Scientific papers citing the SwissParam web server:

  1. Margreitter, C.; Petrov, D.; Zagrovic, B. Vienna-PTM web server: a toolkit for MD simulations of protein post-translational modifications. Nucleic Acids Res. 2013.
  2. Tou, W. I.; Chang, S.-S.; Lee, C.-C.; Chen, C. Y.-C. Drug Design for Neuropathic Pain Regulation from Traditional Chinese Medicine. Sci. Rep. 2013, 3.
  3. Knight, J. L.; Yesselman, J. D.; Brooks, C. L. Assessing the quality of absolute hydration free energies among CHARMM-compatible ligand parameterization schemes. J Comput Chem 2013, 34, 893–903.
  4. Steinmann, C.; Fedorov, D. G.; Jensen, J. H. Mapping Enzymatic Catalysis using the Effective Fragment Molecular Orbital Method: Towards all ab initio Biochemistry. 2012.
  5. Tsou, Y.-A.; Chen, K.-C.; Chang, S.-S.; Wen, Y.-R.; Chen, C. Y.-C. A possible strategy against head and neck cancer: in silicoinvestigation of three-in-one inhibitors. J. Biomol. Struct. Dyn. 2012, 1–12.
  6. Hodzic, A.; Pabst, G.; Rappolt, M.; Mali, G. Comparative study of the AT1 receptor prodrug antagonist candesartan cilexetil with other sartans on the interactions with membrane bilayers. Biochim Biophys Acta. 2012, 1818(12), 3107-20.
  7. Otero, J. M.; Fernández, F.; Estévez, J. C.; Nash, R.; Estévez, R. J. A Nitro Sugar-Mediated Stereocontrolled Synthesis of β2-Amino Acids: Synthesis of a Polyhydroxylated trans-2-Amino­cyclohexanecarboxylic Acid. Eur. J. Org. Chem. 2012, 2012, 2969–2979.
  8. Tuffery, P.; Derreumaux, P. Flexibility and binding affinity in protein-ligand, protein-protein and multi-component protein interactions: limitations of current computational approaches. J R Soc Interface 2012, 9, 20–33.
  9. Hill, E. H.; Stratton, K.; Whitten, D. G.; Evans, D. G. A Molecular Dynamics Simulation Study of the Interaction of Cationic Biocides with Lipid Bilayers: Aggregation Effects and Bilayer Damage. Langmuir. 2012, 28(42), 14849-54.
  10. Nandi, T. K.; Bairagya, H. R.; Mishra, D. K. Structural and Putative Functional Role of Conserved Water Molecular Cluster in the X-ray Structures of Plant Thiol Proteases: A Molecular Dynamics Simulation Study. Journal of Chemical Crystallography, 2012, 42(11), 1105-18.
  11. Kyrychenko, A.; Karpushina, G. V.; Svechkarev, D.; Kolodezny, D.; Bogatyrenko, S. I.; Kryshtal, A. P.; Doroshenko, A. O. Fluorescence Probing of Thiol-Functionalized Gold Nanoparticles: Is Alkylthiol Coating of a Nanoparticle as Hydrophobic as Expected? J. Phys. Chem. C, 2012, 116(39), 21059–68
  12. Mabanglo, M. F.; Serohijos, A. W. R.; Poulter, C. D. The Streptomyces-Produced Antibiotic Fosfomycin Is a Promiscuous Substrate for Archaeal Isopentenyl Phosphate Kinase. Biochemistry 2012, 51, 917–925.
  13. Ericksen, S. S.; Cummings, D. F.; Teer, M. E.; Amdani, S.; Schetz, J. A. Ring Substituents on Substituted Benzamide Ligands Indirectly Mediate Interactions with Position 7.39 of Transmembrane Helix 7 of the D4 Dopamine Receptor. J Pharmacol Exp Ther 2012, 342, 472–485.
  14. Quintal, S.; Viegas, A.; Erhardt, S.; Cabrita, E. J.; Farrell, N. P. Platinated DNA Affects Zinc Finger Conformation. Interaction of a Platinated Single-Stranded Oligonucleotide and the C-Terminal Zinc Finger of Nucleocapsid Protein HIVNCp7. Biochemistry 2012, 51, 1752–1761.
  15. Roberts, J. A.; Kuiper, M. J.; Thorley, B. R.; Smooker, P. M.; Hung, A. Investigation of a predicted N-terminal amphipathic α-helix using atomistic molecular dynamics simulation of a complete prototype poliovirus virion. J. Mol. Graph. Model. 2012.
  16. Li, Y.; Hao, M.; Ren, H.; Zhang, S.; Wang, X.; Ma, M.; Li, G.; Yang, L. Exploring the structure requirement for PKCθ inhibitory activity of pyridinecarbonitrile derivatives: an in silico analysis. J. Mol. Graph. Model. 2012, 34, 76–88.
  17. Kalyaanamoorthy, S.; Chen, Y.-P. P. Exploring Inhibitor Release Pathways in Histone Deacetylases Using Random Acceleration Molecular Dynamics Simulations. J Chem Inf Model 2012, 52, 589–603.
  18. Pacios, L. F.; Gómez-Casado, C.; Tordesillas, L.; Palacín, A.; Sánchez-Monge, R.; Díaz-Perales, A. Computational study of ligand binding in lipid transfer proteins: Structures, interfaces, and free energies of protein-lipid complexes. J Comput Chem 2012, 33, 1831–1844.
  19. Fotakis, C.; Megariotis, G.; Christodouleas, D.; Kritsi, E.; Zoumpoulakis, P.; Ntountaniotis, D.; Zervou, M.; Potamitis, C.; Hodzic, A.; Pabst, G.; Rappolt, M.; Mali, G.; Baldus, J.; Glaubitz, C.; Papadopoulos, M.; Afantitis, A.; Melagraki, G.; Mavromoustakos, T. Comparative study of the AT1 receptor prodrug antagonist candesartan cilexetil with other sartans on the interactions with membrane bilayers. Biochimica et Biophysica Acta (BBA) - Biomembranes 2012.
  20. Liu, H.; Roberts, J. A.; Moore, D.; Anderson, B.; Pallansch, M. A.; Pevear, D. C.; Collett, M. S.; Oberste, M. S. Characterization of Poliovirus Variants Selected for Resistance to the Antiviral Compound V-073. Antimicrob. Agents Chemother. 2012.
  21. O'Reilly, A. O.; Eberhardt, E.; Weidner, C.; Alzheimer, C. Bisphenol A Binds to the Local Anesthetic Receptor Site to Block the Human Cardiac Sodium Channel. PLoS ONE 2012.
  22. Malde, A. K.; Zuo, L.; Breeze, M.; Stroet, M.; Poger, D.; Nair, P. C.; Oostenbrink, C.; Mark, A. E. An Automated Force Field Topology Builder (ATB) and Repository: Version 1.0. J Chem Theory Comput 2011, 7, 4026–4037.
  23. Daily, M. D.; Phillips, G. N.; Cui, Q. Interconversion of Functional Motions between Mesophilic and Thermophilic Adenylate Kinases. PLoS Comput. Biol. 2011, 7, e1002103.
  24. Nanda, T.; Tripathy, K.; Ashwin, P. Integration of Bioinformatics Tools for Proteomics Research. J Comput Sci Syst Biol R 2011.
  25. Shim, J.; MacKerell, A. D. Computational ligand-based rational design: Role of conformational sampling and force fields in model development. Medchemcomm 2011, 2, 356–370.
  26. Nguyen, T. T.; Mai, B. K.; Li, M. S. Study of Tamiflu Sensitivity to Variants of A/H5N1 Virus Using Different Force Fields. J Chem Inf Model 2011, 51, 2266–2276.
  27. Caulfield, T.; Medina-Franco, J. L. Molecular dynamics simulations of human DNA methyltransferase 3B with selective inhibitor nanaomycin A. J Struct Biol 2011, 176, 185–191.
  28. Pantazes, R. J.; Maranas, C. D. OptCDR: a general computational method for the design of antibody complementarity determining regions for targeted epitope binding. Protein Eng. Des. Sel. 2010, 23, 849–858.