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	Dipole Moment, Hydrogen Bonding and IR Spectrum of Confined Water [My Copy] ChemPhysChem, Vol. 7, No. 12. (2006), pp. 2464-2467. by François-Xavier Coudert, Rodolphe Vuilleumier, Anne Boutin posted to moleculardynamics ir by loison on 2009-10-28 11:19:51 as
	Free energy simulations: Use of reverse cumulative averaging to determine the equilibrated region and the time required for convergence [My Copy] The Journal of Chemical Physics, Vol. 120, No. 6. (2004), pp. 2618-2628. by Wei Yang, Ryan B. Putzer, Martin Karplus posted to moleculardynamics inference by tovrstra on 2009-10-01 11:55:42 as
	Constant temperature simulations using the Langevin equation with velocity Verlet integration [My Copy] Chemical Physics, Vol. 236, No. 1-3. (15 September 1998), pp. 243-252. by M. Paterlini, D. Ferguson posted to sampling protein moleculardynamics modeling langevin by tovrstra on 2009-09-17 09:42:26 as
	QUICKSTEP: Fast and accurate density functional calculations using a mixed Gaussian and plane waves approach [My Copy] Computer Physics Communications, Vol. 167, No. 2. (15 April 2005), pp. 103-128. by J. Vandevondele, M. Krack, F. Mohamed, M. Parrinello, T. Chassaing, J. Hutter posted to moleculardynamics modeling abinitio by tovrstra on 2009-09-15 13:33:57 as
	Replica-exchange molecular dynamics method for protein folding [My Copy] Chemical Physics Letters, Vol. 314, No. 1-2. (26 November 1999), pp. 141-151. by Y. Sugita, Y. Okamoto posted to sampling protein moleculardynamics by tovrstra on 2009-09-15 08:08:07 as along with 8 people and 1 group chemrahul82 Diego_Prada oteri Sylvain_Prigent andreasauerwein dgront allmensch rulix Structural Biology Group TorVergata
	On searching in, sampling of, and dynamically moving through conformational space of biomolecular systems: A review [My Copy] Journal of Computational Chemistry, Vol. 29, No. 2. (14 June 2008), pp. 157-166. by Markus Christen, Wilfred F. van Gunsteren posted to moleculardynamics review by tovrstra on 2009-07-15 07:24:55 as along with 5 people BragilMassoud dgront rabio somak dmobley
	From atoms and bonds to three-dimensional atomic coordinates: automatic model builders [My Copy] Chemical Reviews, Vol. 93, No. 7. (1 November 1993), pp. 2567-2581. by Jens Sadowski, Johann Gasteiger posted to forcefields modeling moleculardynamics by tovrstra on 2009-06-24 10:57:05 as
	Molecular Mechanics and Modeling: Overview [My Copy] Chemical Reviews, Vol. 93, No. 7. (1 November 1993), pp. 2337-2337. by Ernest R. Davidson posted to forcefields modeling moleculardynamics by tovrstra on 2009-06-24 10:53:59 as
	APT a next generation QM-based reactive force field model [My Copy] Molecular Physics, Vol. 105, No. 2. (2007), pp. 301-324. by A. K. Rappe, L. M. Bormann-Rochotte, D. C. Wiser, et al.J. R. Hart, M. A. Pietsch, C. J. Casewit, W. M. Skiff posted to esp forcefields modeling moleculardynamics parameterization qmmm transitionstate valence-bond by tovrstra on 2009-06-23 16:18:08 as along with 2 people daevans middledomain
	Similarities between principal components of protein dynamics and random diffusion [My Copy] Physical Review E, Vol. 62, No. 6. (1 December 2000), 8438. by Berk Hess posted to forcefields moleculardynamics by tovrstra on 2009-06-15 08:01:33 as along with 1 person onufriev
	Convergence of sampling in protein simulations [My Copy] Physical Review E, Vol. 65, No. 3. (1 March 2002), 031910. by Berk Hess posted to forcefields moleculardynamics by tovrstra on 2009-06-15 08:01:16 as along with 6 people and 1 group loison anuragsethi klexa oteri onufriev softsimu Structural Biology Group TorVergata
	Binding site detection and druggability index from first principles. [My Copy] Journal of medicinal chemistry, Vol. 52, No. 8. (23 April 2009), pp. 2363-2371. by Jesus Seco, F. Javier Luque, Xavier Barril posted to bindingenergy bindingsites druggability moleculardynamics solvent by sschurer on 2009-04-20 15:16:42 as along with 3 people ubcg08l higueruelo Klapampfer
	Exploring the Binding of Inhibitors Derived from Tetrabromobenzimidazole to the CK2 Protein Using a QM/MM-PB/SA Approach [My Copy] Journal of Chemical Information and Modeling, Vol. 0, No. 0. (0000) by Marius Retegan, Anne Milet, Hélène Jamet posted to bindingenergy kinaseinhibition md mmpbsa moleculardynamics qmmm by sschurer on 2009-04-13 21:31:21 as
	All-atom molecular dynamics simulation studies of fully hydrated gel phase DPPG and DPPE bilayers [My Copy] Journal of Molecular Structure, Vol. 921, No. 1-3. (17 March 2009), pp. 38-50. by Jutarat Pimthon,, Regine Willumeit,, Andreas Lendlein,, Dieter Hofmann, posted to dppg lipids moleculardynamics by loison on 2009-04-10 16:44:50 as
	How to lose a kink and gain a helix: pH independent conformational changes of the fusion domains from influenza hemagglutinin in heterogeneous lipid bilayers [My Copy] Proteins: Structure, Function, and Bioinformatics, Vol. 9999, No. 9999. (2008), NA. by Hyunbum Jang, Naveen Michaud-Agrawal, Jennifer M. Johnston, Thomas B. Woolf posted to moleculardynamics peptides by loison on 2009-03-20 14:03:21 as along with 2 people neils sunhwan
	NMR Structure and Molecular Dynamics of the In-Plane Membrane Anchor of Nonstructural Protein 5A from Bovine Viral Diarrhea Virus†,‡ [My Copy] Biochemistry, Vol. 45, No. 7. (1 February 2006), pp. 2221-2233. by Nicolas Sapay, Roland Montserret, Christophe Chipot, et al.Volker Brass, Darius Moradpour, Gilbert Deleage, Francois Penin posted to membrane moleculardynamics peptide by loison on 2009-03-20 09:32:08 as
	Interaction of a peptide nanotube with a water–membrane interface [My Copy] Physical Biology, Vol. 3, No. 1. (March 2006), S20. by Christophe Chipot, Mounir Tarek posted to membrane moleculardynamics peptide by loison on 2009-03-20 09:31:04 as
	Fundamental Aspects of Protein−Protein Association Kinetics [My Copy] Chemical Reviews, Vol. 109, No. 3. (11 March 2009), pp. 839-860. by G. Schreiber, G. Haran, H. X. Zhou posted to kinetics md moleculardynamics proteincomplex proteinproteininteraction review by sschurer on 2009-03-14 18:11:43 as along with 10 people and 2 groups anuragsethi barry sunhwan jmccammon sobolevnrm willard kafuitay carlosjavierna hadesnumb paulschlesinger McCammon baker-group
	Insight into the Solvation and Isomerization of 3-Halo-1-azaallylic Anions from Ab Initio Metadynamics Calculations and NMR Experiments [My Copy] Chemistry - A European Journal, Vol. 15, No. 3. (2009), pp. 580-584. by Reinout Declerck, Bart De Sterck, Toon Verstraelen, et al.Guido Verniest, Sven Mangelinckx, Jan Jacobs, Norbert De Kimpe, Michel Waroquier, Veronique Van Speybroeck posted to dft moleculardynamics by tovrstra on 2009-03-12 16:32:39 as
	Effect of temperature on the EPR properties of a rhamnose alkoxy radical: A DFT molecular dynamics study [My Copy] Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy, Vol. 69, No. 5. (May 2008), pp. 1388-1394. by E. Pauwels, T. Verstraelen, M. Waroquier posted to epr moleculardynamics by tovrstra on 2009-03-12 16:03:55 as
	Temperature Study of a Glycine Radical in the Solid State Adopting a DFT Periodic Approach: Vibrational Analysis and Comparison with EPR Experiments [My Copy] The Journal of Physical Chemistry B, Vol. 112, No. 25. (1 June 2008), pp. 7618-7630. by Ewald Pauwels, Toon Verstraelen, Hendrik De Cooman, Veronique Van Speybroeck, Michel Waroquier posted to epr moleculardynamics by tovrstra on 2009-03-12 16:03:35 as
	Transition path sampling and the calculation of rate constants [My Copy] The Journal of Chemical Physics, Vol. 108, No. 5. (1998), pp. 1964-1977. by Christoph Dellago, Peter G. Bolhuis, Félix S. Csajka, David Chandler posted to modeling moleculardynamics montecarlo transitionstate by tovrstra on 2009-03-04 14:38:31 as along with 3 people Diego_Prada jrperillaj ruvido
	A novel path sampling method for the calculation of rate constants [My Copy] The Journal of Chemical Physics, Vol. 118, No. 17. (2003), pp. 7762-7774. by Titus S. van Erp, Daniele Moroni, Peter G. Bolhuis posted to modeling moleculardynamics montecarlo transitionstate by tovrstra on 2009-03-04 14:35:47 as
	Iterative fluctuation charge model: A new variable charge molecular dynamics method [My Copy] The Journal of Chemical Physics, Vol. 124, No. 23. (2006) by Ying Ma, Stephen H. Garofalini posted to chargetransfer forcefields moleculardynamics silica by tovrstra on 2009-02-27 14:40:52 as
	Potential of Mean Force for Tetramethylammonium Binding to Cagelike Oligosilicates in Aqueous Solution [My Copy] Journal of the American Chemical Society, Vol. 128, No. 50. (1 December 2006), pp. 16138-16147. by S. Caratzoulas, D. G. Vlachos, M. Tsapatsis posted to modeling moleculardynamics synthesis templates zeolites by tovrstra on 2009-02-21 10:35:17 as
	ZEOBUILDER: A GUI Toolkit for the Construction of Complex Molecular Structures on the Nanoscale with Building Blocks [My Copy] Journal of Chemical Information and Modeling, Vol. 48, No. 7. (1 July 2008), pp. 1530-1541. by T. Verstraelen, V. Van Speybroeck, M. Waroquier posted to moleculardynamics software by tovrstra on 2009-02-20 15:35:38 as
	MD-TRACKS: A Productive Solution for the Advanced Analysis of Molecular Dynamics and Monte Carlo simulations [My Copy] Journal of Chemical Information and Modeling, Vol. 48, No. 12. (22 December 2008), pp. 2414-2424. by Toon Verstraelen, Marc Van Houteghem, Veronique Van Speybroeck, Michel Waroquier posted to moleculardynamics software by tovrstra on 2009-02-20 15:35:19 as
	Homology modeling and molecular dynamics study on N-acetylneuraminate lyase [My Copy] Journal of Molecular Modeling by Hui-Ying Chu, Qing-Chuan Zheng, Yong-Shan Zhao, Hong-Xing Zhang posted to homologymodeling md moleculardynamics by sschurer on 2009-01-29 14:48:44 as
	A conserved protonation-dependent switch controls drug binding in the Abl kinase [My Copy] Proceedings of the National Academy of Sciences, Vol. 106, No. 1. (6 January 2009), pp. 139-144. by Yibing Shan, Markus A. Seeliger, Michael P. Eastwood, et al.Filipp Frank, Huafeng Xu, Morten Jensen, Ron O. Dror, John Kuriyan, David E. Shaw posted to dfgout kinase kinaseinhibition md moleculardynamics by sschurer on 2009-01-08 19:32:04 as along with 2 people and 1 group nanonan sobolevnrm baker-group
	A new method for in-silico drug screening and similarity search using molecular dynamics maximum volume overlap (MD-MVO) method [My Copy] Journal of Molecular Graphics and Modelling, Vol. 27, No. 5. (January 2009), pp. 628-636. by Y. Fukunishi, H. Nakamura posted to ligandoverlap md moleculardynamics pharmacophoremodel volumeoverlap by sschurer on 2008-12-28 14:37:02 as
	Monte Carlo-minimization approach to the multiple-minima problem in protein folding. [My Copy] Proc Natl Acad Sci U S A, Vol. 84, No. 19. (October 1987), pp. 6611-6615. by Z. Li, H. A. Scheraga posted to moleculardynamics by dsekaran on 2008-12-11 19:19:20 as along with 2 people dgront newton1234
	Milestones in the Activation of a G Protein-Coupled Receptor. Insights from Molecular-Dynamics Simulations into the Human Cholecystokinin Receptor-1 [My Copy] Journal of Chemical Theory and Computation, Vol. 4, No. 12. (December 2008), pp. 2150-2159. by Christophe Chipot posted to gpcractivation md moleculardynamics theory by sschurer on 2008-12-11 07:07:12 as
	United-Atom Discrete Molecular Dynamics of Proteins Using Physics-Based Potentials [My Copy] Journal of Chemical Theory and Computation, Vol. 4, No. 12. (December 2008), pp. 2001-2010. by Agustí Emperador, Tim Meyer, Modesto Orozco posted to md moleculardynamics theory by sschurer on 2008-12-11 06:58:54 as
	Novel paradigms for drug discovery: computational multitarget screening [My Copy] Trends in Pharmacological Sciences, Vol. 29, No. 2. (February 2008), pp. 62-71. by Ekachai Jenwitheesuk, Jeremy A. Horst, Kasey L. Rivas, Wesley C. Van Voorhis, Ram Samudrala posted to docking md moleculardynamics multitargetscreening proteinflexibility virtualscreening by sschurer on 2008-12-09 21:31:41 as along with 1 person psique
	Prediction of the 3D Structure and Dynamics of Human DP G-Protein Coupled Receptor Bound to an Agonist and an Antagonist [My Copy] J. Am. Chem. Soc., Vol. 129, No. 35. (5 September 2007), pp. 10720-10731. by Y. Li, F. Zhu, N. Vaidehi, et al.W. A. Goddard, F. Sheinerman, S. Reiling, I. Morize, L. Mu, K. Harris, A. Ardati, A. Laoui posted to agonist antagonist docking gpcr homologymodeling md moleculardynamics by sschurer on 2008-12-07 20:31:34 as along with 2 people daevans superpyrin
	Crystal Structure of a Ten-Amino Acid Protein [My Copy] Journal of the American Chemical Society, Vol. 130, No. 46. (19 November 2008), pp. 15327-15331. by Shinya Honda, Toshihiko Akiba, Yusuke S. Kato, et al.Yoshito Sawada, Masakazu Sekijima, Miyuki Ishimura, Ayako Ooishi, Hideki Watanabe, Takayuki Odahara, Kazuaki Harata posted to daspace md moleculardynamics by sschurer on 2008-12-05 19:25:10 as
	Structure–activity relationships of modified C-terminal endomorphin-2 analogues by molecular dynamics simulations [My Copy] Journal of Molecular Graphics and Modelling, Vol. 27, No. 4. (November 2008), pp. 489-496. by Y. Wang, Y. Wu, J. Chen, L. Huang, F. Tsai, C. Hwang posted to moleculardynamics by sschurer on 2008-12-01 15:43:03 as
	Computing the stability diagram of the Trp-cage miniprotein [My Copy] Proceedings of the National Academy of Sciences, Vol. 105, No. 46. (18 November 2008), pp. 17754-17759. by Dietmar Paschek, Sascha Hempel, Angel E. García posted to moleculardynamics by sschurer on 2008-11-19 18:28:21 as along with 1 person paulschlesinger
	Structure of Met-enkephalin in explicit aqueous solution using replica exchange molecular dynamics [My Copy] Proteins: Structure, Function, and Genetics, Vol. 46, No. 2. (2002), pp. 225-234. by K. Y. Sanbonmatsu, A. E. García posted to moleculardynamics opioid-peptide by dsekaran on 2008-11-05 22:49:32 as along with 1 person Sylvain_Prigent
	Prediction of phase equilibria and transport properties in carbon-dioxide expanded solvents by molecular simulation [My Copy] Molecular Simulation, Vol. 33, No. 9-10. (August 2007), pp. 861-869. by Houndonougbo, Y., Kuczera, et al. K., Subramaniam, B., Laird, B.B. posted to carbondioxide equilibria expanded ionic liquid moleculardynamics phase properties transport rtil by majdula on 2008-09-08 09:35:04 as
	Ab initio RNA folding by discrete molecular dynamics: from structure prediction to folding mechanisms. [My Copy] RNA (New York, N.Y.), Vol. 14, No. 6. (1 June 2008), pp. 1164-1173. by Feng Ding, Shantanu Sharma, Poornima Chalasani, Vadim V. Demidov, Natalia E. Broude, Nikolay V. Dokholyan posted to folding moleculardynamics rna by carmaus on 2008-06-07 16:16:54 as along with 3 people balewis Hosna physics
	On the computation and contribution of conductivity in molecular ionic liquids [My Copy] Journal of Chemical Physics, Vol. 128, No. 13. (2008) by C. Schröder, M. Haberler, O. Steinhauser posted to bf4 bmim conductivity dicyanamide emim ionic liquid moleculardynamics rtil by majdula on 2008-05-09 17:22:16 as
	Aqueous interfaces with hydrophobic room-temperature ionic liquids: A molecular dynamics study [My Copy] Journal of Physical Chemistry B, Vol. 109, No. 40. (2005), pp. 18964-18973. by A. Chaumont, R. Schurhammer, G. Wipff posted to demixing ionic liquids lle mechanisms moleculardynamics rtil by majdula on 2008-04-29 16:56:03 as along with 1 person marcou
	Extended FinnisSinclair potential for bcc and fcc metals and alloys [My Copy] Journal of Physics: Condensed Matter, Vol. 18, No. 19. (17 May 2006), pp. 4527-4542. by X. D. Dai, Y. Kong, J. H. Li, B. X. Liu posted to materials moleculardynamics nanoscience by srkirk on 2008-03-07 05:35:52 as
	Interatomic potentials for atomistic simulations of the Ti-Al system [My Copy] Physical Review B, Vol. 68, No. 2. (14 July 2003), 024102. by Rajendra R. Zope, Y. Mishin posted to materials moleculardynamics nanoscience by srkirk on 2008-03-07 05:34:31 as
	Additive and Classical Drude Polarizable Force Fields for Linear and Cyclic Ethers [My Copy] J. Chem. Theory Comput., Vol. 3, No. 3. (8 May 2007), pp. 1120-1133. by I. Vorobyov, V. M. Anisimov, S. Greene, et al.R. M. Venable, A. Moser, R. W. Pastor, A. D. Mackerell posted to forcefields ionshell moleculardynamics parameterization by tovrstra on 2008-02-05 08:54:13 as along with 1 person marcvanhouteghem
	A domain decomposition parallel processing algorithm for molecular dynamics simulations of systems of arbitrary connectivity [My Copy] pp. 170-186. by D. Brown posted to algorithm domaindecomposition moleculardynamics parallel by rblake to the group uiuc-cs on 2007-02-19 18:17:43 as along with 1 person jwagoner
	Constructing ab initio force fields for molecular dynamics simulations [My Copy] The Journal of Chemical Physics, Vol. 108, No. 12. (1998), pp. 4739-4755. by Yi P. Liu, Kyungsun Kim, B. J. Berne, Richard A. Friesner, Steven W. Rick posted to chargetransfer electronegativity forcefields hardness longrange moleculardynamics parameterization polarizable by tovrstra on 2006-04-24 16:23:52 as
	Molecular Dynamics Study of Hydrated Faujasite-Type Zeolites [My Copy] J. Phys. Chem. B, Vol. 109, No. 8. (3 March 2005), pp. 3446-3453. by K. Shirono, A. Endo, H. Daiguji posted to chargetransfer electronegativity forcefields hardness moleculardynamics zeolites by tovrstra on 2006-04-20 09:48:21 as
	Including the polarization in simulations of hydrated aluminosilicates. Model and application to water in silicalite [My Copy] Chemical Physics, Vol. 292, No. 1. (15 July 2003), pp. 53-70. by K. S. Smirnov, D. Bougeard posted to chargetransfer forcefields moleculardynamics zeoliteguest zeolites by tovrstra on 2006-04-20 09:42:41 as

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