Paul H. Schlesinger's Top Recommendations

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	Computations of Standard Binding Free Energies with Molecular Dynamics Simulations [My Copy] The Journal of Physical Chemistry B, Vol. 113, No. 8. (26 February 2009), pp. 2234-2246. by Yuqing Deng, Benoît Roux posted by 12 people anuragsethi flbarroso mikaellund baker-group sobolevnrm barry McCammon jmccammon willard agrossfield carlosjavierna ibuch
	A minimalist network model for coarse-grained normal mode analysis and its application to biomolecular x-ray crystallography. [My Copy] Proceedings of the National Academy of Sciences of the United States of America (1 October 2008) by Mingyang Lu, Jianpeng Ma posted by 12 people baker-group sobolevnrm aqeel apaydin ruvido agrossfield Nielsen group skoddet structural_bioinformatics McCammon Bioinformatics barry
	How Efficient Is Replica Exchange Molecular Dynamics? An Analytic Approach [My Copy] J. Chem. Theory Comput., Vol. 4, No. 4. (8 April 2008), pp. 626-636. by Hugh Nymeyer posted by 7 people agrossfield sobolevnrm baker-group loison barry structural_bioinformatics McCammon
	What is principal component analysis? [My Copy] Nature biotechnology, Vol. 26, No. 3. (March 2008), pp. 303-304. by Markus Ringnér posted by 71 people 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
	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 19 people Diego_Prada xdeupi viktor21614 ruvido barry pavanghatty chad_davis allmensch choonpeng rsantana cjeans sobolevnrm baker-group wilbur mijam kjell phoenixzxl higueruelo GeeSharpMinor
	Thermodynamically dominant hydration structures of aqueous ions [My Copy] The Journal of Chemical Physics, Vol. 130, No. 19. (2009), 195102. by Safir Merchant, D. Asthagiri posted by 7 people afenley mikaellund flbarroso dlimmer agrossfield baker-group sobolevnrm
	Thermodynamics of Melittin Binding to Lipid Bilayers. Aggregation/Pore Formation. [My Copy] Biochemistry, Vol. 0, No. ja. (0000) by Gabriela Klocek, Therese Schulthess, Yechiel Shai, Joachim Seelig posted by 5 people willard agrossfield baker-group sobolevnrm carlosjavierna
	Intrinsic dynamics of enzymes in the unbound state and relation to allosteric regulation [My Copy] Current Opinion in Structural Biology In Catalysis and regulation / Proteins, Vol. 17, No. 6. (December 2007), pp. 633-640. by Ivet Bahar, Chakra Chennubhotla, Dror Tobi posted by 15 people allmensch jrperillaj barry aqeel ruvido cactus sobolevnrm structural_bioinformatics Bioinformatics baker-group jennifermbui higueruelo LamBras jmccammon McCammon
	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
	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 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation [My Copy] Journal of Chemical Theory and Computation, Vol. 4, No. 3. (1 March 2008), pp. 435-447. by Berk Hess, Carsten Kutzner, David van der Spoel, Erik Lindahl posted by 25 people softsimu parnell rabio oteri krapnik robertvacha rodrigofaccioli pavanghatty janneb ZhangYinhe okapi flbarroso marceavi Structural Biology Group TorVergata A_Coletta_Thesis choonpeng Lombardo_7 jwm daevans mmuecke sobolevnrm baker-group r2s2 middledomain loison
	De Novo Computational Design of Retro-Aldol Enzymes [My Copy] Science, Vol. 319, No. 5868. (7 March 2008), pp. 1387-1391. by Lin Jiang, Eric A. Althoff, Fernando R. Clemente, et al.Lindsey Doyle, Daniela Rothlisberger, Alexandre Zanghellini, Jasmine L. Gallaher, Jamie L. Betker, Fujie Tanaka, Carlos F. Barbas, Donald Hilvert, Kendall N. Houk, Barry L. Stoddard, David Baker posted by 22 people barmak7282 baiaixi fralium Biocatalysis and Biotransformation qbin1304 alexknight barry aalibes jwm aprasad dgront zwang sobolevnrm structural_bioinformatics baker-group davidlott msuarezdiez scienbox ucbcjbm McCammon joseph_x_zhou cambray
	Calculation of protein-ligand binding free energy by using a polarizable potential [My Copy] Proceedings of the National Academy of Sciences, Vol. 105, No. 17. (29 April 2008), pp. 6290-6295. by Dian Jiao, Pavel A. Golubkov, Thomas A. Darden, Pengyu Ren posted by 9 people flbarroso onufriev jmccammon biehl sobolevnrm baker-group barry structural_bioinformatics McCammon
	Accelerating molecular dynamic simulation on graphics processing units [My Copy] Journal of Computational Chemistry, Vol. 30, No. 6. (2009), pp. 864-872. by Mark S. Friedrichs, Peter Eastman, Vishal Vaidyanathan, et al.Mike Houston, Scott Legrand, Adam L. Beberg, Daniel L. Ensign, Christopher M. Bruns, Vijay S. Pande posted by 14 people anuragsethi kevinchannon flbarroso r2s2 iantunbridge ihaque baker-group sobolevnrm ruvido massivemayhem structural_bioinformatics McCammon barry RamuAnandakrishnan
	Cell water dynamics on multiple time scales [My Copy] Proceedings of the National Academy of Sciences, Vol. 105, No. 17. (29 April 2008), pp. 6266-6271. by Erik Persson, Bertil Halle posted by 6 people qshao edws ocs biehl sobolevnrm baker-group
	Computing conformational free energy by deactivated morphing [My Copy] The Journal of Chemical Physics, Vol. 129, No. 13. (2008), 134102. by Sanghyun Park, Albert Y. Lau, Benoît Roux posted by 5 people paddydu baker-group sobolevnrm agrossfield sunhwan
	Protein-protein binding is often associated with changes in protonation state [My Copy] Proteins: Structure, Function, and Bioinformatics, Vol. 9999, No. 9999. (2007), NA. by Aaron C. Mason, Jan H. Jensen posted by 10 people flbarroso onufriev csrocha bicko sobolevnrm baker-group RamuAnandakrishnan barry structural_bioinformatics McCammon
	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
	Computational Methods for Predicting Sites of Functionally Important Dynamics [My Copy] The Journal of Physical Chemistry B, Vol. 0, No. 0. (0000) by Adam D. Schuyler, Heather A. Carlson, Eva L. Feldman posted by 7 people skywalkerus02 agrossfield ubcg08l higueruelo barry baker-group sobolevnrm
	Emerging roles for lipids in shaping membrane-protein function [My Copy] Nature, Vol. 459, No. 7245. (20 May 2009), pp. 379-385. by Rob Phillips, Tristan Ursell, Paul Wiggins, Pierre Sens posted by 9 people girayenkavi viktor21614 agrossfield cjryan kevinchannon hsekiguc baker-group sobolevnrm nelfarargy
	Characterization of Protein Conformational States by Normal-Mode Frequencies [My Copy] J. Am. Chem. Soc. (23 August 2007) by B. A. Hall, S. L. Kaye, A. Pang, R. Perera, P. C. Biggin posted by 11 people Diego_Prada Scis0000002 ubcg08l barry aqeel choonpeng sobolevnrm structural_bioinformatics Bioinformatics baker-group LamBras
	Reassessing a sparse energetic network within a single protein domain [My Copy] Proceedings of the National Academy of Sciences, Vol. 105, No. 12. (25 March 2008), pp. 4679-4684. by Celestine N. Chi, Lisa ElfstrÃ¶m, Yao Shi, Tord SnÃ¤ll, Ãke EngstrÃ¶m, Per Jemth posted by 8 people choonpeng barry apaydin cjeans cactus sunhwan sobolevnrm baker-group
	Membrane Potential and Electrostatics of Phospholipid Bilayers with Asymmetric Transmembrane Distribution of Anionic Lipids [My Copy] J. Phys. Chem. B, Vol. 112, No. 15. (17 April 2008), pp. 4629-4634. by A. A. Gurtovenko, I. Vattulainen posted by 3 people sobolevnrm baker-group robertvacha
	From the Cover: A dry ligand-binding cavity in a solvated protein [My Copy] Proceedings of the National Academy of Sciences, Vol. 105, No. 17. (29 April 2008), pp. 6296-6301. by Johan Qvist, Monika Davidovic, Donald Hamelberg, Bertil Halle posted by 7 people Lombardo_7 jmccammon barry structural_bioinformatics McCammon sobolevnrm baker-group
	Improved Sampling for Simulations of Interfacial Membrane Proteins: Application of Generalized Shadow Hybrid Monte Carlo to a Peptide Toxin/Bilayer System [My Copy] J. Phys. Chem. B, Vol. 112, No. 18. (8 May 2008), pp. 5710-5717. by C. L. Wee, M. S. P. Sansom, S. Reich, E. Akhmatskaya posted by 2 people sobolevnrm baker-group
	Distribution of Amino Acids in a Lipid Bilayer from Computer Simulations [My Copy] Biophys. J., Vol. 94, No. 9. (1 May 2008), pp. 3393-3404. by Justin L. Maccallum, Drew W. F. Bennett, Peter D. Tieleman posted by 3 people agrossfield sobolevnrm baker-group
	A novel algorithm for creating coarse-grained, density dependent implicit solvent models [My Copy] The Journal of Chemical Physics, Vol. 128, No. 15. (2008) by Erik C. Allen, Gregory C. Rutledge posted by 3 people sobolevnrm baker-group agrossfield
	Similarity Measures for Protein Ensembles [My Copy] PLoS ONE, Vol. 4, No. 1. (15 January 2009), e4203. by Kresten Lindorff-Larsen, Jesper Ferkinghoff-Borg posted by 12 people anuragsethi klexa apaydin baker-group sobolevnrm gane5h structural_bioinformatics barry McCammon jmccammon reyez biehl
	United-Atom Acyl Chains for CHARMM Phospholipids [My Copy] J. Phys. Chem. B, Vol. 112, No. 23. (12 June 2008), pp. 7008-7015. by Jérôme Hénin, Wataru Shinoda, Michael L. Klein posted by 2 people sobolevnrm baker-group
	Predicting Allosteric Communication in Myosin via a Pathway ofConserved Residues [My Copy] Journal of Molecular Biology, Vol. In Press, Accepted Manuscript by Susan Tang, Jung-Chi Liao, Alexander R. Dunn, Russ B. Altman, James A. Spudich, Jeanette P. Schmidt posted by 8 people barry choonpeng cactus sobolevnrm jlh64 structural_bioinformatics baker-group melting
	Protein crystallography for non-crystallographers, or how to get the best (but not more) from published macromolecular structures [My Copy] FEBS Journal, Vol. 275, No. 1. (January 2008), pp. 1-21. by Wlodawer, Alexander, Minor, et al. Wladek, Dauter, Zbigniew, Jaskolski, Mariusz posted by 10 people klexa nanonan structural_bioinformatics McCammon barry baker-group sobolevnrm ae1054 aisyahrehan rph
	Electrostatic rate enhancement and transient complex of protein-protein association [My Copy] Proteins: Structure, Function, and Bioinformatics, Vol. 71, No. 1. (11 October 2008), pp. 320-335. by Ramzi Alsallaq, Huan-Xiang Zhou posted by 6 people structural_bioinformatics McCammon barry bicko sobolevnrm baker-group
	ABSINTH: a new continuum solvation model for simulations of polypeptides in aqueous solutions. [My Copy] Journal of computational chemistry, Vol. 30, No. 5. (15 April 2009), pp. 673-699. by A. Vitalis, R. V. Pappu posted by 4 people melo_mcr baker-group sobolevnrm 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
	Solvent-Free Lipid Bilayer Model Using Multiscale Coarse-Graining [My Copy] The Journal of Physical Chemistry B, Vol. 113, No. 13. (2 April 2009), pp. 4443-4455. by Sergei Izvekov, Gregory A. Voth posted by 5 people choonpeng flbarroso agrossfield baker-group sobolevnrm
	A highly parallelizable integral equation theory for three dimensional solvent distribution function: Application to biomolecules [My Copy] The Journal of Chemical Physics, Vol. 130, No. 6. (2009) by Daisuke Yokogawa, Hirofumi Sato, Takashi Imai, Shigeyoshi Sakaki posted by 4 people baker-group sobolevnrm dlimmer agrossfield
	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
	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
	Analysis of the residue-residue coevolution network and the functionally important residues in proteins [My Copy] Proteins: Structure, Function, and Bioinformatics, Vol. 9999, No. 9999. (2008), NA. by Byung-Chul Lee, Keunwan Park, Dongsup Kim posted by 10 people barry neils sobolevnrm structural_bioinformatics baker-group mingzhi penpen926 scienbox wilbur friendpine
	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
	Structural flexibility in proteins: impact of the crystal environment [My Copy] Bioinformatics, Vol. 24, No. 4. (15 February 2008), pp. 521-528. by Konrad Hinsen posted by 8 people Diego_Prada mijogiffin barry sobolevnrm jlh64 baker-group scienbox McCammon
	Lambda-dynamics free energy simulation methods. [My Copy] Journal of computational chemistry, Vol. 30, No. 11. (August 2009), pp. 1692-1700. by J. L. Knight, C. L. Brooks posted by 5 people ibuch klexa agrossfield baker-group sobolevnrm
	Wordom: a program for efficient analysis of molecular dynamics simulations [My Copy] Bioinformatics, Vol. 23, No. 19. (1 October 2007), pp. 2625-2627. by Michele Seeber, Marco Cecchini, Francesco Rao, Giovanni Settanni, Amedeo Caflisch posted by 9 people guhjy barry tmmurali choonpeng hmk sobolevnrm structural_bioinformatics baker-group LamBras
	Correlated substitution analysis and the prediction of amino acid structural contacts [My Copy] Brief Bioinform (13 November 2007), bbm052. by David S. Horner, Walter Pirovano, Graziano Pesole posted by 10 people mgomes qluo RebeccaHamer barry zwang sobolevnrm structural_bioinformatics Bioinformatics baker-group Lombardo_7
	Cloud computing [My Copy] Bioinformatics, Vol. 25, No. 12. (15 June 2009), 1475. by Alex Bateman, Matt Wood posted by 28 people jfr rdiaz fgibson walshtp Jingbo aan pekrau tnhh niallhaslam bertelsen apaydin structural_bioinformatics McCammon barry kiekyon reyez baker-group sobolevnrm cymacs druvus acesforum thegoose mikel_egana dullhunk Bioinformatics dswan jmeppley bmajoros
	Gaussian-Mixture Umbrella Sampling [My Copy] The Journal of Physical Chemistry B, Vol. 0, No. 0. (0000) by Paul Maragakis, Arjan van der Vaart, Martin Karplus posted by 4 people willard agrossfield baker-group sobolevnrm
	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
	Salt-Mediated Electrostatics in the Association of TATA Binding Proteins to DNA: A Combined Molecular Mechanics/Poisson-Boltzmann Study [My Copy] Biophys. J., Vol. 94, No. 12. (15 June 2008), pp. 4634-4645. by Johan H. Bredenberg, Cristina Russo, Marcia O. Fenley posted by 5 people sobolevnrm baker-group barry McCammon structural_bioinformatics
	Pump-probe molecular dynamics as a tool for studying protein motion and long range coupling [My Copy] Proteins: Structure, Function, and Bioinformatics, Vol. 65, No. 2. (2006), pp. 347-361. by Kim Sharp, John J. Skinner posted by 7 people barry lna choonpeng sobolevnrm structural_bioinformatics Bioinformatics baker-group
	High-resolution structure prediction and the crystallographic phase problem [My Copy] Nature, Vol. 450, No. 7167. (14 October 2007), pp. 259-264. by Bin Qian, Srivatsan Raman, Rhiju Das, et al.Philip Bradley, Airlie J. McCoy, Randy J. Read, David Baker posted by 19 people bmduggan newton1234 apaydin aheilbut jwm eckart_bindewald ffranca dgront massivemayhem cjeans zwang cactus sobolevnrm baker-group boris_aguilar Ema chenway ardalby OPIG
	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
	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
	Efficient evaluation of sampling quality of molecular dynamics simulations by clustering of dihedral torsion angles and Sammon mapping [My Copy] Journal of Computational Chemistry, Vol. 30, No. 3. (2009), pp. 479-492. by Stephan Frickenhaus, Srinivasaraghavan Kannan, Martin Zacharias posted by 5 people Diego_Prada scampos baker-group sobolevnrm agrossfield
	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
	Large-scale allosteric conformational transitions of adenylate kinase appear to involve a population-shift mechanism. [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 104, No. 47. (20 November 2007), pp. 18496-18501. by Karunesh Arora, Charles L. Brooks posted by 10 people xdeupi jrperillaj barry allmensch cactus sobolevnrm jlh64 structural_bioinformatics baker-group karunesh
	Spontaneous Formation of a Barrel-Stave Pore in a Coarse-Grained Model of the Synthetic LS3 Peptide and a DPPC Lipid Bilayer [My Copy] The Journal of Physical Chemistry B, Vol. 0, No. 0. (0000) by P. Gkeka, L. Sarkisov posted by 3 people baker-group sobolevnrm agrossfield
	Protein allostery, signal transmission and dynamics: a classification scheme of allosteric mechanisms. [My Copy] Molecular bioSystems, Vol. 5, No. 3. (March 2009), pp. 207-216. by C. J. Tsai, A. Del Sol, R. Nussinov posted by 8 people anuragsethi flbarroso structural_bioinformatics McCammon barry baker-group sobolevnrm higueruelo
	Flexibility and packing in proteins [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 99, No. 3. (5 February 2002), pp. 1274-1279. by Bertil Halle posted by 11 people Diego_Prada edws barry baker-group sobolevnrm ana aqeel allmensch hmk structural_bioinformatics Bioinformatics
	Coarse-grained Models for Simulations of Multiprotein Complexes: Application to Ubiquitin Binding [My Copy] Journal of Molecular Biology, Vol. 375, No. 5. (01 February 2008), pp. 1416-1433. by Young C. Kim, Gerhard Hummer posted by 8 people okapi barry sobolevnrm structural_bioinformatics Bioinformatics baker-group iantunbridge mikaellund
	Probing the Flexibility of Large Conformational Changes in Protein Structures through Local Perturbations [My Copy] PLoS Comput Biol, Vol. 5, No. 4. (3 April 2009), e1000343. by Bosco K. Ho, David A. Agard posted by 9 people skywalkerus02 dimka operon baker-group sobolevnrm structural_bioinformatics McCammon barry bourby
	Trypsin-ligand binding free energies from explicit and implicit solvent simulations with polarizable potential [My Copy] Journal of Computational Chemistry, Vol. 9999, No. 9999. (2009), NA. by Dian Jiao, Jiajing Zhang, Robert E. Duke, Guohui Li, Michael J. Schnieders, Pengyu Ren posted by 4 people agrossfield flbarroso baker-group sobolevnrm
	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
	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
	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
	Restoring Charge Asymmetry in Continuum Electrostatics Calculations of Hydration Free Energies [My Copy] The Journal of Physical Chemistry B, Vol. 113, No. 24. (18 June 2009), pp. 8206-8209. by Enrico O. Purisima, Traian Sulea posted by 5 people Elena_Zubova onufriev agrossfield baker-group sobolevnrm
	Mapping the conformational transition in Src activation by cumulating the information from multiple molecular dynamics trajectories [My Copy] Proceedings of the National Academy of Sciences, Vol. 106, No. 10. (10 March 2009), pp. 3776-3781. by Sichun Yang, Nilesh K. Banavali, BenoÃ®t Roux posted by 10 people anuragsethi Diego_Prada bmduggan allmensch guhjy baker-group sobolevnrm barry McCammon jmccammon
	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
	Four stages of a scientific discipline; four types of scientist. [My Copy] Trends in biochemical sciences, Vol. 34, No. 5. (09 May 2009), pp. 217-223. by Alexander M. Shneider posted by 36 people Sergey_gerbek cyounkin memerman Horduna Gorzomagnificent sfalsharif plosmedicine daforerog Roswell Cancer Crosstalk yyfwuhan CulCog yangjustinc abhishek_tiwari operon brembs ommachi Ryerson U. MMSc marclijour druvus qwermish Centre de Recherches Interdisciplinaires Enro polivares coela BergmanLab cisevol baker-group sobolevnrm McCammon barry reyez silberbauer Zephyrus dullhunk fgibson neils
	Interpreting the Coulomb-field approximation for generalized-Born electrostatics using boundary-integral equation theory [My Copy] The Journal of Chemical Physics, Vol. 129, No. 14. (2008) by Jaydeep P. Bardhan posted by 4 people baker-group sobolevnrm onufriev agrossfield
	Getting Started in Probabilistic Graphical Models [My Copy] PLoS Computational Biology, Vol. 3, No. 12. (1 December 2007), e252. by Edoardo M. Airoldi posted by 16 people buyske mhamada guhjy balicea AbnerCYH stajich cjeans GustavoLacerda GeeSharpMinor sobolevnrm cabbagezs nklee baker-group biehl softsimu jfr
	Determination of electrostatic interaction energies and protonation state populations in enzyme active sites [My Copy] Journal of Molecular Biology, Vol. In Press, Accepted Manuscript by Chresten R. Sondergaard, Lawrence P. Mcintosh, Gianluca Pollastri, Jens E. Nielsen posted by 6 people onufriev barry sobolevnrm structural_bioinformatics baker-group skoddet
	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 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
	2D molecular graphics: a flattened world of chemistry and biology [My Copy] Brief Bioinform (30 March 2009), bbp013. by Peng Zhou, Zhicai Shang posted by 9 people mijogiffin Zephyrus nanonan baker-group sobolevnrm dimka structural_bioinformatics McCammon barry
	Investigating protein dynamics in collective coordinate space [My Copy] Current Opinion in Structural Biology, Vol. 9, No. 2. (April 1999), pp. 164-169. by A. Kitao, N. Go posted by 8 people bmduggan Scis0000002 ttjoseph ffranca barry choonpeng sobolevnrm baker-group
	Trapping Moving Targets with Small Molecules [My Copy] Science, Vol. 324, No. 5924. (10 April 2009), pp. 213-215. by Gregory M. Lee, Charles S. Craik posted by 10 people guhjy nanonan baker-group sobolevnrm structural_bioinformatics McCammon barry pablocarb Fortran friendpine
	Association of Aminoglycosidic Antibiotics with the Ribosomal A-Site Studied with Brownian Dynamics [My Copy] J. Chem. Theory Comput., Vol. 4, No. 4. (8 April 2008), pp. 549-559. by Maciej Długosz, Jan M. Antosiewicz, Joanna Trylska posted by 4 people sobolevnrm baker-group barry McCammon
	Protonation free energy levels in complex molecular systems [My Copy] Biopolymers, Vol. 9999, No. 9999. (2007), NA. by Jan M. Antosiewicz posted by 4 people sobolevnrm baker-group barry McCammon
	Acidic range titration of HEWL using a constant-pH molecular dynamics method [My Copy] Proteins: Structure, Function, and Bioinformatics, Vol. 72, No. 1. (2008), pp. 289-298. by Miguel Machuqueiro, António M. Baptista posted by 6 people flbarroso scampos sobolevnrm baker-group sunhwan skoddet
	Kemp elimination catalysts by computational enzyme design [My Copy] Nature, Vol. 453, No. 7192. (19 March 2008), pp. 190-195. by Daniela Rothlisberger, Olga Khersonsky, Andrew M. Wollacott, et al.Lin Jiang, Jason DeChancie, Jamie Betker, Jasmine L. Gallaher, Eric A. Althoff, Alexandre Zanghellini, Orly Dym, Shira Albeck, Kendall N. Houk, Dan S. Tawfik, David Baker posted by 16 people barmak7282 baiaixi Jiang Research Group whitead Biocatalysis and Biotransformation qbin1304 fralium Diego_Prada apaydin jwm msuarezdiez austin cactus neils sobolevnrm baker-group
	Rational stabilization of enzymes by computational redesign of surface charge-charge interactions. [My Copy] Proceedings of the National Academy of Sciences of the United States of America (5 February 2009) by Alexey V V. Gribenko, Mayank M M. Patel, Jiajing Liu, Scott A A. McCallum, Chunyu Wang, George I I. Makhatadze posted by 7 people baker-group sobolevnrm grahamc amishp structural_bioinformatics McCammon barry
	Allosteric Communication Occurs via Networks of Tertiary and Quaternary Motions in Proteins [My Copy] PLoS Comput Biol, Vol. 5, No. 2. (20 February 2009), e1000293. by Michael D. Daily, Jeffrey J. Gray posted by 13 people anuragsethi skywalkerus02 baker-group sobolevnrm pablocarb AngelB eallain allmensch gane5h apaydin structural_bioinformatics McCammon barry
	Construction of effective free energy landscape from single-molecule time series [My Copy] Proceedings of the National Academy of Sciences, Vol. 104, No. 49. (4 December 2007), pp. 19297-19302. by Akinori Baba, Tamiki Komatsuzaki posted by 8 people hmk zwang cactus sobolevnrm baker-group Diego_Prada arnaudriegert hsekiguc
	Molecular Dynamics Simulation of the Escherichia coli NikR Protein: Equilibrium Conformational Fluctuations Reveal Interdomain Allosteric Communication Pathways [My Copy] Journal of Molecular Biology, Vol. 378, No. 5. (16 May 2008), pp. 1155-1173. by Michael J. Bradley, Peter T. Chivers, Nathan A. Baker posted by 5 people sobolevnrm baker-group skoddet barry structural_bioinformatics
	A mathematical tool for exploring the dynamics of biological networks [My Copy] Proceedings of the National Academy of Sciences (21 November 2007), 0709955104. by Paolo E. Barbano, Marina Spivak, Marc Flajolet, Angus C. Nairn, Paul Greengard, Leslie Greengard posted by 13 people Scis0000002 agomez tmmurali cjeans zwang cactus sobolevnrm forgoston lenov baker-group sdbneuro mdramirez phoenixzxl
	Defining functional distances over gene ontology. [My Copy] BMC bioinformatics, Vol. 9, No. 1. (2008), 50. by A. del Pozo, F. Pazos, A. Valencia posted by 13 people biomcgary MarcoAlvarez sgoetz wilbur barry tny grahamc sobolevnrm Bioinformatics baker-group barriot carlk guhjy
	Transitive homology-guided structural studies lead to discovery of Cro proteins with 40% sequence identity but different folds [My Copy] Proceedings of the National Academy of Sciences, Vol. 105, No. 7. (19 February 2008), pp. 2343-2348. by Christian G. Roessler, Branwen M. Hall, William J. Anderson, et al.Wendy M. Ingram, Sue A. Roberts, William R. Montfort, Matthew H. Cordes posted by 4 people barry cactus sobolevnrm baker-group
	Molecular dynamics simulations of nucleic acid-protein complexes. [My Copy] Current opinion in structural biology, Vol. 18, No. 2. (April 2008), pp. 194-199. by A. D. Mackerell, L. Nilsson posted by 6 people flbarroso ruvido zwang sobolevnrm baker-group phoenixzxl
	Secondary Structure Bias in Generalized Born Solvent Models: Comparison of Conformational Ensembles and Free Energy of Solvent Polarization from Explicit and Implicit Solvation [My Copy] J. Phys. Chem. B, Vol. 111, No. 7. (22 February 2007), pp. 1846-1857. by D. R. Roe, A. Okur, L. Wickstrom, V. Hornak, C. Simmerling posted by 7 people RamuAnandakrishnan flbarroso baaden choonpeng sobolevnrm baker-group onufriev
	Illuminating the mechanistic roles of enzyme conformational dynamics [My Copy] Proceedings of the National Academy of Sciences, Vol. 104, No. 46. (13 November 2007), pp. 18055-18060. by Jeffrey A. Hanson, Karl Duderstadt, Lucas P. Watkins, et al.Sucharita Bhattacharyya, Jason Brokaw, Jhih-Wei Chu, Haw Yang posted by 9 people kjell protein_Dyn joseph_x_zhou quanwang toerst barry sobolevnrm baker-group biehl
	Designed Protein-Protein Association [My Copy] Science, Vol. 319, No. 5860. (11 January 2008), pp. 206-209. by Dirk Grueninger, Nora Treiber, Mathias O. Ziegler, Jochen W. Koetter, Monika-Sarah Schulze, Georg E. Schulz posted by 8 people timg cjeans zwang cactus biomcgary sobolevnrm baker-group higueruelo
	Entropic Cost of Protein−Ligand Binding and Its Dependence on the Entropy in Solution [My Copy] The Journal of Physical Chemistry B, Vol. 0, No. 0. (0000) by Sheeba J. Irudayam, Richard H. Henchman posted by 4 people agrossfield mijam baker-group sobolevnrm
	Molecular dynamics -- potential of mean force calculations as a tool for understanding ion permeation and selectivity in narrow channels [My Copy] Biophysical Chemistry In Ion Hydration Special Issue, Vol. 124, No. 3. (1 December 2006), pp. 251-267. by Toby W. Allen, Olaf S. Andersen, Benoit Roux posted by 6 people ibuch barry sobolevnrm structural_bioinformatics Bioinformatics baker-group
	Polarizable Force Fields: History, Test Cases, and Prospects [My Copy] Journal of Chemical Theory and Computation, Vol. 3, No. 6. (1 November 2007), pp. 2034-2045. by Arieh Warshel, Mitsunori Kato, Andrei V. Pisliakov posted by 6 people edws tovrstra flbarroso sobolevnrm baker-group middledomain
	Simulation Study of Protein-Mediated Vesicle Fusion [My Copy] The Journal of Physical Chemistry B, Vol. 113, No. 3. (22 January 2009), pp. 589-591. by Shaogui Wu, Hongxia Guo posted by 3 people baker-group sobolevnrm agrossfield
	Statistical thermodynamics of residue fluctuations in native proteins [My Copy] The Journal of Chemical Physics, Vol. 130, No. 9. (2009), 095103. by Osman N. Yogurtcu, Mert Gur, Burak Erman posted by 3 people agrossfield baker-group sobolevnrm
	On the origin of the electrostatic potential difference at a liquid-vacuum interface [My Copy] The Journal of Chemical Physics, Vol. 129, No. 23. (2008) by Edward Harder, Benoît Roux posted by 3 people baker-group sobolevnrm agrossfield
	Computer Simulations of Vesicle Fission Induced by External Amphipathic Inclusions [My Copy] The Journal of Physical Chemistry B, Vol. 113, No. 4. (29 January 2009), pp. 1048-1057. by Kai Yang, Yu-Qiang Ma posted by 3 people baker-group sobolevnrm agrossfield
	Hybrid Coarse-Graining Approach for Lipid Bilayers at Large Length and Time Scales [My Copy] The Journal of Physical Chemistry B, Vol. 0, No. 0. (0000) by Gary S. Ayton, Gregory A. Voth posted by 3 people agrossfield baker-group sobolevnrm
	Solvent dramatically affects protein structure refinement [My Copy] Proceedings of the National Academy of Sciences, Vol. 105, No. 51. (23 December 2008), pp. 20239-20244. by Gaurav Chopra, Christopher M. Summa, Michael Levitt posted by 12 people rabio pavanghatty mijam dgront structural_bioinformatics McCammon Bioinformatics barry baker-group sobolevnrm biehl itmeson