 Istanbul, Turkey, cCancer and Inflammation Program, Leidos Biomedical Research Inc., National Cancer Institute, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA, dSackler Institute of Molecular Medicine, Department of Human Genetics and Molecular Medicine, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel, and eComputer Engineering, Koc University, 34450 Istanbul, Turkey
*Correspondence e-mail: okeskin@ku.edu.tr, agursoy@ku.edu.tr

Edited by G. J. Kleywegt, EMBL-EBI, Hinxton, England (Received 30 November 2016; accepted 12 December 2017)

A revised Table 6[link] and Supporting Information are provided for the article by Kuzu et al. [(2016[Kuzu, G., Keskin, O., Nussinov, R. & Gursoy, A. (2016). Acta Cryst. D72, 1137-1148.]), Acta Cryst. D72, 1137–1148].

Table 6
Performance of our method on the HADDOCK-EM set (van Zundert et al., 2015[Zundert, G. C. P. van, Melquiond, A. S. J. & Bonvin, A. M. J. J. (2015). Structure, 23, 949-960.]) where cases were selected from the ZDOCK benchmark set

Models were compared with the PDB structures and the results are presented with i.r.m.s.d. values. The first column gives the PDB code of the complex. The second column indicates the difficulty level assigned as in the benchmark data set. The third column lists the HADDOCK-EM results using unbound structures (listed in the benchmark). The fourth column gives the PRISM-EM results using the same set of unbound structures. Note that for equal comparison, columns 3 and 4 should be used. The fifth column lists the i.r.m.s.d. values of PRISM-EM using the alternative structures of the same proteins available in the PDB. The sixth column lists the i.r.m.s.d. values when the individual proteins are from the bound complex structures. A dash indicates a case where PRISM-EM could not find a model. Asterisks indicate use of the self-template interfaces of bound structures.

    I.r.m.s.d. (Å)
    HADDOCK-EM (itw) PRISM-EM
Complex Difficulty Query (unbound) proteins Query (unbound) proteins Query proteins and their alternatives Bound proteins
1avx Easy 0.67 1.72 1.01 0.51
2oul Easy 0.63 0.83 0.83 0.55
1ay7 Easy 0.66 1.25 1.19 0.75
4cpa Easy 0.94
1ahw Easy 0.91 1.23 1.23 0.47*
7cei Easy 0.78 0.90 0.90 0.53
2oob Easy 0.97 7.43 7.43 0.73*
2fd6 Easy 1.13 1.43 0.94 0.45
1ak4 Easy 1.22 1.40 1.40 1.01
1b6c Easy 1.88 2.22 2.22 0.74
1bgx Medium 4.85 7.18* 7.18* 0.53*
1r6q Medium 1.26 9.38 0.95 0.72
1m10 Medium 2.82 2.59 0.93 0.47
1acb Medium 2.43 9.24 0.68 0.59*
1jk9 Hard 2.32 3.11 3.11 0.49
1bkd Hard 3.62 4.61 0.92 0.49
1jmo Hard 4.23 15.62 15.62 3.43*

After the online publication of the article by Kuzu et al. (2016[Kuzu, G., Keskin, O., Nussinov, R. & Gursoy, A. (2016). Acta Cryst. D72, 1137-1148.]), Drs Sjoer de Vries and Alexandre Bonvin noticed an apparent anomaly in the i.r.m.s.d. values in Table 6[link]. Indeed, there were erroneous and duplicate entries in this table. (i) The values in the old Table 6[link] were computed using a definition which is different from that used in CAPRI. In the paper, the superposition was performed for the entire protein, and the r.m.s.d. was then computed only for the interface residues. We have revised Table 6[link] by recalculating i.r.m.s.d. values as described in CAPRI evaluations (Mendez et al., 2003[Mendez, R., Leplae, R., De Maria, L. & Wodak, S. J. (2003). Proteins, 52, 51-67.]) using the script irsmd.py (Viswanath et al., 2013[Viswanath, S., Ravikant, D. V. & Elber, R. (2013). Proteins, 81, 592-606.]), considering only the interface backbone atoms. (ii) The results for alternative conformations were compared with the rigid-body docking of HADDOCK-EM (it0) in the old table. We now compare these results with their explicit solvent docking results (itw), which are their best generated complexes among the top 400 solutions, with our results for both unbound and alternative structures. We have revised Table 6[link] accordingly. Using only unbound structures, HADDOCK-EM (itw) models all 17 cases, where 15 of them have i.r.m.s.d. values less than 4 Å. PRISM-EM models ten of the 17 cases using unbound structures, where only one model has a better i.r.m.s.d. (1m10) than HADDOCK-EM models. Therefore, using unbound structures, HADDOCK-EM outperforms PRISM-EM (comparison of columns 3 and 4). When PRISM-EM considers alternative structures, the following cases additionally become better than HADDOCK-EM: 2fd6 (easy), 1r6q (medium), 1acb (medium) and 1bkd (hard). The supplementary tables have been revised to provide the alternative structures which have been used in the calculations. All of the models of Table 6[link] are also provided in the Supporting Information.

The authors apologize for any inconvenience that this has caused.

Supporting information


Footnotes

Current address: Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA.

References

First citationKuzu, G., Keskin, O., Nussinov, R. & Gursoy, A. (2016). Acta Cryst. D72, 1137–1148.  CrossRef IUCr Journals
First citationMendez, R., Leplae, R., De Maria, L. & Wodak, S. J. (2003). Proteins, 52, 51–67.  Web of Science CrossRef PubMed CAS
First citationViswanath, S., Ravikant, D. V. & Elber, R. (2013). Proteins, 81, 592–606.  CrossRef CAS PubMed
First citationZundert, G. C. P. van, Melquiond, A. S. J. & Bonvin, A. M. J. J. (2015). Structure, 23, 949–960.  Web of Science PubMed

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Journal logoSTRUCTURAL
BIOLOGY
ISSN: 2059-7983
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