Publications which have used AMMP.

The publications below have used AMMP to build structural models, to analyze binding of ligands cofactors, or other proteins, and to aid in the understanding of enzyme biochemistry. These publications show the range of tasks for which AMMP is designed. If you use AMMP please cite either of:

• Harrison R. W. "Stiffness and Energy Conservation in Molecular Dynamics: an Improved Integrator" (1993) J. Comp. Chem. 14 1112-1122.
• Harrison, R.W., Chatterjee D., and Weber I.T. "Analysis of six protein structures predicted by comparative modeling techniques." (1995) Proteins: Structure Function and Genetics 23:463-471.

If you have used AMMP in published work and would like to be included in this list please send email to the author and give the reference.

• Harrison R. W. "Stiffness and Energy Conservation in Molecular Dynamics: an Improved Integrator" (1993) J. Comp. Chem. 14 1112-1122.

• Harrison R. W. "Randomized Optimizers: a Scalable Probabilistic Optimizer" Proceedings of the Convex Worldwide User Group 1993.

• Takeda, J., Gidh-Jain, M., Xu, L.Z., Froguel, P., Velho, G., Vaxillaire, M., Cohen, D., Shimada, F., Makino, H., Nishi, S., Stoffel, M., Vionnet, N., St. Charles, R., Harrison, R.W., Weber, I.T., Bell, G.I. and Pilkis, S.J. "Structure/Function Studies of Human b-Cell Glucokinase" (1993) J. Biol. Chem. 263, 15200-15204.

• Menendez-Arias, L., Weber, I.T., Soss, J., Harrison, R.W., Gotte, D. and Oroszlan, S. "Kinetic and Modeling Studies of Subsites S4-S3í of Moloney-Murine Leukemia Virus Protease." (1994) J. Biol. Chem. 269, 16795-16801.

• Harrison R.W. and Kurinov I.V. (1994) "Prediction of Novel Serine Protease Inhibitors" Nature Structural Biology 1(10) 735-743.

• Pilkis, S.J., Weber, I.T., Harrison, R.W. and Bell, G.I. "Glucokinase: A Genetic Model for Studying Diabetes Mellitus, Regulation of Glycolysis, and Conformation-driven Catalysis." (1994) J. Biol. Chem., 269, 21925-21928.

• Harrison, R.W. and Weber, I.T. "Molecular Dynamics Simulation of HIV-1 Protease with Peptide Substrate." (1994) Protein Engineering, 7, 1353-1363.

• Xu, L.Z., Zhang, W., Weber, I.T., Harrison, R.W. and Pilkis, S.J. "Site-directed Mutagenesis Studies on the Determinants of Sugar Specificity and Cooperative Behavior of Human b-cell Glucokinase." (1994) J. Biol. Chem. 269, 27458-27465.

• Xu, L.Z., Weber, I.T., Harrison, R.W., Gidh-Jain, M. and Pilkis, S.J. "Sugar Specificity of Human Pancreatic b-cell Glucokinase." (1995) Biochemistry. 34,6083-6092.

• Harrison, R.W., Chatterjee D., and Weber I.T. "Analysis of six protein structures predicted by comparative modeling techniques." (1995) Proteins: Structure Function and Genetics 23:463-471.

• Fu, Z.-Q, Harrison, R.W., Reed, C., Wu, J., Xue, Y.-N., Chen, M.-J. and Weber, I.T. "Model Complexes of Tumor Necrosis Factor-a with Receptors R1 and R2." (1995) Protein Engineering, 8:1233-1241

• Aramini J.M., Kalisch B.W., Pon, R.T., van de Sande, J.H. and Germann, M.W. "Structure of a DNA Duplex That Contains a-Anomeric Nucleotides and 3'-3' and 5'-5' Phosphodiester Linkages: Coexistance of Parallel and Antiparallel DNA" (1996) Biochemistry 35:9355-9365

• Ridky, T., Cameron, C.E., Cameron, J., Leis, J., Copeland, T., Wlodawer, A., Weber, I.T. and Harrison, R.W. "Human Immunodeficiency Virus Type 1 Protease Substrate Specificity is Limited by Interactions Between Substrate Amino Acids Bound in Adjacent Enzyme Subsites." (1996) J. Biol. Chem. 271:4709-4717.

• Scott S.P., Harrison R.W., Weber I.T., and Tanaka J.C. "Predicted ligand interactions for 3',5'-cyclic nucleotide gated channel binding sites: Comparison of retina and olfactory binding site models" (1996) Protein Engineering, 9, 333-344.

• Weber, I.T. and Harrison, R.W. "Molecular Mechanics Calculations on HIV-1 Protease with Peptide Substrates Correlate with Experimental Data." (1996) Protein Engineering, 9: 679-690.

• Zeng C.B., Aleshin A.E., Hardie J.B., Harrison R.W. and Fromm H.J. "ATP-binding Site of Human Brain Hexokinase as Studied by Molecular Modeling and Site-directed Mutagenesis" (1996) Biochemistry, 35 13157-13164.

• Weber, I.T., Cavanaugh, D.S. and Harrison, R.W. "Models of HIV-1 Protease With Peptides Representing Its Natural Substrates." (1996) Theochem, accepted.

• Weber, I.T., Harrison, R.W. and Iozzo, R.V. "Model Structure of Decorin and Implications for Collagen Fibrillogenesis." (1996) J. Biol. Chem. 271:31767-31770.

• Tozser, J., Yin, F.H., Cheng, Y.-S.E., Bagossi, P., Weber, I.T., Harrison, R.W. and Oroszlan, S. "Activity of Tethered HIV-1 Proteases Containing Mutations in the Flap Region of One Subunit." (1997) Eur. J. Biol. 244, 235-241.

• Aramini J.M., van de Sande J.H. and Germann, M.W. "Spectroscopic and Thermodynamic Studies of DNA Duplexes Containing a-Anomeric C, A, and G Nucleotides and Polarity Reversals: Coexistance of Localized Parallel and Antiparallel DNA" (1997) Biochemistry 36:9715-9725.

• Reed, C., Fu, Z.-Q., Wu, J., Xue, Y.-N., Harrison, R.W., Chen, M.-J. and Weber, I.T. "Crystal Structure of TNF-a Mutant R31D with Five-fold Greater Affinity for Receptor R1 Compared to R2." (1997) Prot. Eng. in press.

• Weber, I.T. and Harrison, R.W. (1997) "Molecular Mechanics Calculations on Rous sarcoma virus Protease with Peptide Substrates" Prot. Sci. in press

• Weber, I.T. and Harrison, R.W. (1997) "Molecular Mechanics Calculations on Protein-Ligand Complexes." in 3D QSAR in Drug Design. Recent Advances. eds. Kubinyi, H., Folkers, G. and Martin, Y. ESCOM Science Publishers, Leiden, the Netherlands, in press.

• Harrison, R.W., Reed, C.C. and Weber, I.T. "Analysis of Comparative Modeling Predictions for CASP2 Targets 1, 3, 9 and 17" (1997) Proteins: Struct. Funct. & Genet., accepted.