2. Acetyl-CoA enolization in citrate synthase: Quantum mechanical and quantum mechanical/molecular mechanical (QM/MM) studies.
Adrian Mullholland* and W. G. Richards.
3. Molecular mechanics with QM charge recalculation applied to leucine aminopeptidase, a two-metal ion metallo-protease.
Tim Mitchell*, Alex J. Turner, and Ian H. Williams.
4. Development of hybrid density functional of Hartee Fock-MM methods for application to solution phase chemistry.
Paul Lyne* and Martin Karplus.
5. Stability of water pentamer in solution.
6. Implementation of polarizable solvent model for combined QM/MM simulations on distributed memory parallel computers.
7. Comparison of the hybrid ab initio quantum mechanical 3-21-G-QM/TIP3P-MM, the hybrid semiempirical quantum mechanical AM1-QM/TIP3P-MM and the empirical OPLS functions through Monte Carlo simulations of N-methyl-acetamide in water.
Marek Freindorf* and Jiali Gao.
8. HIV-1 protease reaction mechanism investigated with QM/MM potential.
David Chatfield* and Bernard Brooks.
9. Free-energy simulations of carbohydrate protein interactions.
Ahammadunny Pathiaseril and Robert Woods*.
10. Hamiltonian parameterization methods for free energy calculations.
11. Free energy simulation of anomeric equilibria of monosaccharides.
Ahammadunny Pathiaseril* and Robert Woods.
12. Free energy of cavity formation in water and hexane.
Isabel Tomas Oliveira*, Jean-Pierre Kocher, Martine Prevost, and Shoshana J. Wodak.
13. Insights into protein-ligand binding for FK506 binding protein and HIV protease from Monte Carlo simulations.
Michelle Lamb*, Vickie Tsui, Julian Tirado-Rives, and William L. Jorgensen.
14. Thermodynamic decomposition of solvation free energy.
Mashito Kubo* and Ronald M. Levy.
15. Non-Boltzmann thermodynamic integration.
Nobuyuki Ota* and Axel T. Brunger.
16. Free energy of solvation: Simulations using MMFF force field in CHARMm.
Bruce L. Bush, Thomas A. Halgren, and Jay Banks*.
17. Molecular modeling of the photoactive yellow protein.
Feng Zhou*, Alex Mackerell Jr., Keith Moffat, and Paul Bash.
18. Molecular dynamics simulations of individual bacteriorhodopsin helices.
19. Molecular dynamics simulations of protein S and Gas-6: A comparison with the solution structure of bovine prothrombine.
Lalith Perera*, Leping Li, Tom Darden, Richard G. Hiskey, and Lee G. Pedersen.
20. Predicted solution structure of the Gla domain of human coagulation factor VII.
Leping Li, Tom Darden, Richard G. Hiskey, and Lee Pedersen*.
21. Speculations on the mechanism of hormone-receptor interactions of the secretin/glucagon family of polypeptide hormones derived from computational structural studies.
Frank Momany* and C. Y. Bowers.
22. Comparison of continuum and explicit models of solvation: Potentials of mean force for alanine dipeptide.
Tami Marrone*, Michael Gilson, and J. Andrew McCammon.
23. Simulation of translational and rotational diffusion of anthracene in solution.
Gouri Jas*, Yan Wang, and Krzysztof Kuczera.
24. A new approach to the universal kinetic energy functional.
25. Linear scaling semiempirical molecular orbital calculations.
Steven Dixon* and Kenneth M. Merz.
26. Distinguishing feature of amino acid side-chain radicals and their radical cations.
Yue Qin, Susan E. Walden, and Ralph Wheeler*.
27. A comparison of the structures of bistriazenes: Hartee Fock and density functional structures.
Ann Schmiedekamp*, Mark Schwartz, and Christopher J. Michejda.
28. The ring-opening reaction of triaziribind: Woodward-Hoffmann reactivity in an inorganic ring.
Carl Salter*, Tom Hartle, Ryan Hinrichs, Gretchen, and Alan Salter.
29. Diacylhydrazines are twisted: Theoretical determination of the structure and rotational flexibility of diformylhydrazine and its derivatives.
Chuck Reynolds* and Robert E. Hormann.
30. Complete basis set transition states.
31. The TINKER force field: A polarizable atomic multipole-based water model.
Yong Kong and Jay Ponder*.
32. Correction of self-consistent reaction filed continuum dielectric theory for short range hydrogen bonding effects.
Bryan Marten*, Kyungsun Kim, Christian Cortis, Richard Friesner, Robert B. Murphy, Murco N. Ringnalda, Doree Sitkoff, and Barry Honig.
33. Ab initio and DFT calculations of geometry and solution tautomerism of purine and some purine derivatives.
Ander Holmen* and Anders Broo.
34. Stereoelectronic effects in negatively and positively (protonated) charged dioxa species.
Bishwajit Ganguly and Benzion Fuchs*.
35. Ab initio computational study of electronic structure and related properties of dinuclear transition-metal complexes.
Albert Cotton and Xuejun Feng*.
36. Models for protein-zinc ion binding sites II. The catalytic sites.
37. Tetrahedral intermediates and related structures.
38. Ab initio Hartee-Fock/Moller-Plesset energy perturbation studies of monophosphate esters: Different phosphorylated amino acids exhibit unique conformational preferences.
39. A molecular dynamics study of the stability of a proposed NMR structure of putidaredoxin.
40. Theoretical studies of the kinetics and mechanism of lipid peroxidation.
41. An algorithm to calculate dynamic trajectory between two predefined points on potential energy surface.
42. Generation of models for "unusual" DNA and RNA: A computer language for structural exploration.
Tom Macke and Dave Case*.
43. A progress report on the development of CEX. A language for the exchange of information between computational methods.
Frank Brown*, David Weininger, Roger Sayle, David Spellmeyer, Conrad Hung, Anthony Nicholls, and George Purvis.
44. Modeling peptidomimetic angiotensin II receptor antagonists.
Donald B. Boyd* and Greg Pearl.
45. Modeling an antibody Fab to 7, 8-dihydro-8-oxoguanine.
Jeffrey Bond*, Ivan A. Bespalov, Andrei A. Purmal, Susan Wallace, and Robert J. Melamede.
46. A neural network based method for determining MHC binding peptides.
Kamalakar Gulukota* and Charles DeLisi.
47. Molecular dynamics elucidation of binding properties of the peptide - Major Histocompatibility Complex type II.
Steve Bogusz*, Bernard R. Brooks, and Robert H. Reid.
48. Application of artificial neural network to optimize water-in-oil emulsions.
Stelian Grigoras*, Wen-Lan Lee, and James W. Mentele.
2. Parallel molecular dynamics simulations in NWChem.
3. Charge screening in proteins: Molecular dynamics studies of cytochrome in aqueous solution.
4. A molecular dynamics simulation study of polarizable solute solvation in water.
Badry D. Bursulaya, Dominic A. Zichi, and Hyung Kim*.
5. An efficient split integration symplectic method for molecular dynamics simulations of complex systems.
Dusanka Janezic* and Franci Merzel.
6. Towards large scale simulation of biomolecules in solution: Fast multiple method, reversible integrators and massively parallel machines.
Francisco Figuerirido*, Gabriela S. Del Buono, and Ronald Levy.
7. Docking enzyme-inhibitor complexes using a preferenced based free-energy surface.
Anders Wallquist* and D. G. Covell.
8. Analysis of thermodynamic determinants in helix propensities of nonpolar amino acids through novel free energy calculation.
Jing Wang* and Enrico O. Purisima.
9. Complicated energy landscapes: The connection between structure and function by multivariate methods.
10. Molecular dynamics simulations of individual bacteriorhodopsin helices.
11. Molecular docking to ensembles of protein structures.
Ronald Knegtel*, C. M. Oshiro, and I. D. Kuntz.
12. Docking in a flexible binding site.
Joannis Apostolakis* and Amedeo Caflisch.
13. LEAPS profiles of protein main chain conformations.
14. Exploring peptide conformational free energy surfaces.
15. Conformational analysis utilizing and improved low mode search algorithm: Applications to constrained and intermolecular potential energy surfaces.
Istvan Kolossvary* and Wayne C. Guida.
16. CHASM: An algorithm for predicting polymer and polypeptide conformations at inorganic interfaces.
Nicholas J. Reeves and John Evans*.
17. New algorithms for simulating drugs and drug-like molecules.
18. The conformational distribution of tetramethoxy calixarenes.
Willem van Hoorn*, W. Briels, J. P. M. van Duynhoven, F. C. J. M. van Veggel, and D. N. Reinhoudt.
19. pH dependent conformational preferences of peptides.
Paul Smith*, Herb D. Blatt, and B. Montgomery Pettitt.
20. Mining minima: Direction computation of configurational integrals.
Martha S. Head, James A. Given, and Michael K. Gilson*.
21. Solvation free energies derived from the GB/SA model: Sensitivity of results on charge sets, protocols and force fields.
Vellarkad Viswanadhan*, M. Rami Reddy, and Mark D. Erion.
22. Solvation models for empirical binding free energy calculation.
Zhiping Weng and Sandor Vajda*.
23. The GB/SA continuum model for solvation. A fast analytical method for the calculation of approximate Born radii.
Di Qiu*, P. Shenkin, F. P. Hollinger, and W. C. Still.
24. Modeling electrostatic interactions: A comparative study.
Arno Papazyan* and Arieh Warshel.
25. Calculation of electrostatic interactions in molecular simulations.
26. Rapid estimation of relative ligand binding energetics: Application to FKBP inhibitors.
Xinjun Hou*, Robert E. Babine, Wesley K. M. Chong, Peter S. Dragovich, Thomas F. Hendrickson, Vincent J. Kalish, Susumu Katoh, Hiroshi Kawakami, Chuck R. Kissinger, Daniel R. Knighton, Cristina T. Lewis, Hans E. Parge, John H. Tatlock, and J. Ernest Villafranca.
27. The fast estimation of solvent-induced forces from continuum solvent models.
Dragos Horvath*, D. van Belle, and G. Lippens.
28. Electrostatic complementarity at protein-protein interfaces.
J. McCoy and V. C. Epa*.
29. Realistic simulation of nucleic acids in solution: Application of the particle mesh Ewald method within AMBER.
Thomas Cheatham* and Peter Kollman.
30. Electrostatic steering during enzyme-substrate encounter.
Jim Briggs* and J. Andrew McCammon.
31. Multiple conformation changes and pH-titration.
R. Gunner and Emil Alexov*.
32. De Novo design of templating agents for the synthesis of microporous materials.
W. Lewis and David Willock*.
33. Computer-generated chemical kinetics models.
Roberta Susnow*, W. H. Green, A. M. Dean, P. K. Peczak, and L. J. Broadbelt.
34. Prediction of research and motor octane numbers of alkanes and alkenes.
P. Firmstone, Pallavour Subramanian*, and K. J. Chou.
35. Understanding the activities of aldose reductase inhibitors and their relationship to the mutagenesis data.
Suresh Singh*, Michael S. Malamas, Douglas Kitchen, Thomas C. Hohman, and Deborah A. Carper.
36. Spectroscopically determined force field for linear and branched saturated hydrocarbons.
Kim Palmo, Noemi Mirkin*, and Samuel Krimm.
37. Role of multiple minima in protein vibrational spectroscopy. Anharmonic eigenfunctions for different conformers.
38. New methods for aligning molecules with a known ligand.
G. Klebe, Thomas Mietzner*, and F. J. Pfreundt.
39. Using ab initio calculations to construct accurate force fields for use in simulations of large molecules.
Daniel Mainz* and Richard Friesner.
40. Favourable modes of interaction between catechol and serine residues in helix V of catecholaminergic neurotransmitter receptors as calculated by molecular mechanics.
Tommy Liljefors* and Per-Ola Norrby.
41. Application of enhanced side chain placement algorithms.
Andrew Lemon* and A. R. Leach.
42. Design of picornavirus capsid-binding drugs and computational analysis of binding energetics.
Diane Joseph-McCarthy*, M. Karplus, and J. M. Hogle.
43. A statistical mechanical description of biomolecular hydration.
G. Hummer and Angel Garcia*.
44. Hierarchial protein folding routines with improved reduced inter-residue potentials.
Anthony Felts* and Richard Friesner.
45. The calculation of relative binding constants in protein/inhibitor systems using Monte Carlo simulations.
Jonathan Essex*, W. L. Jorgensen, and D. L. Severance.
46. Measuring conformational diversity in combinatorial libraries with CLICHE. Diversity from core structures.
Mika Lindvall*, George Lauri, and Paul A. Bartlett.
47. Probing the stability of an RNA tetraloop with unrestrained molecular dynamics.
Jennifer Miller* and Peter A. Kollman.
48. The AIDD combinatorial chemistry - HTS program at Neurogen Pharmaceuticals.
Charles Manly* and Deborah Jones-Hertzog.
49. Constraining molecular diversity calculations to ensure enhanced diversity with respect to already synthesised libraries.
Andy Good*, Stephen D. Pickett, and Richard A. Lewis.
50. Calculated one-electron reduction potentials for biochemically important p-benzoquinones.
Kevin S. Raymond, Anthony Kurt Grafton, and Ralph Wheeler*.
Copyright (c) 2007-2009. All rights reserved.
Updated March 2009.
Webmaster: Donald B. Boyd, Ph.D., Indiana University-Purdue University at Indianapolis (IUPUI)