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	The MARTINI Coarse-Grained Force Field: Extension to Proteins [My Copy] Journal of Chemical Theory and Computation, Vol. 4, No. 5. (1 May 2008), pp. 819-834. by Luca Monticelli, Senthil K. Kandasamy, Xavier Periole, Ronald G. Larson, D. Peter Tieleman, Siewert-Jan Marrink posted by 17 people arnaucordomi dimka oteri sunrise flbarroso Structural Biology Group TorVergata A_Coletta_Thesis krapnik Molecular dynamics in MSU Marine middledomain sobolevnrm baker-group Ema aqeel DanielParton softsimu
	GROMACS: fast, flexible, and free. [My Copy] Journal of computational chemistry, Vol. 26, No. 16. (December 2005), pp. 1701-1718. by David Van Der Spoel, Erik Lindahl, Berk Hess, Gerrit Groenhof, Alan E. Mark, Herman J. Berendsen posted by 23 people arifor krapnik r2s2 janneb dsmueller oteri choonpeng sebk dimka jwm ttjoseph bilab rabio Dinler Radiation_Damage Stressosome tji softsimu ashaytan robertvacha sunnytov Diego_Prada A_Coletta_Thesis
	Hydrogen bonding definitions and dynamics in liquid water [My Copy] The Journal of Chemical Physics, Vol. 126, No. 20. (2007), 204107. by R. Kumar, J. R. Schmidt, J. L. Skinner posted by 5 people softsimu samjlord ruvido moernerlab kdesmond
	The MARTINI Force Field: Coarse Grained Model for Biomolecular Simulations [My Copy] The Journal of Physical Chemistry B, Vol. 111, No. 27. (1 July 2007), pp. 7812-7824. by Siewert J. Marrink, H. Jelger Risselada, Serge Yefimov, D. Peter Tieleman, Alex H. de Vries posted by 10 people anuragsethi sunrise Structural Biology Group TorVergata A_Coletta_Thesis Molecular dynamics in MSU Marine choonpeng softsimu dimka sunnytov
	Settle: An analytical version of the SHAKE and RATTLE algorithm for rigid water models [My Copy] Journal of Computational Chemistry, Vol. 13, No. 8. (1992), pp. 952-962. by Shuichi Miyamoto, Peter A. Kollman posted by 9 people oteri Lombardo_7 choonpeng A_Coletta_Thesis jwagoner tji softsimu ashaytan robertvacha
	Multi-Channel Receptors and Their Relation to Guest Chemosensing and Reconfigurable Molecular Logic Gates [My Copy] European Journal of Inorganic Chemistry, Vol. 2005, No. 12. (2005), pp. 2393-2403. by Diego Jiménez, Ramón Martínez-Máñez, Félix Sancenón, et al.José V. Ros-Lis, Juan Soto, Ángel Benito, Eduardo García-Breijo posted by 2 people samjlord moernerlab
	Comparison of simple potential functions for simulating liquid water [My Copy] The Journal of Chemical Physics, Vol. 79, No. 2. (1983), pp. 926-935. by William L. Jorgensen, Jayaraman Chandrasekhar, Jeffry D. Madura, Roger W. Impey, Michael L. Klein posted by 19 people jmparks fralium bmduggan kulinskii ibuch Lombardo_7 paddydu dfgreen softsimu mleis ttjoseph ffranca easybakemuffin ashaytan RamuAnandakrishnan r2s2 CMB pavanghatty Diego_Prada
	Continuum molecular electrostatics, salt effects, and counterion binding--a review of the Poisson-Boltzmann theory and its modifications. [My Copy] Biopolymers, Vol. 89, No. 2. (February 2008), pp. 93-113. by P. Grochowski, J. Trylska posted by 6 people onufriev flbarroso sobolevnrm baker-group softsimu mikaellund
	Explicit ion, implicit water solvation for molecular dynamics of nucleic acids and highly charged molecules [My Copy] Journal of Computational Chemistry, Vol. 29, No. 7. (2008), pp. 1113-1130. by Ninad V. Prabhu, Manoranjan Panda, Qingyi Yang, Kim A. Sharp posted by 7 people ras Elena_Zubova sobolevnrm baker-group RamuAnandakrishnan onufriev dimka
	Molecular dynamics with coupling to an external bath [My Copy] The Journal of Chemical Physics, Vol. 81, No. 8. (1984), pp. 3684-3690. by H. J. C. Berendsen, J. P. M. Postma, W. F. van Gunsteren, A. Dinola, J. R. Haak posted by 14 people georgwachter Structural Biology Group TorVergata A_Coletta_Thesis rdf r2s2 dsmueller Lombardo_7 gsub lillekatt allmensch jwagoner tji choonpeng jteyra
	Full correlation analysis of conformational protein dynamics [My Copy] Proteins: Structure, Function, and Bioinformatics, Vol. 9999, No. 9999. (2007), NA. by Oliver F. Lange, Helmut Grubmüller posted by 9 people anuragsethi jeargle Diego_Prada softsimu barry choonpeng sobolevnrm baker-group LamBras
	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 by 18 people jmparks rpetrenko Structural Biology Group TorVergata A_Coletta_Thesis r2s2 charris5 pavanghatty baker-group sobolevnrm choonpeng lillekatt and_ped10 easybakemuffin RamuAnandakrishnan ashaytan mikaellund 6rheology jteyra
	Convergence of sampling in protein simulations [My Copy] Physical Review E, Vol. 65, No. 3. (1 March 2002), 031910. by Berk Hess posted by 7 people anuragsethi klexa tovrstra Structural Biology Group TorVergata oteri onufriev softsimu
	Equilibrium Information from Nonequilibrium Measurements in an Experimental Test of Jarzynski's Equality [My Copy] Science, Vol. 296, No. 5574. (7 June 2002), pp. 1832-1835. by Jan Liphardt, Sophie Dumont, Steven B. Smith, Ignacio Tinoco, Carlos Bustamante posted by 6 people kulinskii stephenbond melting samjlord softsimu ruudvanleeuwen
	The Structure of the First Coordination Shell in Liquid Water [My Copy] Science, Vol. 304, No. 5673. (14 May 2004), pp. 995-999. by Ph Wernet, D. Nordlund, U. Bergmann, et al.M. Cavalleri, M. Odelius, H. Ogasawara, L. A. Naslund, T. K. Hirsch, L. Ojamae, P. Glatzel, L. G. M. Pettersson, A. Nilsson posted by 10 people kulinskii Diego_Prada Jiang Research Group whitead mlg gane5h samjlord rabio ruvido moernerlab
	Coarse-grained models for proteins [My Copy] Current Opinion in Structural Biology, Vol. 15, No. 2. (April 2005), pp. 144-150. by V. Tozzini posted by 11 people saravan flbarroso krapnik RamuAnandakrishnan baaden aqeel ltrabuco simone cottrell choonpeng iantunbridge
	Hydration Thermodynamic Properties of Amino Acid Analogues: A Systematic Comparison of Biomolecular Force Fields and Water Models [My Copy] The Journal of Physical Chemistry B, Vol. 110, No. 35. (1 September 2006), pp. 17616-17626. by Berk Hess, Nico F. A. van der Vegt posted by 8 people softsimu arnaucordomi krapnik flbarroso Diego_Prada Molecular dynamics in MSU Marine ashaytan
	Efficient Exploration of Reactive Potential Energy Surfaces Using Car-Parrinello Molecular Dynamics [My Copy] Physical Review Letters, Vol. 90, No. 23. (June 2003), 238302. by M. Iannuzzi, A. Laio, M. Parrinello posted by 3 people Structural Biology Group TorVergata A_Coletta_Thesis and_ped10
	The multiscale coarse-graining method. I. A rigorous bridge between atomistic and coarse-grained models [My Copy] The Journal of Chemical Physics, Vol. 128, No. 24. (2008), 244114. by W. G. Noid, Jhih W. Chu, Gary S. Ayton, et al.Vinod Krishna, Sergei Izvekov, Gregory A. Voth, Avisek Das, Hans C. Andersen posted by 4 people edws sunrise softsimu A_Coletta_Thesis
	The multiscale coarse-graining method. II. Numerical implementation for coarse-grained molecular models [My Copy] The Journal of Chemical Physics, Vol. 128, No. 24. (2008), 244115. by W. G. Noid, Pu Liu, Yanting Wang, et al.Jhih W. Chu, Gary S. Ayton, Sergei Izvekov, Hans C. Andersen, Gregory A. Voth posted by 5 people edws sunrise softsimu A_Coletta_Thesis agrossfield
	Multiscale Simulation of Soft Matter: From Scale Bridging to Adaptive Resolution [My Copy] Annual Review of Physical Chemistry, Vol. 59, No. 1. (2008), pp. 545-571. by Matej Praprotnik, Luigi Delle Site, Kurt Kremer posted by 6 people Jiang Research Group whitead flbarroso rok softsimu RamuAnandakrishnan
	Assessing Atomistic and Coarse-Grained Force Fields for Protein−Lipid Interactions: the Formidable Challenge of an Ionizable Side Chain in a Membrane [My Copy] J. Phys. Chem. B (18 July 2008) by Igor Vorobyov, Libo Li, Toby W. Allen posted by 4 people softsimu A_Coletta_Thesis middledomain agrossfield
	Supercharging Proteins Can Impart Unusual Resilience [My Copy] J. Am. Chem. Soc., Vol. 129, No. 33. (22 August 2007), pp. 10110-10112. by M. S. Lawrence, K. J. Phillips, D. R. Liu posted by 6 people barry samjlord sobolevnrm structural_bioinformatics moernerlab baker-group
	Local electrostatics algorithm for classical molecular dynamics simulations [My Copy] The Journal of Chemical Physics, Vol. 127, No. 13. (2007), 134104. by Jörg Rottler posted by 7 people sobolevnrm baker-group afenley softsimu mikaellund OndrejMarsalek michaelbussmann
	Some Fundamental Issues in Ground-State Density Functional Theory: A Guide for the Perplexed [My Copy] Journal of Chemical Theory and Computation, Vol. 5, No. 4. (14 April 2009), pp. 902-908. by John P. Perdew, Adrienn Ruzsinszky, Lucian A. Constantin, Jianwei Sun, Gábor I. Csonka posted by 4 people softsimu Fortran Structural Biology Group TorVergata A_Coletta_Thesis
	Effect of Ions on a Dipalmitoyl Phosphatidylcholine Bilayer. A Molecular Dynamics Simulation Study [My Copy] J. Phys. Chem. B (15 January 2008) by A. Cordomi, O. Edholm, J. J. Perez posted by 6 people arnaucordomi robertvacha sobolevnrm baker-group softsimu dimka
	Equilibrium Free Energies from Nonequilibrium Metadynamics [My Copy] Physical Review Letters, Vol. 96, No. 9. (2006) by Giovanni Bussi, Alessandro Laio, Michele Parrinello posted by 2 people Structural Biology Group TorVergata A_Coletta_Thesis
	Efficient, Multiple-Range Random Walk Algorithm to Calculate the Density of States [My Copy] Physical Review Letters, Vol. 86, No. 10. (5 March 2001), 2050. by Fugao Wang, D. P. Landau posted by 5 people Structural Biology Group TorVergata A_Coletta_Thesis mc1975 Akimasa softsimu
	Recent progress in understanding hydrophobic interactions [My Copy] Proceedings of the National Academy of Sciences, Vol. 103, No. 43. (24 October 2006), pp. 15739-15746. by Emily E. Meyer, Kenneth J. Rosenberg, Jacob Israelachvili posted by 7 people softsimu sunrise Cristiano sobolevnrm paulschlesinger baker-group hsekiguc
	Determining the density of states for classical statistical models: A random walk algorithm to produce a flat histogram [My Copy] Physical Review E, Vol. 64, No. 5. (Oct 2001), 056101. by Fugao Wang, D. P. Landau posted by 7 people mc1975 Structural Biology Group TorVergata A_Coletta_Thesis pcarbo dsanders Akimasa softsimu
	A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules [My Copy] Journal of the American Chemical Society, Vol. 117, No. 19. (1 May 1995), pp. 5179-5197. by Wendy D. Cornell, Piotr Cieplak, Christopher I. Bayly, et al.Ian R. Gould, Kenneth M. Merz, David M. Ferguson, David C. Spellmeyer, Thomas Fox, James W. Caldwell, Peter A. Kollman posted by 7 people Lombardo_7 softsimu coomteng flbarroso kgutwin pavanghatty dfgreen
	Improving implicit solvent simulations: a Poisson-centric view [My Copy] Current Opinion in Structural Biology, Vol. 15, No. 2. (April 2005), pp. 137-143. by N. Baker posted by 6 people oteri flbarroso softsimu ttjoseph qwermish RamuAnandakrishnan
	Potential of Mean Force of Hydrophobic Association: Dependence on Solute Size [My Copy] The Journal of Physical Chemistry B, Vol. 111, No. 36. (1 September 2007), pp. 10765-10774. by Emil Sobolewski, Mariusz Makowski, Cezary Czaplewski, Adam Liwo, Stanislaw Oldziej, Harold A. Scheraga posted by 4 people softsimu sobolevnrm paulschlesinger baker-group
	Energetics of Cholesterol Transfer between Lipid Bilayers. [My Copy] J Phys Chem B (29 February 2008) by Zhancheng Zhang, Lanyuan Lu, Max L. Berkowitz posted by 4 people dimka sobolevnrm baker-group softsimu
	Development of an improved four-site water model for biomolecular simulations: TIP4P-Ew [My Copy] The Journal of Chemical Physics, Vol. 120, No. 20. (2004), pp. 9665-9678. by Hans W. Horn, William C. Swope, Jed W. Pitera, et al.Jeffry D. Madura, Thomas J. Dick, Greg L. Hura, Teresa H. Gordon posted by 5 people bmduggan Lombardo_7 Jiang Research Group whitead softsimu
	Locating missing water molecules in protein cavities by the three-dimensional reference interaction site model theory of molecular solvation. [My Copy] Proteins, Vol. 66, No. 4. (1 March 2007), pp. 804-813. by Takashi Imai, Ryusuke Hiraoka, Andriy Kovalenko, Fumio Hirata posted by 4 people oteri baker-group sobolevnrm softsimu
	Nonlinear scaling schemes for Lennard-Jones interactions in free energy calculations [My Copy] The Journal of Chemical Physics, Vol. 127, No. 21. (2007), 214108. by Thomas Steinbrecher, David L. Mobley, David A. Case posted by 4 people arnaucordomi sobolevnrm baker-group dmobley
	Dynamic personalities of proteins [My Copy] Nature, Vol. 450, No. 7172. (12 December 2007), pp. 964-972. by Katherine Henzler-Wildman, Dorothee Kern posted by 21 people victorclaessen saravan Diego_Prada xdeupi viktor21614 ruvido barry pavanghatty chad_davis allmensch choonpeng rsantana cjeans sobolevnrm baker-group wilbur mijam kjell phoenixzxl higueruelo GeeSharpMinor
	Significance of Cholesterol Methyl Groups [My Copy] J. Phys. Chem. B, Vol. 112, No. 10. (13 March 2008), pp. 2922-2929. by S. Poyry, T. Rog, M. Karttunen, I. Vattulainen posted by 4 people sobolevnrm baker-group softsimu dimka
	Lateral Diffusion in Lipid Membranes through Collective Flows [My Copy] J. Am. Chem. Soc., Vol. 130, No. 1. (9 January 2008), pp. 44-45. by E. Falck, T. Rog, M. Karttunen, I. Vattulainen posted by 8 people Scis0000002 priyaps mc1975 ARobson sobolevnrm paulschlesinger baker-group softsimu
	Recent advances in implicit solvent-based methods for biomolecular simulations. [My Copy] Current opinion in structural biology, Vol. 18, No. 2. (04 April 2008), pp. 140-148. by Jianhan Chen, Charles L. Brooks, Jana Khandogin posted by 10 people RamuAnandakrishnan mikaellund Structural Biology Group TorVergata oteri nickolay flbarroso choonpeng sobolevnrm baker-group onufriev
	Multicolor Super-Resolution Imaging with Photo-Switchable Fluorescent Probes [My Copy] Science, Vol. 317, No. 5845. (21 September 2007), pp. 1749-1753. by Mark Bates, Bo Huang, Graham T. Dempsey, Xiaowei Zhuang posted by 12 people OliverHarriman cloudsforest paulschlesinger lechristophe samjlord rodney zwang karmarae moernerlab Kopelman_Group markusbeck melting
	The Implementation of Slab Geometry for Membrane-Channel Molecular Dynamics Simulations [My Copy] Biophys. J., Vol. 85, No. 1. (1 July 2003), pp. 97-107. by David Bostick, Max L. Berkowitz posted by 4 people paulschlesinger softsimu sobolevnrm baker-group
	Escaping free-energy minima. [My Copy] Proc Natl Acad Sci U S A, Vol. 99, No. 20. (1 October 2002), pp. 12562-12566. by A. Laio, M. Parrinello posted by 8 people Jiang Research Group howerja ibuch apaydin baaden and_ped10 Diego_Prada AndreaColetta
	Test of the Gouy-Chapman Theory for a Charged Lipid Membrane against Explicit-Solvent Molecular Dynamics Simulations [My Copy] Physical Review Letters, Vol. 101, No. 3. (2008) by Myunggi Yi, Hugh Nymeyer, Huan X. Zhou posted by 5 people softsimu j_vinals sobolevnrm baker-group agrossfield
	Parallel multigrid summation for the N-body problem [My Copy] Journal of Parallel and Distributed Computing, Vol. 65, No. 8. (August 2005), pp. 949-962. by Jesus A. Izaguirre, Scott S. Hampton, Thierry Matthey posted by 4 people baker-group sobolevnrm r2s2 softsimu
	The Role of Solvent Fluctuations in Hydrophobic Assembly [My Copy] J. Phys. Chem. B (30 January 2008) by A. P. Willard, D. Chandler posted by 4 people softsimu sobolevnrm baker-group mikaellund
	Ordering effects of cholesterol and its analogues [My Copy] Biochimica et Biophysica Acta (BBA) - Biomembranes, Vol. In Press, Accepted Manuscript by Tomasz Róg, Marta Pasenkiewicz-Gierula, Ilpo Vattulainen, Mikko Karttunen posted by 4 people softsimu baker-group sobolevnrm paulschlesinger
	Remeasuring the Double Helix [My Copy] Science, Vol. 322, No. 5900. (17 October 2008), pp. 446-449. by Rebecca S. Mathew-Fenn, Rhiju Das, Pehr A. Harbury posted by 9 people baker-group sobolevnrm jbhiatt Elena_Zubova melting kshundyak marck moernerlab samjlord
	Differential Effects of Cholesterol and its Immediate Biosynthetic Precursors on Membrane Organization [My Copy] Biochemistry (29 April 2008) by Sandeep:paila Shrivastava posted by 4 people paulschlesinger sobolevnrm baker-group softsimu
	Molecular Dynamics Simulations of Discoidal Bilayers Assembled from Truncated Human Lipoproteins [My Copy] Biophys. J., Vol. 88, No. 1. (1 January 2005), pp. 548-556. by Amy Y. Shih, Ilia G. Denisov, James C. Phillips, Stephen G. Sligar, Klaus Schulten posted by 5 people baker-group sobolevnrm paulschlesinger gjuggler softsimu
	Pressure-Area Isotherm of a Lipid Monolayer from Molecular Dynamics Simulations [My Copy] Langmuir (1 November 2007) by S. Baoukina, L. Monticelli, S. J. Marrink, D. P. Tieleman posted by 4 people sobolevnrm paulschlesinger baker-group softsimu
	Effect of Cholesterol and Ergosterol on the Compressibility and Volume Fluctuations of Phospholipid-Sterol Bilayers in the Critical Point Region - A Molecular Acoustic and Calorimetric Study [My Copy] Biophys. J. (16 January 2008), biophysj.107.122549. by Roland Krivanek, Linus Okoro, Roland Winter posted by 4 people sobolevnrm paulschlesinger baker-group softsimu
	Clustering Molecular Dynamics Trajectories: 1. Characterizing the Performance of Different Clustering Algorithms [My Copy] Journal of Chemical Theory and Computation, Vol. 3, No. 6. (1 November 2007), pp. 2312-2334. by Jianyin Shao, Stephen W. Tanner, Nephi Thompson, Thomas E. Cheatham posted by 13 people anuragsethi Diego_Prada scampos Structural Biology Group TorVergata oteri barry daevans sobolevnrm structural_bioinformatics baker-group LamBras allmensch GermanErlenkamp
	A systematic study of water models for molecular simulation: Derivation of water models optimized for use with a reaction field [My Copy] The Journal of Chemical Physics, Vol. 108, No. 24. (1998), pp. 10220-10230. by David van der Spoel, Paul J. van Maaren, Herman J. C. Berendsen posted by 4 people r2s2 A_Coletta_Thesis jwagoner softsimu
	A Quantitative Coarse-Grain Model for Lipid Bilayers [My Copy] J. Phys. Chem. B, Vol. 112, No. 3. (24 January 2008), pp. 802-815. by M. Orsi, D. Y. Haubertin, W. E. Sanderson, J. W. Essex posted by 4 people sobolevnrm paulschlesinger baker-group softsimu
	Replacing the Cholesterol Hydroxyl Group with the Ketone Group Facilitates Sterol Flip-Flop and Promotes Membrane Fluidity [My Copy] J. Phys. Chem. B (25 January 2008) by T. Rog, L. M. Stimson, M. Pasenkiewicz-Gierula, I. Vattulainen, M. Karttunen posted by 4 people sobolevnrm paulschlesinger baker-group softsimu
	Coarse Grained Model for Semiquantitative Lipid Simulations [My Copy] The Journal of Physical Chemistry B, Vol. 108, No. 2. (1 January 2004), pp. 750-760. by Siewert J. Marrink, Alex H. de Vries, Alan E. Mark posted by 7 people dsmueller Elena_Zubova Molecular dynamics in MSU Marine choonpeng softsimu sunnytov
	Why are lipid rafts not observed in vivo? [My Copy] Biophys J (27 July 2007) by Arun Yethiraj, James C C. Weisshaar posted by 5 people sobolevnrm char paulschlesinger baker-group softsimu
	What is principal component analysis? [My Copy] Nature Biotechnology, Vol. 26, No. 3. (01 March 2008), pp. 303-304. by Markus Ringner posted by 73 people singhsh Jporci tnhh ruvido ucbcjbm daforerog Diego_Prada abellogin nguizard thegoose2 arsyed Zephyrus flips svozil VGreiff kaniko ssgong Yanno guhjy operon barry baaic dullhunk Bevan_Weir zeji gareth massivemayhem zwang GustavoLacerda GeeSharpMinor bmaust zambujo mingzhi starz1010101 maralena wchannels sunhwan jennifermbui kdelavega zhouyu rsantana sobolevnrm baker-group fryanpan kengg rvosa FAB-lab dekay23 adacier Bioinformatics hpaces waghsk rchauhan pavanghatty kristgy jfr bibay2004 xingxu quianominorleo craigwilson06 ashko markusd dayjm dimka i-stevenson chrissp100 tharris ale mjoach HugoMarcelo jdiezperezj rrbarb Nici
	Imaging and Tracking of Tat Peptide-Conjugated Quantum Dots in Living Cells: New Insights into Nanoparticle Uptake, Intracellular Transport, and Vesicle Shedding [My Copy] J. Am. Chem. Soc., Vol. 129, No. 47. (28 November 2007), pp. 14759-14766. by G. Ruan, A. Agrawal, A. I. Marcus, S. Nie posted by 5 people samjlord sobolevnrm moernerlab baker-group ml115
	Determination of Electrostatic Parameters for a Polarizable Force Field Based on the Classical Drude Oscillator [My Copy] Journal of Chemical Theory and Computation, Vol. 1, No. 1. (1 January 2005), pp. 153-168. by Victor M. Anisimov, Guillaume Lamoureux, Igor V. Vorobyov, Niu Huang, Benoit Roux, Alexander D. MacKerell posted by 3 people Jiang Research Group whitead softsimu
	Distinct Water Species Confined at the Interface of a Phospholipid Membrane [My Copy] Physical Review Letters, Vol. 99, No. 7. (2007) by Victor V. Volkov, Jason D. Palmer, Roberto Righini posted by 4 people sunrise sobolevnrm baker-group softsimu
	A guide to choosing fluorescent proteins [My Copy] Nature Methods, Vol. 2, No. 12. (18 November 2005), pp. 905-909. by Nathan C. Shaner, Paul A. Steinbach, Roger Y. Tsien posted by 18 people OliverHarriman pmcarlton abhishek_tiwari ajaymalik reidw moernerlab samjlord Oyinlola balabu anwazo lmcf Fritz eeruowl rodney neurolit UFS Kopelman_Group frampton
	HaloTag Protein-Mediated Site-Specific Conjugation of Bioluminescent Proteins to Quantum Dots [My Copy] Angewandte Chemie International Edition, Vol. 45, No. 30. (2006), pp. 4936-4940. by Yan Zhang, Min-Kyung So, Andreas M. Loening, Hequan Yao, Sanjiv S. Gambhir, Jianghong Rao posted by 5 people samjlord sobolevnrm moernerlab baker-group ml115
	An interpretation of fluctuations in enzyme catalysis rate, spectral diffusion, and radiative component of lifetimes in terms of electric field fluctuations [My Copy] Proceedings of the National Academy of Sciences, Vol. 104, No. 41. (9 October 2007), pp. 15982-15987. by Meher K. Prakash, R. A. Marcus posted by 5 people devries samjlord sobolevnrm moernerlab baker-group
	Coarse-Graining in Interaction Space: A Systematic Approach for Replacing Long-Range Electrostatics with Short-Range Potentials [My Copy] J. Phys. Chem. B (27 March 2008) by S. Izvekov, J. M. J. Swanson, G. A. Voth posted by 4 people softsimu sunhwan sobolevnrm baker-group
	Cell-Penetrating Quantum Dots Based on Multivalent and Endosome-Disrupting Surface Coatings [My Copy] J. Am. Chem. Soc., Vol. 129, No. 11. (21 March 2007), pp. 3333-3338. by H. Duan, S. Nie posted by 5 people samjlord sobolevnrm moernerlab baker-group ml115
	Low-dimensional, free-energy landscapes of protein-folding reactions by nonlinear dimensionality reduction [My Copy] PNAS, Vol. 103, No. 26. (27 June 2006), pp. 9885-9890. by Payel Das, Mark Moll, Hernan Stamati, Lydia E. Kavraki, Cecilia Clementi posted by 5 people samjlord hmk sobolevnrm moernerlab baker-group
	Fluorescence Imaging of Membrane Dynamics [My Copy] Annual Review of Biomedical Engineering, Vol. 10, No. 1. (2008), pp. 311-338. by Jay T. Groves, Raghuveer Parthasarathy, Martin B. Forstner posted by 6 people moernerlab samjlord ARobson zwang sobolevnrm baker-group
	Calculation of protein-ligand binding affinities. [My Copy] Annual review of biophysics and biomolecular structure, Vol. 36 (2007), pp. 21-42. by Michael K. Gilson, Huan-Xiang X. Zhou posted by 19 people mijogiffin Chang group flbarroso GermanErlenkamp onufriev arlam Structural Biology Group TorVergata oteri McCammon jmccammon bmduggan dimka neils hmk ashaytan ras cchang boris_aguilar qaiser_fatmi
	Molecular Mechanism for Lipid Flip-Flops [My Copy] J. Phys. Chem. B, Vol. 111, No. 48. (6 December 2007), pp. 13554-13559. by A. A. Gurtovenko, I. Vattulainen posted by 4 people softsimu robertvacha sobolevnrm baker-group
	Environmentally Controlled Invasion of Cancer Cells by Engineered Bacteria [My Copy] Journal of Molecular Biology, Vol. 355, No. 4. (27 January 2006), pp. 619-627. by J. Christopher Anderson, Elizabeth J. Clarke, Adam P. Arkin, Christopher A. Voigt posted by 16 people ic2009 antonkratz dantarjan albertlu ClaireFB rklancer imouthesmp marcius JKelly555 samjlord rodney BioinfoCIPF SGU-CIPF moernerlab Kopelman_Group heliopais
	Role of sterol type on lateral pressure profiles of lipid membranes affecting membrane protein functionality: Comparison between cholesterol, desmosterol, 7-dehydrocholesterol and ketosterol [My Copy] Journal of Structural Biology In 3rd International Conference on Structure, Dynamics and Function of Proteins in Biological Membranes, Vol. 159, No. 2. (August 2007), pp. 311-323. by Samuli, Tomasz Rog, Mikko Karttunen, Ilpo Vattulainen posted by 3 people sobolevnrm baker-group softsimu
	Monitoring Biological Membrane-Potential Changes: A CI QM/MM Study [My Copy] J. Phys. Chem. B, Vol. 112, No. 8. (28 February 2008), pp. 2445-2455. by C. F. Rusu, H. Lanig, O. G. Othersen, C. Kryschi, T. Clark posted by 3 people sobolevnrm baker-group softsimu
	Effect of Double Bond Position on Lipid Bilayer Properties: Insight through Atomistic Simulations [My Copy] J. Phys. Chem. B (31 August 2007) by H. Martinez-Seara, T. Rog, M. Pasenkiewicz-Gierula, I. Vattulainen, M. Karttunen, R. Reigada posted by 3 people sobolevnrm baker-group softsimu
	Is Random Close Packing of Spheres Well Defined? [My Copy] Physical Review Letters, Vol. 84, No. 10. (6 Mar 2000), pp. 2064-2067. by S. Torquato, T. M. Truskett, P. G. Debenedetti posted by 7 people dchen LGNR Jiang Research Group whitead kdesmond weeks softsimu
	An improved pairwise decomposable finite-difference Poisson-Boltzmann method for computational protein design [My Copy] Journal of Computational Chemistry, Vol. 9999, No. 9999. (2007), NA. by Christina L. Vizcarra, Naigong Zhang, Shannon A. Marshall, Ned S. Wingreen, Chen Zeng, Stephen L. Mayo posted by 2 people sobolevnrm baker-group
	Coupled composition-deformation phase-field method for multicomponent lipid membranes [My Copy] Physical Review E (Statistical, Nonlinear, and Soft Matter Physics), Vol. 76, No. 1. (2007) by Chloe M. Funkhouser, Francisco J. Solis, K. Thornton posted by 3 people sobolevnrm baker-group softsimu
	Glycolipid Membranes through Atomistic Simulations: Effect of Glucose and Galactose Head Groups on Lipid Bilayer Properties [My Copy] J. Phys. Chem. B, Vol. 111, No. 34. (30 August 2007), pp. 10146-10154. by T. Rog, I. Vattulainen, A. Bunker, M. Karttunen posted by 3 people sobolevnrm baker-group softsimu
	Poisson-Boltzmann Theory for Membranes with Mobile Charged Lipids and the pH-Dependent Interaction of a DNA Molecule with a Membrane [My Copy] Biophys. J., Vol. 82, No. 1. (1 January 2002), pp. 76-92. by Christian Fleck, Roland R. Netz, Hans H. von Grunberg posted by 4 people softsimu sobolevnrm baker-group rok
	Flexible docking in solution using metadynamics. [My Copy] J Am Chem Soc, Vol. 127, No. 8. (2 March 2005), pp. 2600-2607. by F. L. Gervasio, A. Laio, M. Parrinello posted by 5 people A_Coletta_Thesis apaydin baaden yongzhao TSRI_MGL
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	Two-photon laser scanning fluorescence microscopy [My Copy] Science, Vol. 248, No. 4951. (6 April 1990), pp. 73-76. by W. Denk, J. H. Strickler, W. W. Webb posted by 11 people moernerlab samjlord schmidtm victorclaessen marissalee fbaroni paulschlesinger cgguido eeruowl kcrawlik NicMag
	Molecular Dynamics of a Protein Surface: Ion-Residues Interactions [My Copy] Biophys. J., Vol. 89, No. 2. (1 August 2005), pp. 768-781. by Ran Friedman, Esther Nachliel, Menachem Gutman posted by 3 people sobolevnrm baker-group softsimu
	Effect of Lipid Peroxidation on the Properties of Lipid Bilayers: A Molecular Dynamics Study [My Copy] Biophys. J., Vol. 93, No. 12. (15 December 2007), pp. 4225-4236. by Jirasak Wong-Ekkabut, Zhitao Xu, Wannapong Triampo, I-Ming Tang, Peter D. Tieleman, Luca Monticelli posted by 3 people sobolevnrm baker-group softsimu
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	Debye-Hückel theory of mixed charged-zwitterionic lipid layers [My Copy] The European Physical Journal E - Soft Matter, Vol. 26, No. 3. (17 July 2008), pp. 251-260. by D. Mengistu, S. May posted by 3 people softsimu sobolevnrm baker-group
	Lessons of Slicing Membranes: Interplay of Packing, Free Area, and Lateral Diffusion in Phospholipid/Cholesterol Bilayers [My Copy] Biophys. J., Vol. 87, No. 2. (1 August 2004), pp. 1076-1091. by Emma Falck, Michael Patra, Mikko Karttunen, Marja T. Hyvonen, Ilpo Vattulainen posted by 3 people sobolevnrm baker-group softsimu
	Energy of an Ion crossing a Low Dielectric Membrane: Solutions to Four Relevant Electrostatic Problems [My Copy] Nature, Vol. 221, No. 5183. (1 March 1969), pp. 844-846. by Adrian Parsegian posted by 4 people softsimu chiufanlee sobolevnrm baker-group
	Scalable molecular dynamics with NAMD [My Copy] Journal of Computational Chemistry, Vol. 26, No. 16. (December 2005), pp. 1781-1802. by James C. Phillips, Rosemary Braun, Wei Wang, et al.James Gumbart, Emad Tajkhorshid, Elizabeth Villa, Christophe Chipot, Robert D. Skeel, Laxmikant Kalé, Klaus Schulten posted by 26 people krapnik pjkiley flbarroso yxue r2s2 grondina rpetrenko oteri oceanwind dfgreen vahmurk gisle dimka jwm ttjoseph sangeetha yoel_rf bilab wilsoros sobolevnrm Radiation_Damage Stressosome Bioinformatics insilicodrug baker-group ibuch
	The implementation of a fast and accurate QM/MM potential method in Amber [My Copy] Journal of Computational Chemistry, Vol. 29, No. 7. (2008), pp. 1019-1031. by Ross C. Walker, Michael F. Crowley, David A. Case posted by 3 people onufriev RamuAnandakrishnan softsimu
	A detailed look at vesicle fusion. [My Copy] J Phys Chem B, Vol. 110, No. 26. (6 July 2006), pp. 13212-13219. by A. F. Smeijers, A. J. Markvoort, K. Pieterse, P. A. Hilbers posted by 3 people sobolevnrm baker-group softsimu
	A particle-particle, particle-density algorithm for the calculation of electrostatic interactions of particles with slablike geometry [My Copy] The Journal of Chemical Physics, Vol. 127, No. 22. (2007) by Alireza S. Ghasemi, Alexey Neelov, Stefan Goedecker posted by 3 people sobolevnrm baker-group softsimu
	Single-Molecule Fluorescence Resonance Energy Transfer [My Copy] Methods, Vol. 25, No. 1. (September 2001), pp. 78-86. by T. Ha posted by 9 people samjlord kjell joseolucha toerst yanjiang rodney moernerlab Kopelman_Group yusdi
	Barriers to Ion Translocation in Cationic and Anionic Receptors from the Cys-Loop Family [My Copy] J. Am. Chem. Soc., Vol. 129, No. 26. (4 July 2007), pp. 8217-8224. by I. Ivanov, X. Cheng, S. M. Sine, J. A. Mccammon posted by 2 people sobolevnrm baker-group
	Simultaneous determination of protein structure and dynamics [My Copy] Nature, Vol. 433, No. 7022. (13 January 2005), pp. 128-132. by Kresten Lindorff-Larsen, Robert B. Best, Mark A. Depristo, Christopher M. Dobson, Michele Vendruscolo posted by 19 people Diego_Prada xdeupi Structural Biology Group TorVergata A_Coletta_Thesis karbak apaydin barry lillekatt baaden lna dgront allmensch daevans rsantana jlh64 structural_bioinformatics Bioinformatics biehl rph
	Molecular Dynamics of Water at the Protein-Solvent Interface [My Copy] J. Phys. Chem. B, Vol. 106, No. 26. (4 July 2002), pp. 6617-6633. by A. R. Bizzarri, S. Cannistraro posted by 4 people rabio ruvido softsimu saravan
	REACH Coarse-Grained Biomolecular Simulation: Transferability between Different Protein Structural Classes [My Copy] Biophys. J. (9 May 2008), biophysj.108.131714. by Kei Moritsugu, Jeremy C. Smith posted by 10 people barry baker-group sobolevnrm A_Coletta_Thesis paulschlesinger choonpeng aqeel jmccammon McCammon rok
	Canonical sampling through velocity rescaling. [My Copy] The Journal of chemical physics, Vol. 126, No. 1. (7 January 2007), 014101. by Giovanni Bussi, Davide Donadio, Michele Parrinello posted by 6 people arnaucordomi Soft Matter janneb daevans OndrejMarsalek michaelbussmann