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Alternative approaches to potential of mean force calculations: Free energy perturbation versus thermodynamic integration. Case study of some representative nonpolar interactions.

C. Chipot, P. Kollman, and D. Pearlman. J. Comput. Chem., 17 (9): 1112-1131 (1996)

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Peter A Schmid

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Peter A Stegmaier

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The application of three approximate free energy calculations methods to structure based ligand design: Trypsin and its complex with inhibitors.R. Radmer, and P. Kollman. J. Comput. Aided Mol. Des., 12 (3): 215-227 (1998)Structural changes by sulfoxidation of phenothiazine drugs.S. Dahl, P. Kollman, S. Rao, and U. Singh. J. Comput. Aided Mol. Des., 6 (3): 207-222 (1992)AMBERCUBE MD, parallelization of Amber's molecular dynamics module for distributed-memory hypercube computers.S. DeBolt, and P. Kollman. J. Comput. Chem., 14 (3): 312-329 (1993)Direct hydroxide attack is a plausible mechanism for amidase antibody 43C9.L. Chong, P. Bandyopadhyay, T. Scanlan, I. Kuntz, and P. Kollman. J. Comput. Chem., 24 (12): 1371-1377 (2003)Free Energy Peturbation Calculations on Parallel Computers: Demonstrations of Scalable Linear Speedup.S. DeBolt, D. Pearlman, and P. Kollman. J. Comput. Chem., 15 (3): 351-374 (1994)Molecular dynamics simulation studies of liquid acetonitrile: New six-site model.X. Grabuleda, C. Jaime, and P. Kollman. J. Comput. Chem., 21 (10): 901-908 (2000)Application of a simple diagonal force field to the simulation of cyclopentane conformational dynamics.W. Cornell, M. Ha, Y. Sun, and P. Kollman. J. Comput. Chem., 17 (13): 1541-1548 (1996)Peptide mimetics as enzyme inhibitors: Use of free energy perturbation calculations to evaluate isosteric replacement for amide bonds in a potent HIV protease inhibitor.P. Cieplak, and P. Kollman. J. Comput. Aided Mol. Des., 7 (3): 291-304 (1993)Announcement.D. Boyd, and P. Kollman. J. Comput. Aided Mol. Des., 1 (3): 269 (1987)Grand challenges in computational science: Simulations on biological macromolecules.P. Kollman. Future Gener. Comput. Syst., 5 (2-3): 207-211 (1989)