Parameter Sweep Workflows for Modelling Carbohydrate Recognition

Jacq, N. et al.: Grid-enabled virtual Screening against malaria. Journal of Grid Computing 6(1), 29–43 (2008). Springer Netherlands, 2007. doi: 10.1007/s10723-007-9085-5

Goble, C.A., De Roure, D.C.: myExperiment: social networking for workflow-using e-scientists. In: Proceedings of the 2nd Workshop on Workflows in Support of Large-Scale Science, Monterey, California, USA (2007), ISBN:978-1-59593-715-5

Kacsuk, P., Sipos, G.: Multi-Grid, multi-user workflows in the P-GRADE Grid Portal. Journal of Grid Computing 3(3–4), (2005). Springer, 1570–7873; 221–238. doi: 10.1007/s10723-005-9012-6

Ruvinsky, A.M.: Role of binding entropy in the refinement of protein-ligand docking predictions: analysis based on the use of 11 scoring functions. J. Comput. Chem. 28(8), 1364–1372 (2007)

Teixeira, C., Barbault, F., et al.: Molecular modeling studies of N-substituted pyrrole derivatives-Potential HIV-1 gp41 inhibitors. Bioorg. Med. Chem. 16(6), 3039–3048 (2008)

Morris, G.M., et al.: Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function. J. Comput. Chem. 19(14), 1639–1662

Case, D.A. et al.: The Amber bio-molecular simulation programs. J. Comput. Chem. 26, 1668–1688 (2005)

MacKerell, A.D. et al.: CHARMM: the energy function and its parameterization with an overview of the program, in The Encyclopedia of Computational Chemistry. 1, 271–277, P. v. R. Schleyer et al., editors. John Wiley & Sons, Chichester (1998)

Lindahl, E., et al.: GROMACS 3.0: a package for molecular simulation and trajectory analysis. Journal of Molecular Modeling 7, 306–317 (2001)

Bernstein, F., et al.: The protein data bank: a computer-based archival file for macromolecular structures. J. Mol. Biol. 112, 535–542 (1977)

Berman, H.M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T.N., Weissig, H., Shindyalov, I.N., Bourne, P.E.: The protein data bank. Nucleic Acids Res. 28, 235–242 (2000). http://www.rcsb.org/pdb/home/home.do

Morris, A.L., MacArthur, M.W. et al.: Stereochemical quality of protein structure coordinates. Proteins 12(4), 345–364 (1992)

Lovell, S.C., Davis, I.W. et al.: Structure validation by Calpha geometry: phipsi and Cbeta deviation. Proteins 50(3), 437–450 (2003)

Ramachandran, G.N. et al.: Stereochemistry of polypeptide chain configurations. J. Mol. Biol. 7, 95–99 (1963)

Kacsuk, P. et al.: WS-PGRADE: supporting parameter sweep applications in workflows, 3rd Workshop on Workflows in Support of Large-Scale Science, In conjunction with SC 2008, pp. 1–10. IEEE, Austin, TX, USA (2008). doi: 10.1109/WORKS.2008.4723955

Novotny, J., et al.: GridSphere: an advanced portal framework, Euromicro Conference, 2004. In: Proceedings. 30th Volume, Issue, pp. 412–419, 31 Aug.–3 Sept. 2004

Kacsuk, P., et al.: Supporting dynamic parameter sweep applications in workflows—lessons learnt from the CancerGrid project, PARA ‘08, 9th International Workshop on State-of-the-Art in Scientific and Parallel Computing, Trondheim, Norway (2008)

Zhang, X.L.: Roles of glycans and glycopeptides in immune system and immune-related diseases. Curr. Med. Chem. 13(10), 1141–1147 (2006)

Crocker, P.R., Paulson, J.C., Varki, A.: Siglecs and their roles in the immune system. Nat Rev Immunol. 7(4), 255–266 (2007)

Erbacher, A., Gieseke, F., Handgretinger, R., Müller, I.: Dendritic cells: functional aspects of glycosylation and lectins. Hum. Immunol. 70(5), 308–312 (2009)

Reading, P.C., Tate, M.D., Pickett, D.L., Brooks, A.G.: Glycosylation as a target for recognition of influenza viruses by the innate immune system. Adv. Exp. Med. Biol. 598, 279 (2007)

Hricovíni, M.: Structural aspects of carbohydrates and the relation with their biological properties. Curr. Med. Chem. 11(19), 2565–2583 (2004)

Davis, I.W., Chen, V.B.: The KiNG manual (2007). http://kinemage.biochem.duke.edu/software/king.php

Delaittre, T. et al.: GEMLCA: running legacy code applications as Grid services. Journal of Grid Computing 3, 1–2 (2005). Springer, 1570–7873, pp. 75–90

Kiefer, F., Arnold, K., Künzli, M., Bordoli, L., Schwede, T.: The SWISS-MODEL repository and associated resources. Nucleic Acids Res. 37, D387–D392 (2009). http://swissmodel.expasy.org/

Kenny, P.W., Sadowski, J.: Structure modification in chemical databases. In: Oprea, T. I. (ed.) Chemoinformatics in Drug Discovery, pp. 271–285. Wiley (2005)

Weininger, D.: SMILES, a chemical language and information system. 1. Introduction to methodology and encoding rules. J. Chem. Inf. Comput. Sci. 28, 31–36 (1988)

Tantoso, E. et al.: Molecular Docking, an example of Grid enabled applications. New Gener. Comput. 22(2) (2004). Page numbers

Tantar, A.-A., et al.: A Grid-based genetic algorithm combined with an adaptive simulated annealing for protein structure prediction. Soft Computing Journal, Springer Verlag, Special issue on Distributed Bioinspired Algorithms (2008)

Roh, Y. et al.: A molecular docking system using CUDA, ACM International Conference Proceeding Series; In: Proceedings of the 2009 International Conference on Hybrid Information Technology, vol. 321, pp. 28–33, Daejeon, Korea (2009)

The UK National Grid Service. http://www.ngs.ac.uk/

Laure, E., Jones, B.: Enabling Grids for e-Science: The EGEE Project, Grid Computing: Infrastructure, Service, and Application. CRC Press (2008). http://www.eu-egee.org/

Gibbins, H. et al.: The Australian BioGrid Portal: empowering the molecular docking research community. In: Proceedings of the 3rd APAC Conference and Exhibition on Advanced Computing, Grid Applications and eResearch (APAC 2005), Gold Coast, Australia, 26–30 Sept. 2005

Ewing, A. (ed.): DOCK Version 4.0 Reference Manual. University of California at San Francisco (UCSF), U.S.A. (1998). http://www.cmpharm.ucsf.edu/kuntz/dock.html

Foster, I.: Globus toolkit version 4: software for service-oriented systems. IFIP International Conference on Network and Parallel Computing. LNCS, vol. 3779, pp. 2–13. Springer-Verlag (2006). http://www.globus.org/

Sukhwani, B., Herbordt, M.: GPU acceleration of a production molecular docking code. In: Proceedings of 2nd Workshop on General Purpose Processing on Graphics Processing Units, ACM International Conference Proceeding Series, vol. 383, pp. 19–27 (2009)

Friedrichs, M.S. et al.: Accelerating molecular dynamic simulation on graphics processing units. J. Comp. Chem. 30(6), 864–872 (2009)

Buyya, R., et al.: The virtual laboratory: enabling molecular modelling for drug design on the world wide Grid, Concurrency and Computation: Practice and Experience (CCPE) Journal, vol. 15, Issue 1, pp. 1–25. Wiley Press, USA (2003)

Tantar, A.-A., et al.: Docking and biomolecular simulations on computer Grids: status and trends, Current Computer-Aided Drug Design, vol. 4, No 3, pp. 235–249, Bentham Science Publishers (2008)

Tantar, A.-A., Melab, N., Talbi, E.-G.: A grid-based genetic algorithm combined with an adaptive simulated annealing for protein structure prediction. Soft Computing Journal, Springer Verlag, Special issue on Distributed Bioinspired Algorithms (2008). doi: 10.1007/s00500-008-0298-8

The Chemomentum Project. http://www.chemomentum.org/c9m

Schuller, B., et al.: Chemomentum—UNICORE 6 based infrastructure for complex applications in science and technology, Euro-Par 2007 Workshops: Parallel Processing, Lecture Notes in Computer Science, vol. 4854/2008, pp. 82–93, Springer (2008)

Kluszczyński, R., Bała, P.: Supporting NAMD application on the Grid using GPE, In: Parallel Processing and Applied Mathematics, Lecture Notes in Computer Science, vol. 4967, pp. 762–769, Springer (2008)

Keator, D.B., Wei, D., Gadde, S., Bockholt, J., Grethe, J.S., Marcus, D., Aucoin, N., Ozyurt, I.B.: Derived data storage and exchange workflow for large-scale neuroimaging analyses on the BIRN grid. Frontiers in Neuroscience (2009, in press). http://www.birncommunity.org/

Baru, C., et al.: The SDSC Storage Resource Broker. In: Proceedings of the 1998 conference of the Centre for Advanced Studies on Collaborative research, IBM press (1998)

Anderson, D.P.: BOINC: a system for public-resource computing and storage. In: Fifth IEEE/ACM International Workshop on Grid Computing (GRID’04), pp. 4–10, IEE Computer Society (2004)