The DisVis and PowerFit Web Servers: Explorative and Integrative Modeling of Biomolecular Complexes

Journal of Molecular Biology

Volumn 429, Issue 3, 2017, Pages 399-407

  van Zundert, G C P ^a   Trellet, M ^a   Schaarschmidt, J ^a   Kurkcuoglu, Z ^a   David, M ^b   Verlato, M ^c   Rosato, A ^d   Bonvin, A M J J ^a  

^a UTRECHT UNIVERSITY   (Netherlands)

^b LIP   (Portugal)

^c SEZIONE DI PADOVA   (Italy)

^d UNIVERSITY OF FLORENCE   (Italy)

Author keywords

chemical cross links coupled with mass spectrometry; cryo electron microscopy; fast Fourier transform; GPGPU acceleration

Indexed keywords

ARTICLE; COMPLEX FORMATION; CROSS LINKING; ELECTRON MICROSCOPY; FALSE POSITIVE RESULT; LIGAND BINDING; MASS SPECTROMETRY; METHODOLOGY; PRIORITY JOURNAL; SOFTWARE; STRUCTURAL MODEL; WORKFLOW; BIOLOGY; CHEMISTRY; CRYOELECTRON MICROSCOPY; INTERNET; MACROMOLECULE; MOLECULAR MODEL; PROTEIN CONFORMATION; PROTEIN DATABASE; REPRODUCIBILITY;

MACROMOLECULE;

COMPUTATIONAL BIOLOGY; CRYOELECTRON MICROSCOPY; DATABASES, PROTEIN; INTERNET; MACROMOLECULAR SUBSTANCES; MASS SPECTROMETRY; MODELS, MOLECULAR; PROTEIN CONFORMATION; REPRODUCIBILITY OF RESULTS; SOFTWARE;

EID: 85009349446     PISSN: 00222836     EISSN: 10898638     Source Type: Journal    
DOI: 10.1016/j.jmb.2016.11.032     Document Type: Article

References (16)

1. [1] Bai, X.-C.B., McMullan, G., Scheres, S.H.W., How cryo-EM is revolutionizing structural biology. Trends Biochem. Sci. 40 (2015), 49–57.
2. [2] Leitner, A., Faini, M., Stengel, F., Aebersold, R., Crosslinking and mass spectrometry: an integrated technology to understand the structure and function of molecular machines. Trends Biochem. Sci. 41 (2016), 20–32.
3. [3] Van Zundert, G.C.P., Bonvin, A.M.J.J., Fast and sensitive rigid-body fitting into cryo-EM density maps with PowerFit. AIMS Biophys. 2 (2015), 73–87.
4. [4] Van Zundert, G.C.P., Bonvin, A.M.J.J., DisVis: quantifying and visualizing the accessible interaction space of distance-restrained biomolecular complexes. Bioinformatics 31 (2015), 3222–3224.
5. [5] Van Zundert, G.C.P., Bonvin, A.M.J.J., Defining the limits and reliability of rigid-body fitting in cryo-EM maps using multi-scale image pyramids. J. Struct. Biol. 195 (2016), 252–258.
6. [6] Karney, C.F., Quaternions in molecular modeling. J. Mol. Graph. Model. 25 (2007), 595–604.
7. [7] Wu, X., Milne, J.L., Borgnia, M.J., Rostapshov, A.V., Subramaniam, S., Brooks, B.R., A core-weighted fitting method for docking atomic structures into low-resolution maps: application to cryo-electron microscopy. J. Struct. Biol. 141 (2003), 63–76.
8. [8] Chacón, P., Wriggers, W., Multi-resolution contour-based fitting of macromolecular structures. J. Mol. Biol. 317 (2002), 375–384.
9. [9] Fisher, R.A., On the “probable error” of a coefficient of correlation deduced from a small sample. Metron 1 (1921), 1–32.
10. [10] Volkmann, N., Confidence intervals for fitting of atomic models into low-resolution densities. Acta Crystallogr. D Biol. Crystallogr. 65 (2009), 679–689.
11. [11] Katchalski-Katzir, E., Shariv, I., Eisenstein, M., Friesem, A.A., Aflalo, C., Vakser, I.A., Molecular surface recognition: determination of geometric fit between proteins and their ligands by correlation techniques. Proc. Natl. Acad. Sci. U. S. A. 89 (1992), 2195–2199.
12. [12] Hwang, H., Vreven, T., Janin, J., Weng, Z., Protein–protein docking benchmark version 4.0. Proteins 78 (2010), 3111–3114.
13. [13] Pettersen, E.F., Goddard, T.D., Huang, C.C., Couch, G.S., Greenblatt, D.M., Meng, E.C., Ferrin, T.E., UCSF chimera—a visualization system for exploratory research and analysis. J. Comput. Chem. 25 (2004), 1605–1612.
14. [14] Dominguez, C., Boelens, R., Bonvin, A.M.J.J., HADDOCK: a protein–protein docking approach based on biochemical or biophysical information. J. Am. Chem. Soc. 125 (2003), 1731–1737.
15. [15] Van Zundert, G.C.P., Rodrigues, J.P.G.L.M., Trellet, M., Schmitz, C., Kastritis, P.L., Karaca, E., Melquiond, A.S.J., van Dijk, M., de Vries, S.J., Bonvin, A.M.J.J., The HADDOCK2.2 web server: user-friendly integrative modeling of biomolecular complexes. J. Mol. Biol. 428 (2016), 720–725.
16. [16] Ferrari, T., Gaido, L., Resources and services of the EGEE production infrastructure. J. Grid Comput. 9 (2011), 119–133.