If you use this server, please cite: Sandal M, Duy TP, Cona M, Zung H, Carloni P, et al. (2013) GOMoDo: A GPCRs Online Modeling and Docking Webserver. PLoS ONE 8(9): e74092. doi:10.1371/journal.pone.0074092

Please always cite the relevant papers for the software you have used thanks to this server.

Alignment

BLAST

  1. Altschul, S; Gish, W; Miller, W; Myers, E; Lipman, D (October 1990). "Basic local alignment search tool". Journal of Molecular Biology 215 (3): 403–410.
  2. Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ. (September 1997) "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.", Nucleic Acids Res. 25(17):3389-402.

HHSEARCH / HHPRED

  1. Söding J (2005). "Protein homology detection by HMM-HMM comparison". Bioinformatics 21 (7): 951–960
  2. Söding J, Biegert A, Lupas AN. (2005) "The HHpred interactive server for protein homology detection and structure prediction." Nucleic Acids Res. Jul 1;33(Web Server issue):W244-8.

Homology modeling and model assessment

MODELLER

  1. N. Eswar, M. A. Marti-Renom, B. Webb, M. S. Madhusudhan, D. Eramian, M. Shen, U. Pieper, A. Sali. (2006) "Comparative Protein Structure Modeling With MODELLER." Current Protocols in Bioinformatics, John Wiley and Sons, Inc., Supplement 15, 5.6.1-5.6.30, 2006.
  2. M.A. Marti-Renom, A. Stuart, A. Fiser, R. Sánchez, F. Melo, A. Sali. "Comparative protein structure modeling of genes and genomes." Annu. Rev. Biophys. Biomol. Struct. 29, 291-325, 2000.
  3. A. Sali, T.L. Blundell. (1993) "Comparative protein modelling by satisfaction of spatial restraints." J. Mol. Biol. 234, 779-815, 1993.
  4. A. Fiser, R.K. Do, A. Sali. (2000) "Modeling of loops in protein structures", Protein Science 9. 1753-1773, 2000.

DOPE scoring function

  1. Shen MY, Sali A. (2006) "Statistical potential for assessment and prediction of protein structures." Protein Sci. 2006 Nov;15(11):2507-24.

GA341 scoring function

  1. John B, Sali A. (2003) Comparative protein structure modeling by iterative alignment, model building and model assessment." Nucleic Acids Res. 2003 Jul 15;31(14):3982-92.

VADAR

  1. Leigh Willard, Anuj Ranjan,Haiyan Zhang,Hassan Monzavi, Robert F. Boyko, Brian D. Sykes, and David S. Wishart (2003) "VADAR: a web server for quantitative evaluation of protein structure quality" Nucleic Acids Res. 2003 July 1; 31 (13): 3316.3319

Docking

AUTODOCK VINA

  1. Trott O, Olson AJ. (2010) "AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading." J Comput Chem. 2010 Jan 30;31(2):455-61.

HADDOCK

  1. Cyril Dominguez, Rolf Boelens and Alexandre M.J.J. Bonvin (2003). "HADDOCK: a protein-protein docking approach based on biochemical and/or biophysical information.", J. Am. Chem. Soc. 125, 1731-1737.
  2. S.J. de Vries, A.D.J. van Dijk, M. Krzeminski, M. van Dijk, A. Thureau, V. Hsu, T. Wassenaar and A.M.J.J. Bonvin (2007) "HADDOCK versus HADDOCK: New features and performance of HADDOCK2.0 on the CAPRI targets.", Proteins: Struc. Funct. & Bioinformatic 69, 726-733
  3. A.D.J. van Dijk and A.M.J.J. Bonvin (2006) "Solvated docking: introducing water into the modelling of biomolecular complexes." Bioinformatics, 22 2340-2347 (2006).

Other utilities

LOVOALIGN

  1. L. Martínez, R. Andreani, J. M. Martínez, (2007) "Convergent algorithms for protein structural alignment." , BMC Bioinformatics, 2007, 8:306.

FPOCKET

  1. Vincent Le Guilloux, Peter Schmidtke and Pierre Tuffery (2009) "Fpocket: An open source platform for ligand pocket detection", BMC Bioinformatics, 2009, 10:168

MGLTOOLS

  1. Morris, G. M., Huey, R., Lindstrom, W., Sanner, M. F., Belew, R. K., Goodsell, D. S. and Olson, A. J. (2009) Autodock4 and AutoDockTools4: automated docking with selective receptor flexiblity. J. Computational Chemistry 2009, 16: 2785-91

OPENBABEL

  1. N M O'Boyle, M Banck, C A James, C Morley, T Vandermeersch, and G R Hutchison. (2011) "Open Babel: An open chemical toolbox." J. Cheminf., 3, 33. DOI:10.1186/1758-2946-3-33

MATPLOTLIB

  1. Hunter, J.D. (2007) "Matplotlib: A 2D Graphics Environment", Computing in Science and Engineering, 9(3):90-95
  2. John Hunter, creator of Matplotlib, passed away in August 2012. Please consider donating to the memorial fund.