Citation Information

ePMV

Please acknowledge the use of the ePMV software that results in any published work, including scientific papers, textbooks, covers, animations, slides, etc. by citing the following reference:

• • Johnson, G.T. and Autin, L., Goodsell, D.S., Sanner, M.F., Olson, A.J. (2011). ePMV Embeds Molecular Modeling into Professional Animation Software Environments. Structure 19, 293-303.

PMV

Please acknowledge the use of the PMV software that results in any published work, including scientific papers, films and videotapes, by citing the following reference:

• • Michel F. Sanner. Python: A Programming Language for Software Integration and Development. J. Mol. Graphics Mod., 1999, Vol 17, February. pp57-61

MSMS molecular surface

The MSMS library is used by the Pmv module msmsCommands. Please acknowledge the use of the MSMS library that results in any published work, including scientific papers, films and videotapes, by citing the following reference:

• • Sanner, M.F., Spehner, J.-C., and Olson, A.J. (1996) Reduced surface: an efficient way to compute molecular surfaces. Biopolymers, Vol. 38, (3),305-320.

ADT

Please acknowledge the use of the ADT software that results in any published work, including scientific papers, films and videotapes, by citing the following reference:

• • Michel F. Sanner. Python: A Programming Language for Software Integration and Development. J. Mol. Graphics Mod., 1999, Vol 17, February. pp57-61

Volume rendering

The PCVolRen library is used in the PMV module .... Please acknowledge the use of the FAST VOLUME RENDERING library that results in any published work, including scientific papers, films and videotapes, by citing the following reference:

• • Bajaj, C, Park, S., Thane, A., (2002), A Parallel Multi-PC Volume Rendering System, ICES and CS Technical Report, University of Texas, 2002.

Isocontouring

The isocontour library is used by the Pmv module .... Please acknowledge the use of the isocontour library that results in any published work, including scientific papers, films, videos and videotapes, by citing the following reference:

• • Bajaj, C, Pascucci, V., Schikore, D., (1996), Fast IsoContouring for Improved Interactivity, Proceedings of ACM Siggraph/IEEE Symposium on Volume Visualization, ACM Press, 1996, pages 39 - 46, San Francisco, CA

APBS

APBS is used in the Pmv Module.... Please acknowledge the use of APBS that results in any published work, including scientific papers,films and videotapes, by citing the following reference:

• • Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA *98*, 10037-10041 2001

Stride

stride is used in Pmv Module...... Please acknowledge the use of stride that results in any published work, including scientific papers,films and videotapes, by citing the following reference:

• • Frishman,D & Argos,P. (1995) Knowledge-based secondary structure assignment. Proteins: structure, function and genetics, 23, 566-579.

PROSS Secondary Structure assignation

PROSS is used in Pmv for Secondary Structure prediction. Please acknowledge the use of PROSS that results in any published work, including scientific papers,films and videotapes, by citing the following reference:

• • Srinivasan R, Rose GD. (1999) A physical basis for protein secondary structure. Proc. Natl. Acad. Sci. USA 96, 14258-63.

PyRosetta

• • Chaudhury, S., Lyskov, S., Gray, J.J. (2010) PyRosetta: a script-based interface for implementing custom molecular modeling algorithms using Rosetta. Bioinformatics

Modeller

• • N. Eswar, M. A. Marti-Renom, B. Webb, M. S. Madhusudhan, D. Eramian, M. Shen, U. Pieper, A. Sali. Comparative Protein Structure Modeling With MODELLER. Current Protocols in Bioinformatics, John Wiley & Sons, Inc., Supplement 15, 5.6.1-5.6.30, 2006.

  • 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.

  • A. Sali & T.L. Blundell. Comparative protein modelling by satisfaction of spatial restraints. J. Mol. Biol. 234, 779-815, 1993.

  • A. Fiser, R.K. Do, & A. Sali. Modeling of loops in protein structures, Protein Science 9. 1753-1773, 2000.

Early citations of the ePMV paper in Structure

Please acknowledge the use of the ePMV software that results in any published work, including scientific papers, textbooks, covers, animations, slides, etc. by citing the following reference:

• • Gökhan Tolun, Alexander M. Makhov, Steven J. Ludtke, and Jack D. Griffith, Details of ssDNA annealing revealed by an HSV-1 ICP8–ssDNA binary complex, Nucl. Acids Res. April 19, 2013 doi:10.1093/nar/gkt266

  • Lv, Z., Tek, A., Da Silva, F., Empereur-mot, C., Chavent, M., Baaden, M. (2013). Game On, Science - How Video Game Technology May Help Biologists Tackle Visualization Challenges, PLoS ONE 8 (3), art. no. e57990

  • Hornus, S., Lévy, B., Larivière, D., Fourmentin, E. (2013) Easy DNA Modeling and More with GraphiteLifeExplorer. PLoS ONE 8 (1), art. no. e53609.

  • Autin, L., Johnson, G., Hake, J., Olson, A., Sanner, M. (2012). uPy: A ubiquitous CG python API with biological-modeling applications. IEEE Computer Graphics and Applications 32 (5), art. no. 6311371.

  • Jacob, R.B., Andersen, T., McDougal, O.M. Accessible high-throughput virtual screening molecular docking software for students and educators. PLoS Computational Biology 8 (5), art. no. e1002499.

  • Jenkinson, J., McGill, G. (2012) Visualizing protein interactions and dynamics: Evolving a visual language for molecular animation, CBE Life Sciences Education 11 (1).

  • Baugh, E.H., Lyskov, S., Weitzner, B.D., Gray, J.J., (2011) Real-time PyMOL visualization for Rosetta and PyRosetta, PLoS ONE 6 (8), art. no. e21931.