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	Electronic Structure of (6−4) DNA Photoproduct Repair Involving a Non-Oxetane Pathway [My Copy] Journal of the American Chemical Society, Vol. 0, No. 0. (0000) by Tatiana Domratcheva, Ilme Schlichting posted to photoproduct photolyase oxetane dna 6-4 by charris5 on 2009-11-22 11:58:53 as
	A Quick Guide to Organizing Computational Biology Projects [My Copy] PLoS Comput Biol, Vol. 5, No. 7. (31 July 2009), e1000424. by William S. Noble posted to how-tos by charris5 on 2009-08-21 14:12:15 as along with 57 people and 7 groups skembel pekrau Sergey_gerbek mordiano remoteFuture Yanno aaltenburger marekrud guhjy dolchan frohike operon CorinYeats artaban421 antonkratz tomhebbron maren bayesian daveGerrard JoeBanks jcaddy somak bertelsen ptrobajo nperoni daforerog mmwoodman GustavoLacerda pmendes fgibson rdiaz Zephyrus heliopais franklu310 lmichan silberbauer leemond31 jlangdon robfsouza Stew pmung reyez kshameer djkt pawelsobko jjray dswan apaydin renatomilani VGreiff cabbagesofdoom wei_tang fenghezi cisevol barry sdaehne druvus Pedro Martinez EvoDevo lab Barcelona Orengo Group Journal Picks Bioinformatics - CRUK ccsbs BergmanLab structural_bioinformatics McCammon
	Quantum Chemistry on Graphical Processing Units. 2. Direct Self-Consistent-Field Implementation [My Copy] Journal of Chemical Theory and Computation, Vol. 5, No. 4. (14 April 2009), pp. 1004-1015. by Ivan S. Ufimtsev, Todd J. Martinez posted to qmgpu qm gpu by charris5 on 2009-04-24 21:17:17 as along with 2 people Fortran RamuAnandakrishnan
	Beyond Förster Resonance Energy Transfer in Biological and Nanoscale Systems [My Copy] The Journal of Physical Chemistry B, Vol. 0, No. 0. (0000) by David Beljonne, Carles Curutchet, Gregory D. Scholes, Robert J. Silbey posted to energytransfer by charris5 on 2009-04-19 16:57:15 as along with 2 people and 1 group marissalee samjlord moernerlab
	Evaluating Boundary Dependent Errors in QM/MM Simulations [My Copy] The Journal of Physical Chemistry B, Vol. 0, No. 0. (0000) by Iván Solt, Petr Kulhánek, István Simon, et al.Steven Winfield, Mike C. Payne, Gábor Csányi, Monika Fuxreiter posted to qmmm by charris5 on 2009-04-19 14:35:16 as
	Structure-Based Discovery of Triphenylmethane Derivatives as Inhibitors of Hepatitis C Virus Helicase∞ [My Copy] Journal of Medicinal Chemistry, Vol. 0, No. 0. (0000) by Chien-Shu Chen, Chun-Tang Chiou, Grace S. Chen, et al.Sheng-Chia Chen, Chih-Yung Hu, Wei-Kuang Chi, Yi-Ding Chu, Lih-Hwa Hwang, Pei-Jer Chen, Ding-Shinn Chen, Shwu-Huey Liaw, Ji-Wang Chern posted to helicase by charris5 on 2009-04-18 22:43:45 as
	Implementation of the SCC-DFTB Method for Hybrid QM/MM Simulations within the Amber Molecular Dynamics Package. [My Copy] J Phys Chem A (24 May 2007) by Gustavo D. Seabra, Ross C. Walker, Marcus Elstner, David A. Case, Adrian E. Roitberg posted to sccdftb qmmm amber by charris5 on 2009-04-17 14:55:50 as along with 3 people and 1 group krapnik vahmurk xdeupi LabCompMed
	LocalSCF method for semiempirical quantum-chemical calculation of ultralarge biomolecules [My Copy] The Journal of Chemical Physics, Vol. 121, No. 3. (2004), pp. 1266-1270. by N. A. Anikin, V. M. Anisimov, V. L. Bugaenko, V. V. Bobrikov, A. M. Andreyev posted to no-tag by charris5 on 2009-04-17 11:16:01 as
	Efficient Multipole Model and Linear Scaling of NDDO-Based Methods [My Copy] The Journal of Physical Chemistry A, Vol. 109, No. 33. (1 August 2005), pp. 7613-7620. by A. M. Tokmachev, A. L. Tchougreeff posted to no-tag by charris5 on 2009-04-17 11:12:17 as
	Comparison of SCC-DFTB and NDDO-Based Semiempirical Molecular Orbital Methods for Organic Molecules [My Copy] The Journal of Physical Chemistry A, Vol. 110, No. 50. (1 December 2006), pp. 13551-13559. by Kurt W. Sattelmeyer, Julian Tirado-Rives, William L. Jorgensen posted to no-tag by charris5 on 2009-04-17 11:05:57 as
	Linear-scaling semiempirical quantum calculations for macromolecules [My Copy] The Journal of Chemical Physics, Vol. 105, No. 7. (1996), pp. 2744-2750. by Tai S. Lee, Darrin M. York, Weitao Yang posted to no-tag by charris5 on 2009-04-17 04:39:08 as along with 1 person and 1 group sobolevnrm baker-group
	Quantum Mechanical Study of Aqueous Polarization Effects on Biological Macromolecules [My Copy] Journal of the American Chemical Society, Vol. 118, No. 44. (1 January 1996), pp. 10940-10941. by Darrin M. York, Tai-Sung Lee, Weitao Yang posted to no-tag by charris5 on 2009-04-17 04:38:02 as
	Parameterization and efficient implementation of a solvent model for linear-scaling semiempirical quantum mechanical calculations of biological macromolecules [My Copy] Chemical Physics Letters, Vol. 263, No. 1-2. (06 December 1996), pp. 297-304. by D. York posted to no-tag by charris5 on 2009-04-17 04:36:42 as
	Quantum descriptors for biological macromolecules from linear-scaling electronic structure methods. [My Copy] Proteins, Vol. 56, No. 4. (1 September 2004), pp. 724-737. by J. Khandogin, D. M. York posted to no-tag by charris5 on 2009-04-17 04:30:39 as along with 1 person superpyrin
	Improvement of semiempirical response properties with charge-dependent response density [My Copy] The Journal of Chemical Physics, Vol. 123, No. 16. (2005), 164108. by Timothy J. Giese, Darrin M. York posted to no-tag by charris5 on 2009-04-17 04:28:49 as
	An Efficient Linear-Scaling Ewald Method for Long-Range Electrostatic Interactions in Combined QM/MM Calculations [My Copy] Journal of Chemical Theory and Computation, Vol. 1, No. 1. (1 January 2005), pp. 2-13. by Kwangho Nam, Jiali Gao, Darrin M. York posted to no-tag by charris5 on 2009-04-17 04:27:43 as
	Multilevel and Density Functional Electronic Structure Calculations of Proton Affinities and Gas-Phase Basicities Involved in Biological Phosphoryl Transfer† [My Copy] The Journal of Physical Chemistry A, Vol. 110, No. 2. (1 January 2006), pp. 791-797. by Kevin Range, Carlos S. Lopez, Adam Moser, Darrin M. York posted to no-tag by charris5 on 2009-04-17 04:26:03 as
	A charge-scaling implementation of the variational electrostatic projection method [My Copy] Journal of Computational Chemistry, Vol. 27, No. 1. (2006), pp. 103-115. by Brent A. Gregersen, Darrin M. York posted to no-tag by charris5 on 2009-04-17 04:24:06 as
	A Semiempirical Quantum Model for Hydrogen-Bonded Nucleic Acid Base Pairs [My Copy] Journal of Chemical Theory and Computation, Vol. 1, No. 6. (1 November 2005), pp. 1275-1285. by Timothy J. Giese, Edward C. Sherer, Christopher J. Cramer, Darrin M. York posted to no-tag by charris5 on 2009-04-17 04:21:08 as
	Charge-dependent model for many-body polarization, exchange, and dispersion interactions in hybrid quantum mechanical/molecular mechanical calculations [My Copy] The Journal of Chemical Physics, Vol. 127, No. 19. (2007), 194101. by Timothy J. Giese, Darrin M. York posted to no-tag by charris5 on 2009-04-17 04:18:38 as
	Extension of the Self-Consistent-Charge Density-Functional Tight-Binding Method: Third-Order Expansion of the Density Functional Theory Total Energy and Introduction of a Modified Effective Coulomb Interaction [My Copy] The Journal of Physical Chemistry A, Vol. 111, No. 42. (1 October 2007), pp. 10861-10873. by Yang, Haibo Yu, Darrin York, Qiang Cui, Marcus Elstner posted to no-tag by charris5 on 2009-04-17 04:17:35 as
	A Mesoscopic Model for Protein-Protein Interactions in Solution [My Copy] Biophys. J., Vol. 85, No. 5. (1 November 2003), pp. 2940-2947. by M. Lund, B. Jönsson posted to protein-protein-interactions mesoscale by charris5 on 2009-04-17 01:11:58 as along with 1 person mikaellund
	Accelerating molecular modeling applications with graphics processors [My Copy] Journal of Computational Chemistry, Vol. 28, No. 16. (25 September 2007), pp. 2618-2640. by John E. Stone, James C. Phillips, Peter L. Freddolino, David J. Hardy, Leonardo G. Trabuco, Klaus Schulten posted to mdgpu md gpu by charris5 on 2009-04-17 01:11:48 as along with 9 people and 1 group ihaque naoya timg BragilMassoud ruvido sobolevnrm yalexeev mikaellund afenley baker-group
	Protein Stability Prediction: A Poisson-Boltzmann Approach [My Copy] J. Phys. Chem. B (23 January 2008) by Y. H. Tan, R. Luo posted to protein-folding poisson-boltzman go-model by charris5 on 2009-04-17 01:11:39 as along with 2 people and 1 group sobolevnrm mikaellund baker-group
	Water at Hydrophobic Surfaces: When Weaker Is Better [My Copy] J. Am. Chem. Soc. (18 January 2008) by D. K. Hore, D. S. Walker, G. L. Richmond posted to water hydrophobic by charris5 on 2009-04-17 01:11:31 as along with 2 people sunrise mikaellund
	Energy Landscape and Transition State of Protein-Protein Association [My Copy] Biophys. J., Vol. 92, No. 5. (1 March 2007), pp. 1486-1502. by Ramzi Alsallaq, Huan-Xiang Zhou posted to tst protein-protein-interactions pes by charris5 on 2009-04-17 01:11:24 as along with 1 person mikaellund
	Thermodynamics and an Introduction to Thermostatistics, 2nd Edition [My Copy] (29 August 1985) by Herbert B. Callen posted to thermo stat-mech by charris5 on 2009-04-17 01:11:16 as along with 3 people cager robertoalamino mikaellund
	Understanding Molecular Simulation, Second Edition: From Algorithms to Applications (Computational Science Series, Vol 1) [My Copy] (07 November 2001) by Daan Frenkel, B. Smit posted to md by charris5 on 2009-04-17 01:11:10 as along with 6 people pjkiley georgwachter kkims ptupper mikaellund OndrejMarsalek
	Computer Simulation of Liquids [My Copy] (29 June 1989) by M. P. Allen, D. J. Tildesley posted to stat-mech by charris5 on 2009-04-17 01:11:03 as along with 6 people horaciotm kkims agupta0318 mikaellund OndrejMarsalek alexispaz
	An Introduction to Statistical Thermodynamics [My Copy] (01 January 1987) by Terrell L. Hill posted to stat-mech by charris5 on 2009-04-17 01:10:57 as along with 4 people and 1 group chiufanlee thaliana ssomani mikaellund structure-bii
	The C++ Programming Language (Special 3rd Edition) [My Copy] (15 February 2000) by Bjarne Stroustrup posted to c by charris5 on 2009-04-17 01:10:49 as along with 12 people and 1 group MSukruKuran jmmcg lostcoder matjes danfcook gardak aespinosa alexzeh chandlerc mikaellund michaelbussmann sven_luzar Catalysts Bookshelf
	Amber 9 [My Copy] (2006) by D. A. Case, T. A. Darden, Cheatham, et al.C. L. Simmerling, J. Wang, R. E. Duke, R. Luo, K. M. Merz, D. A. Pearlman, M. Crowley, R. C. Walker, W. Zhang, B. Wang, S. Hayik, A. Roitberg, G. Seabra, K. F. Wong, F. Paesani, X. Wu, S. Brozell, V. Tsui, H. Gohlke, L. Yang, C. Tan, J. Mongan, V. Hornak, G. Cui, P. Beroza, D. H. Mathews, C. Schafmeister, W. S. Ross, P. A. Kollman posted to amber by charris5 on 2009-04-17 01:09:00 as along with 1 person mikaellund
	How well does a restrained electrostatic potential(RESP) model perform in calculating conformational energies of organic and biological molecules? [My Copy] J. Comp. Chem., Vol. 21, No. 12. (2000), pp. 1049-1074. by J. Wang, P. Cieplak, P. A. Kollman posted to electrostatics conformational-change by charris5 on 2009-04-17 01:08:52 as along with 1 person mikaellund
	Electrostatic aspects of protein–protein interactions [My Copy] Current Opinion in Structural Biology, Vol. 10, No. 2. (1 April 2000), pp. 153-159. by F. Sheinerman posted to protein-protein-interactions electrostatics by charris5 on 2009-04-17 01:08:44 as along with 4 people flbarroso cjeans carlescorbi mikaellund
	Potentials of mean force for biomolecular simulations: Theory and test on alanine dipeptide [My Copy] The Journal of Chemical Physics, Vol. 104, No. 21. (1996), pp. 8639-8648. by Matteo Pellegrini, Niels, Sebastian Doniach posted to pmf nanma by charris5 on 2009-04-17 01:08:36 as along with 1 person mikaellund
	Protein-protein binding is often associated with changes in protonation state [My Copy] Proteins: Structure, Function and Bioinformatics, Vol. 71 (2007), pp. 81-91. by A. C. Mason, J. H. Jensen posted to protein-protein-interactions by charris5 on 2009-04-17 01:08:26 as along with 1 person mikaellund
	On the driving forces for protein-protein association [My Copy] The Journal of Chemical Physics, Vol. 125, No. 2. (2006) by Arieh B. Naim posted to protein-protein-interactions by charris5 on 2009-04-17 01:08:11 as along with 1 person mikaellund
	The Amber biomolecular simulation programs. [My Copy] Journal of computational chemistry, Vol. 26, No. 16. (December 2005), pp. 1668-1688. by David A. Case, Thomas E. Cheatham, Tom Darden, et al.Holger Gohlke, Ray Luo, Kenneth M. Merz, Alexey Onufriev, Carlos Simmerling, Bing Wang, Robert J. Woods posted to amber by charris5 on 2009-04-17 00:43:44 as along with 18 people and 3 groups krapnik csrocha nickolay mmuecke flbarroso pavanghatty tahereh62 lna jwm ttjoseph xdeupi tovrstra bilab RamuAnandakrishnan IrinaMoreira adilson_mohr mikaellund gisle Radiation_Damage Stressosome LabCompMed
	Electric fields at the active site of an enzyme: direct comparison of experiment with theory. [My Copy] Science (New York, N.Y.), Vol. 313, No. 5784. (14 July 2006), pp. 200-204. by Ian T. Suydam, Christopher D. Snow, Vijay S. Pande, Steven G. Boxer posted to electrostatics by charris5 on 2009-04-17 00:43:36 as along with 5 people onufriev flbarroso mikaellund jbchang kjell
	VMD -- Visual Molecular Dynamics [My Copy] J. Mol. Graphics, Vol. 14 (1996), pp. 31-38. by W. F. Humphrey, A. Dalke, K. Schulten posted to vmd by charris5 on 2009-04-17 00:40:47 as along with 1 person mikaellund
	On the evaluation and optimization of protein X-ray structures for pKa calculations. [My Copy] Protein science : a publication of the Protein Society, Vol. 12, No. 2. (February 2003), pp. 313-326. by J. E. Nielsen, J. A. McCammon posted to pka by charris5 on 2009-04-17 00:38:47 as along with 3 people onufriev softsimu RamuAnandakrishnan
	A reciprocal space based method for treating long range interactions in ab initio and force-field-based calculations in clusters [My Copy] The Journal of Chemical Physics, Vol. 110, No. 6. (1999), pp. 2810-2821. by Glenn J. Martyna, Mark E. Tuckerman posted to qmmm pme by charris5 on 2009-04-17 00:35:08 as along with 1 person softsimu
	A new reciprocal space based treatment of long range interactions on surfaces [My Copy] The Journal of Chemical Physics, Vol. 116, No. 13. (2002), pp. 5351-5362. by Peter Minary, Mark E. Tuckerman, Katianna A. Pihakari, Glenn J. Martyna posted to pme by charris5 on 2009-04-17 00:34:47 as along with 1 person and_ped10
	Gaussian split Ewald: A fast Ewald mesh method for molecular simulation [My Copy] The Journal of Chemical Physics, Vol. 122, No. 5. (2005) by Yibing Shan, John L. Klepeis, Michael P. Eastwood, Ron O. Dror, David E. Shaw posted to pme by charris5 on 2009-04-17 00:34:17 as along with 4 people stephenbond r2s2 sjplimp ruvido
	Is the Ewald summation still necessary? Pairwise alternatives to the accepted standard for long-range electrostatics [My Copy] The Journal of Chemical Physics, Vol. 124, No. 23. (2006) by Christopher J. Fennell, Daniel J. Gezelter posted to pme by charris5 on 2009-04-17 00:32:51 as along with 4 people and 1 group mikaellund OndrejMarsalek michaelbussmann sobolevnrm baker-group
	A smooth particle mesh Ewald method [My Copy] The Journal of Chemical Physics, Vol. 103, No. 19. (1995), pp. 8577-8593. by Ulrich Essmann, Lalith Perera, Max L. Berkowitz, Tom Darden, Hsing Lee, Lee G. Pedersen posted to pme by charris5 on 2009-04-17 00:32:04 as along with 15 people and 2 groups jmparks rpetrenko A_Coletta_Thesis r2s2 pavanghatty sobolevnrm choonpeng lillekatt and_ped10 easybakemuffin RamuAnandakrishnan ashaytan mikaellund 6rheology jteyra Structural Biology Group TorVergata baker-group
	A dual length scale method for plane-wave-based, simulation studies of chemical systems modeled using mixed ab initio/empirical force field descriptions [My Copy] The Journal of Chemical Physics, Vol. 115, No. 8. (2001), pp. 3531-3539. by Dawn A. Yarne, Mark E. Tuckerman, Glenn J. Martyna posted to qmmm pme by charris5 on 2009-04-17 00:30:27 as
	A fine grained parallel smooth particle mesh Ewald algorithm for biophysical simulation studies: Application to the 6-D torus QCDOC supercomputer [My Copy] Computer Physics Communications, Vol. 177, No. 4. (15 August 2007), pp. 362-377. by B. Fang, G. Martyna, Y. Deng posted to pme by charris5 on 2009-04-17 00:27:40 as
	Dispensable residues in the active site of the cytochrome c biogenesis protein CcmH. [My Copy] FEBS letters (4 August 2008) by Ian B B. Robertson, Julie M M. Stevens, Stuart J J. Ferguson posted to cyt-c by charris5 on 2008-08-11 14:21:53 as
	Quality Assurance for Biomolecular Simulations [My Copy] J. Chem. Theory Comput., Vol. 2, No. 6. (14 November 2006), pp. 1477-1481. by S. E. Murdock, K. Tai, M. H. Ng, et al.S. Johnston, B. Wu, H. Fangohr, C. A. Laughton, J. W. Essex, M. S. P. Sansom posted to dynamics simulation by charris5 on 2006-11-24 02:24:45 as

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pme	7
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c	1
conformational-change	1
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