Hebrew University of Jerusale

Prof. Amiram Goldblum's


School of Pharmacy
Molecular Modeling and Drug Design Group


Papers


Since 2000

  1. Glick, M. & Goldblum, A. A novel energy-based stochastic method for positioning polar protons in protein structures from X-rays. Proteins-Structure Function and Genetics 38, 273-287 (2000).
     
  2. Goldblum, A. & Glick, M. Novel stochastic algorithm for structure predictions in proteins and for biomolecular interactions. Abstracts of Papers of the American Chemical Society 220, U286-U287 (2000).
     
  3. Rayan, A., Siew, N., Cherno-Schwartz, S., Matzner, Y., Bautsch, W. & Goldblum, A. A novel computational method for predicting the transmembrane structure of G-protein coupled receptors: Application to human C5aR and C3aR. Receptors & Channels 7, 121-+ (2000).
     
  4. Goren, I., Tavor, E., Goldblum, A. & Honigman, A. Two cysteine residues in the DNA-binding domain of CREB control binding to CRE and CREB-mediated gene expression. Journal of Molecular Biology 313, 695-709 (2001).
     
  5. Cherno-Schwartz, S., Rayan, A. & Goldblum, A. Novel measures of variability in multiple alignments as a basis for modeling 3D structures of G-protein coupled receptors. Abstracts of Papers of the American Chemical Society 223, U503-U503 (2002).
     
  6. Glick, M., Rayan, A. & Goldblum, A. A stochastic algorithm for global optimization and for best populations: A test case of side chains in proteins. Proceedings of the National Academy of Sciences of the United States of America 99, 703-708 (2002).
     
  7. Goldblum, A., Vardi-Kilshtain, A. & Shoham, G. Mechanism of action of zinc proteinases: New indications from a combined study by X-ray crystallography and semiempirical quantum mechanics. Abstracts of Papers of the American Chemical Society 223, C76-C76 (2002).
     
  8. Goldblum, A., Glick, M., Rayan, A., Gorelik, B. & Brinker, G. A novel stochastic search method finds global minima and low-energy populations. Abstracts of Papers of the American Chemical Society 223, U499-U500 (2002).
     
  9. Kilshtain-Vardi, A., Shoham, G. & Goldblum, A. Mechanism of action of zinc proteinases: A MNDO/d/H study of alternative general-acid general-base catalytic pathways for carboxypeptidase-A. International Journal of Quantum Chemistry 88, 87-98 (2002).
     
  10. Chema, D. & Goldblum, A. 'nearest single neighbor method: Finding families of conformations within large samples. Abstracts of Papers of the American Chemical Society 225, U789-U789 (2003).
     
  11. Chema, D. & Goldblum, A. The "Nearest single neighbor" method - Finding families of conformations within a sample. Journal of Chemical Information and Computer Sciences 43, 208-217 (2003).
     
  12. Kilshtain-Vardi, A., Shoham, G. & Goldblum, A. Theoretical studies of catalysis by carboxypeptidase A: Could gas-phase calculations support a mechanism? Collection of Czechoslovak Chemical Communications 68, 2055-2079 (2003).
     
  13. Kilshtain-Vardi, A., Glick, M., Greenblatt, H.M., Goldblum, A. & Shoham, G. Refined structure of bovine carboxypeptidase A at 1.25 angstrom resolution. Acta Crystallographica Section D-Biological Crystallography 59, 323-333 (2003).
     
  14. Noy, E., Gorelik, B., Rayan, A. & Goldblum, A. Stochastic path to form ensembles and to quantify flexibility in proteins. Abstracts of Papers of the American Chemical Society 225, U781-U781 (2003).
     
  15. Rayan, A., Barasch, D., Brinker, G., Cycowitz, A., Geva-Dotan, I., Scaiewicz, A. & Goldblum, A. New stochastic algorithm to determine drug-likeness. Abstracts of Papers of the American Chemical Society 226, U297-U297 (2003).
     
  16. Vardi-Kilshtain, A., Shoham, G. & Goldblum, A. Anhydride formation is not a valid mechanism for peptide cleavage by carboxypeptidase-A: a semiempirical reaction pathway study. Molecular Physics 101, 2715-2724 (2003).
     
  17. Vaya, J., Mahmood, S., Goldblum, A., Aviram, M., Volkova, N., Shaalan, A., Musa, R. & Tamir, S. Inhibition of LDL oxidation by flavonoids in relation to their structure and calculated enthalpy. Phytochemistry 62, 89-99 (2003).
     
  18. Chema, D., Eren, D., Yayon, A., Goldblum, A. & Zaliani, A. Identifying the binding mode of a molecular scaffold. Journal of Computer-Aided Molecular Design 18, 23-40 (2004).
     
  19. Rayan, A., Scaiewicz, A., Geva-Dotan, I., Barasch, D. & Goldblum, A. Screening molecules for their drug-like index. Abstracts of Papers of the American Chemical Society 228, U358-U358 (2004).
     
  20. Rayan, A., Senderowitz, H. & Goldblum, A. Exploring the conformational space of cyclic peptides by a stochastic search method. Journal of Molecular Graphics & Modelling 22, 319-333 (2004).
     
  21. Rayan, A., Noy, E., Chema, D., Levitzki, A. & Goldblum, A. Stochastic algorithm for kinase homology model construction. Current Medicinal Chemistry 11, 675-692 (2004).
     
  22. Goldberg, M. and Goldblum, A. (2006) Computational protein design: a novel path to future protein drugs. Current Pharmaceutical Design 31, 3973-97.
     
  23. Noy, E, Tabakman, T & Goldblum, A (2007) Constructing ensembles of flexible fragments in native proteins by Iterative Stochastic Elimination is relevant to protein-protein interfaces, Proteins 68, 702-11
     
  24. Ittah S., Michaeli A., Goldblum A. et al. (2007) A model for the structure of the C-terminal domain of dragline spider silk and the role of its conserved cysteins, Biomacromolecules 8, 2768-73
     
  25. Gorelik B. and Goldblum A. (2008) High Quality Binding Modes in Docking Ligands to Proteins, Proteins 71, 1373-86

  26. Marcus, D and Goldblum A. (2008) Molecular Selectivity Index for Ligand Based Drug Design, Abs. Pap. Amer. Chem. Soc. 235, 61-CINF

  27. Marcus, D, Rayan, A, Barasch, D, Elias, M and Goldblum A. (2008) Learning from failures: Discontinued Compounds as a source for knowledge in drug discovery. Abs. Pap. Amer. Chem. Soc. 236, 67-CINF

  28. Zucker, D, Marcus, D, Barenholz, Y and Goldblum A.. (2009) Liposome Drugs’ loading efficiency: A working model based on loading conditions and drug’s physicochemical properties. J. Control. Release 139, 73-80

  29. Rayan, A, Marcus, D and Goldblum A.(2010) Predicting Oral Drug-Likeness by Iterative Stochastic Elimination, J. Chem. Inf. Model. 50, 437-445

  30. Noy, E  and Goldblum A. (2010) Flexible protein-protein docking based on best-First search algorithm, J. Comput. Chem. 31, 1929-1943 ( Journal cover)

  31. Dorman, G et al. (2010). Towards accelerated anti-cancer drug discovery: integration of chemoinformatics, cell-based screening and grid computing. Medicinal Chemistry Research 19, S14-S15

  32. Lavy, T, Harries, D and Goldblum A. (2011)  Molecular properties from conformational ensembles: I. dipole moments of molecules with multiple internal rotations, J Phys Chem A, 115, 5794-5809

  33. Ursu, O, Rayan, A, Goldblum A. and Oprea, T (2011). Understanding Drug Likeness. Computational Molecular Science, .Wiley Interdisciplinary Reviews - Computational Molecular Science 1, 760-781

  34. Cern A, Golbraikh, A, Sedykh, A, Tropsha A., Barenholz Y and Goldblum A. (2011) Quantitative Structure – Property Relationship Modeling of Remote Liposome Loading Of Drugs, J. Control. Release http://dx.doi.org/10.1016/j.jconrel.2011.11.029

  35. DeRazon Y,. Ta-Shma Z. & Goldblum, A. (2011). Aging of Acetylcholinesterase with Soman diastereomers: a conformational analysis. Journal of the American Chemical Society, Submitted.
       
Last Update : January 19, 2011 | Copyright ©, 2009, The Hebrew University of Jerusalem. All Rights Reserved.