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	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 by 13 people anuragsethi barry sunhwan McCammon jmccammon baker-group sobolevnrm willard kafuitay carlosjavierna sschurer hadesnumb paulschlesinger
	Protein Dynamism and Evolvability [My Copy] Science, Vol. 324, No. 5924. (10 April 2009), pp. 203-207. by Nobuhiko Tokuriki, Dan S. Tawfik posted by 26 people skywalkerus02 paulymer dfdong tomhebbron anuragsethi ahmetbakan kevinchannon klexa lauresultan dbikard ibuch ramiro2k structural_bioinformatics McCammon barry pablocarb ramanuja baker-group sobolevnrm biomcgary hsekiguc VGreiff phoenixzxl zwang jdoconnell paulschlesinger
	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 13 people skywalkerus02 anuragsethi klexa apaydin baker-group sobolevnrm gane5h structural_bioinformatics barry McCammon jmccammon reyez biehl
	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
	Using the local elevation method to construct optimized umbrella sampling potentials: Calculation of the relative free energies and interconversion barriers of glucopyranose ring conformers in water [My Copy] Journal of Computational Chemistry, Vol. 31, No. 1. (2010), pp. 1-23. by Halvor S. Hansen, Philippe H. Hünenberger posted by 4 people anuragsethi McCammon jmccammon agrossfield
	Inclusion of ionization states of ligands in affinity calculations [My Copy] Proteins: Structure, Function, and Bioinformatics, Vol. 76, No. 1. (2009), pp. 138-150. by Serena Donnini, Alessandra Villa, Gerrit Groenhof, Alan E. Mark, Rik K. Wierenga, André H. Juffer posted by 8 people flbarroso onufriev McCammon rbaron ibuch baker-group sobolevnrm RamuAnandakrishnan
	Chapter 9 Analyzing Enzymatic pH Activity Profiles and Protein Titration Curves Using Structure-Based pKa Calculations and Titration Curve Fitting [My Copy] Methods in enzymology In Computer Methods, Part A, Vol. 454 (2009), pp. 233-258. by Jens E. Nielsen posted by 7 people sobolevnrm scampos anuragsethi McCammon jmccammon flbarroso baker-group
	Dynamics of protein-protein encounter: A Langevin equation approach with reaction patches [My Copy] The Journal of Chemical Physics, Vol. 129, No. 15. (2008) by Jakob Schluttig, Denitsa Alamanova, Volkhard Helms, Ulrich S. Schwarz posted by 6 people anuragsethi barry baker-group sobolevnrm McCammon jmccammon
	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
	Coarse-grained modeling of allosteric regulation in protein receptors [My Copy] Proceedings of the National Academy of Sciences, Vol. 106, No. 34. (25 August 2009), pp. 14253-14258. by Ilya A. Balabin, Weitao Yang, David N. Beratan posted by 6 people sobolevnrm pmung McCammon jmccammon agrossfield okapi
	Linear response theory in dihedral angle space for protein structural change upon ligand binding [My Copy] Journal of Computational Chemistry, Vol. 30, No. 16. (2009), pp. 2602-2608. by Satoshi Omori, Sotaro Fuchigami, Mitsunori Ikeguchi, Akinori Kidera posted by 4 people barry baker-group sobolevnrm RamuAnandakrishnan
	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
	Effective force coarse-graining [My Copy] Phys. Chem. Chem. Phys. In Phys. Chem. Chem. Phys., Vol. 11, No. 12. (2009), pp. 2002-2015. by Yanting Wang, W. G. Noid, Pu Liu, Gregory A. Voth posted by 7 people loison baker-group sobolevnrm McCammon jmccammon mbeeby flbarroso
	Hydration Water Dynamics Near Biological Interfaces† [My Copy] The Journal of Physical Chemistry B, Vol. 113, No. 13. (2 April 2009), pp. 4082-4092. by Margaret E. Johnson, Cecile Malardier-Jugroot, Rajesh K. Murarka, Teresa Head-Gordon posted by 8 people Jiang Research Group whitead willard flbarroso Lombardo_7 kvilonen baker-group sobolevnrm
	Boxed Molecular Dynamics: A Simple and General Technique for Accelerating Rare Event Kinetics and Mapping Free Energy in Large Molecular Systems [My Copy] The Journal of Physical Chemistry B, Vol. 113, No. 52. (31 December 2009), pp. 16603-16611. by David R. Glowacki, Emanuele Paci, Dmitrii V. Shalashilin posted by 7 people McCammon jmccammon agrossfield mfajer yangsiyang anuragsethi sobolevnrm
	Multiscale simulation of soft matter systems - from the atomistic to the coarse-grained level and back [My Copy] Soft Matter In Soft Matter, Vol. 5, No. 22. (2009), pp. 4357-4366. by Christine Peter, Kurt Kremer posted by 6 people loison McCammon jmccammon flbarroso anuragsethi sobolevnrm
	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
	Ion channel gates: comparative analysis of energy barriers [My Copy] European Biophysics Journal by Kaihsu Tai, Shozeb Haider, Alessandro Grottesi, Mark Sansom posted by 5 people McCammon jmccammon baker-group sobolevnrm paulschlesinger
	Prediction of membrane protein structures with complex topologies using limited constraints [My Copy] Proceedings of the National Academy of Sciences, Vol. 106, No. 5. (3 February 2009), pp. 1409-1414. by P. Barth, B. Wallner, D. Baker posted by 13 people rph dgront OPIG sebk structural_bioinformatics barry krapnik viktor21614 paulschlesinger zwang apaydin agrossfield amishp
	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
	Long-timescale molecular dynamics simulations of protein structure and function. [My Copy] Current opinion in structural biology, Vol. 19, No. 2. (08 April 2009), pp. 120-127. by John L. Klepeis, Kresten Lindorff-Larsen, Ron O. Dror, David E. Shaw posted by 14 people loison xdeupi agrossfield allmensch bmduggan r2s2 apaydin kiekyon Borelli idoerg baker-group sobolevnrm edws paulschlesinger
	Biophysical dissection of membrane proteins [My Copy] Nature, Vol. 459, No. 7245. (20 May 2009), pp. 344-346. by Stephen H. White posted by 13 people amoszlj rph girayenkavi ColumbusLabs viktor21614 kevinchannon hsekiguc structural_bioinformatics McCammon barry baker-group sobolevnrm paulschlesinger
	Standard Free Energy of Binding from a One-Dimensional Potential of Mean Force [My Copy] Journal of Chemical Theory and Computation In Journal of Chemical Theory and Computation, Vol. 5, No. 4. (14 April 2009), pp. 909-918. by Slimane Doudou, Neil A. Burton, Richard H. Henchman posted by 9 people dcheong McCammon jmccammon Structural Biology Group TorVergata A_Coletta_Thesis carlosjavierna ibuch baker-group sobolevnrm
	A Systematic Methodology for Defining Coarse-Grained Sites in Large Biomolecules [My Copy] Biophysical Journal, Vol. 95, No. 11. (01 December 2008), pp. 5073-5083. by Z. Zhang, L. Lu, W. Noid, V. Krishna, J. Pfaendtner, G. Voth posted by 9 people loison okapi structural_bioinformatics McCammon barry sobolevnrm choonpeng agrossfield paulschlesinger
	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 11 people loison barry baker-group sobolevnrm A_Coletta_Thesis paulschlesinger choonpeng aqeel jmccammon McCammon rok
	Systematic multiscale simulation of membrane protein systems [My Copy] Current Opinion in Structural Biology, Vol. 19, No. 2. (09 April 2009), pp. 138-144. by Gary Ayton,, Gregory Voth, posted by 6 people loison baker-group sobolevnrm McCammon barry paulschlesinger
	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
	Allosteric Transitions of Supramolecular Systems Explored by Network Models: Application to Chaperonin GroEL [My Copy] PLoS Comput Biol, Vol. 5, No. 4. (17 April 2009), e1000360. by Zheng Yang, Peter Májek, Ivet Bahar posted by 5 people barry McCammon jmccammon baker-group sobolevnrm
	Striking Effects of Hydrodynamic Interactions on the Simulated Diffusion and Folding of Proteins [My Copy] Journal of Chemical Theory and Computation, Vol. 5, No. 2. (10 February 2009), pp. 242-256. by Tamara Frembgen-Kesner, Adrian H. Elcock posted by 5 people baker-group sobolevnrm barry McCammon jmccammon
	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 10 people krapnik flbarroso onufriev jmccammon biehl sobolevnrm baker-group barry structural_bioinformatics McCammon
	Protein Ionizable Groups: pK Values and Their Contribution to Protein Stability and Solubility [My Copy] Journal of Biological Chemistry, Vol. 284, No. 20. (15 May 2009), pp. 13285-13289. by C. Nick Pace, Gerald R. Grimsley, J. Martin Scholtz posted by 10 people pjkiley scampos klexa nanonan structural_bioinformatics McCammon barry baker-group sobolevnrm paulschlesinger
	The work-Hamiltonian connection and the usefulness of the Jarzynski equality for free energy calculations [My Copy] The Journal of Chemical Physics, Vol. 130, No. 17. (2009), 171102. by Eric N. Zimanyi, Robert J. Silbey posted by 3 people dlimmer agrossfield paulschlesinger
	Resampling improves the efficiency of a “fast-switch” equilibrium sampling protocol [My Copy] The Journal of Chemical Physics, Vol. 130, No. 8. (2009) by Edward Lyman, Daniel M. Zuckerman posted by 4 people agrossfield Jiang Research Group whitead dlimmer
	On the Range of Water Structure Models Compatible with X-ray and Neutron Diffraction Data [My Copy] The Journal of Physical Chemistry B, Vol. 113, No. 18. (7 May 2009), pp. 6246-6255. by Kjartan T. Wikfeldt, Mikael Leetmaa, Mathias P. Ljungberg, Anders Nilsson, Lars G. M. Pettersson posted by 5 people qshao willard flbarroso baker-group sobolevnrm
	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
	Effect of cholesterol on the structure of a phospholipid bilayer [My Copy] Proceedings of the National Academy of Sciences, Vol. 106, No. 10. (10 March 2009), pp. 3654-3658. by FrÃ©dÃ©rick de Meyer, Berend Smit posted by 7 people softsimu kevinchannon baker-group sobolevnrm paulschlesinger chiufanlee cjryan
	Diffusion with Moving Boundary on Spherical Surfaces [My Copy] ChemPhysChem, Vol. 10, No. 9-10. (2009), pp. 1593-1602. by Christian Amatore, Oleksiy V. Klymenko, Alexander I. Oleinick, Irina Svir posted by 3 people dlimmer sobolevnrm paulschlesinger
	Surface Sites for Engineering Allosteric Control in Proteins [My Copy] Science, Vol. 322, No. 5900. (17 October 2008), pp. 438-442. by Jeeyeon Lee, Madhusudan Natarajan, Vishal C. Nashine, et al.Michael Socolich, Tina Vo, William P. Russ, Stephen J. Benkovic, Rama Ranganathan posted by 13 people kokphinchooi baker-group sobolevnrm jbhiatt lflorez cactus marck i000 structural_bioinformatics McCammon Bioinformatics barry paulschlesinger
	Dynamical networks in tRNA:protein complexes [My Copy] Proceedings of the National Academy of Sciences, Vol. 106, No. 16. (21 April 2009), pp. 6620-6625. by Anurag Sethi, John Eargle, Alexis A. Black, Zaida Luthey-Schulten posted by 7 people anuragsethi jeargle AbnerCYH McCammon jmccammon baker-group sobolevnrm
	A force field for virtual atom molecular mechanics of proteins [My Copy] Proceedings of the National Academy of Sciences, Vol. 106, No. 37. (15 September 2009), pp. 15667-15672. by Anil Korkut, Wayne A. Hendrickson posted by 4 people jmccammon structural_bioinformatics McCammon barry
	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
	Computational evaluation of protein-small molecule binding. [My Copy] Current opinion in structural biology, Vol. 19, No. 1. (20 February 2009), pp. 56-61. by O. Guvench, A. D. MacKerell posted by 8 people sobolevnrm flbarroso csrocha ucbcjbm baker-group phoenixzxl McCammon barry
	Recognition Dynamics Up to Microseconds Revealed from an RDC-Derived Ubiquitin Ensemble in Solution [My Copy] Science, Vol. 320, No. 5882. (13 June 2008), pp. 1471-1475. by Oliver F. Lange, Nils-Alexander Lakomek, Christophe Fares, et al.Gunnar F. Schroder, Korvin F. A. Walter, Stefan Becker, Jens Meiler, Helmut Grubmuller, Christian Griesinger, Bert L. de Groot posted by 10 people anna_yershova edws paulschlesinger higueruelo barry structural_bioinformatics McCammon jmccammon Chang group cchang
	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
	Conservation of Side-Chain Dynamics Within a Protein Family [My Copy] Journal of the American Chemical Society, Vol. 0, No. 0. (0000) by Anthony B. Law, Ernesto J. Fuentes, Andrew L. Lee posted by 8 people anuragsethi skywalkerus02 pablocarb structural_bioinformatics McCammon barry baker-group sobolevnrm
	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
	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 6 people loison choonpeng flbarroso agrossfield baker-group sobolevnrm
	Computation of Conformational Coupling in Allosteric Proteins [My Copy] PLoS Comput Biol, Vol. 5, No. 8. (28 August 2009), e1000484. by Brian A. Kidd, David Baker, Wendy E. Thomas posted by 11 people richardbickerton apaydin skywalkerus02 sobolevnrm klexa oteri boris_aguilar bmduggan McCammon barry zwang
	Localizing normal modes in large molecules [My Copy] The Journal of Chemical Physics, Vol. 130, No. 8. (2009) by Christoph R. Jacob, Markus Reiher posted by 3 people baker-group sobolevnrm dlimmer
	A one-dimensional dipole lattice model for water in narrow nanopores [My Copy] The Journal of Chemical Physics, Vol. 130, No. 15. (2009), 154110. by Jürgen Köfinger, Gerhard Hummer, Christoph Dellago posted by 3 people dlimmer baker-group sobolevnrm
	Computational Identification of Slow Conformational Fluctuations in Proteins [My Copy] The Journal of Physical Chemistry B, Vol. 113, No. 52. (31 December 2009), pp. 16669-16680. by Arvind Ramanathan, Pratul K. Agarwal posted by 5 people anuragsethi McCammon jmccammon agrossfield qshao
	Electric multipole moment fluctuations in polar liquids [My Copy] The Journal of Chemical Physics, Vol. 130, No. 12. (2009), 124521. by Joakim Stenhammar, Per Linse, Per, Gunnar Karlström posted by 3 people dlimmer baker-group sobolevnrm
	Predictions of Hydration Free Energies from All-Atom Molecular Dynamics Simulations† [My Copy] The Journal of Physical Chemistry B, Vol. 0, No. 0. (0000) by David L. Mobley, Christopher I. Bayly, Matthew D. Cooper, Ken A. Dill posted by 6 people ucbcjbm willard baker-group sobolevnrm Jiang Research Group whitead
	Molecular origin of the negative heat capacity of hydrophilic hydration [My Copy] The Journal of Chemical Physics, Vol. 130, No. 14. (2009), 144705. by Masahiro Kinoshita, Takashi Yoshidome posted by 3 people baker-group sobolevnrm dlimmer
	Multiscale characterization of protein conformational ensembles [My Copy] Proteins: Structure, Function, and Bioinformatics, Vol. 76, No. 4. (2009), pp. 837-851. by Amarda Shehu, Lydia E. Kavraki, Cecilia Clementi posted by 8 people anuragsethi okapi structural_bioinformatics McCammon barry baker-group sobolevnrm apaydin
	BlockMaster: Partitioning Protein Kinase Structures Using Normal-Mode Analysis† [My Copy] The Journal of Physical Chemistry A, Vol. 113, No. 26. (2 July 2009), pp. 7528-7534. by Marina Shudler, Masha Y. Niv posted by 5 people carlosjavierna McCammon barry sobolevnrm paulschlesinger
	How to obtain statistically converged MM/GBSA results [My Copy] Journal of Computational Chemistry, Vol. 9999, No. 9999. (2009), NA. by Samuel Genheden, Ulf Ryde posted by 5 people pmung McCammon barry sobolevnrm RamuAnandakrishnan
	Backbone relaxation coupled to the ionization of internal groups in proteins: A self-guided Langevin dynamics study [My Copy] Biophys. J. (18 July 2008), biophysj.108.130906. by Ana Damjanovic, Xiongwu Wu, Bertrand Garcia-Moreno, Bernard R. Brooks posted by 5 people baker-group sobolevnrm McCammon jmccammon paulschlesinger
	Origin of the change in solvation enthalpy of the peptide group when neighboring peptide groups are added [My Copy] Proceedings of the National Academy of Sciences, Vol. 106, No. 9. (3 March 2009), pp. 3137-3141. by Franc Avbelj, Robert L. Baldwin posted by 4 people baker-group sobolevnrm paulschlesinger amishp
	Computation of Absolute Hydration and Binding Free Energy with Free Energy Perturbation Distributed Replica-Exchange Molecular Dynamics [My Copy] Journal of Chemical Theory and Computation, Vol. 5, No. 10. (13 October 2009), pp. 2583-2588. by Wei Jiang, Milan Hodoscek, Benoît Roux posted by 5 people loison McCammon jmccammon qshao sobolevnrm
	A Quick Guide to Organizing Computational Biology Projects [My Copy] PLoS Comput Biol In PLoS Comput Biol, Vol. 5, No. 7. (31 July 2009), e1000424. by William S. Noble posted by 86 people aprasad okapi abhishek_tiwari agomez songpku shikin kemamy2 chvlyl freesci dfdong dutilh leliavski dgront paulymer FAB-lab rvosa installe burak annakcroft brianb nuin skembel pekrau Sergey_gerbek mordiano remoteFuture Yanno Pedro Martinez EvoDevo lab Barcelona aaltenburger marekrud guhjy dolchan frohike operon Orengo Group Journal Picks CorinYeats artaban421 antonkratz tomhebbron maren bayesian daveGerrard JoeBanks jcaddy somak bertelsen ptrobajo nperoni daforerog mmwoodman charris5 GustavoLacerda pmendes fgibson rdiaz Zephyrus heliopais franklu310 lmichan silberbauer leemond31 jlangdon robfsouza Bioinformatics - CRUK Stew pmung reyez kshameer djkt pawelsobko jjray dswan apaydin renatomilani VGreiff cabbagesofdoom ccsbs wei_tang fenghezi BergmanLab cisevol structural_bioinformatics McCammon barry sdaehne druvus
	Solubility and Molecular Conformations of n-Alkane Chains in Water [My Copy] The Journal of Physical Chemistry B, Vol. 113, No. 18. (7 May 2009), pp. 6405-6414. by Andrew L. Ferguson, Pablo G. Debenedetti, Athanassios Z. Panagiotopoulos posted by 4 people willard flbarroso baker-group sobolevnrm
	What are the Sites Water Occupies at the Interface of a Phospholipid Membrane?† [My Copy] The Journal of Physical Chemistry B, Vol. 113, No. 13. (2 April 2009), pp. 4119-4124. by Victor V. Volkov, Yuji Takaoka, Roberto Righini posted by 4 people sobolevnrm flbarroso willard baker-group
	From Franklin to Today: Toward a Molecular Level Understanding of Bonding and Adsorption at the Oil−Water Interface† [My Copy] The Journal of Physical Chemistry C, Vol. 113, No. 4. (29 January 2009), pp. 1171-1188. by Cathryn L. Mcfearin, Daniel K. Beaman, Fred G. Moore, Geraldine L. Richmond posted by 4 people flbarroso baker-group sobolevnrm willard
	Biophysical characterization of intrinsically disordered proteins. [My Copy] Current opinion in structural biology, Vol. 19, No. 1. (21 February 2009), pp. 23-30. by D. Eliezer posted by 7 people sobolevnrm girayenkavi flbarroso laurenm baker-group paulschlesinger viktor21614
	On using a too large integration time step in molecular dynamics simulations of coarse-grained molecular models [My Copy] Phys. Chem. Chem. Phys., Vol. 11, No. 12. (28 March 2009), pp. 1934-1941. by Moritz Winger, Daniel Trzesniak, Riccardo Baron, Wilfred F. Gunsteren posted by 7 people sunnytov arnaucordomi patvarilly baker-group sobolevnrm mbeeby flbarroso
	Efficient Drug Lead Discovery and Optimization [My Copy] Accounts of Chemical Research, Vol. 0, No. 0. (0000) by William L. Jorgensen posted by 9 people nanonan tbinbal Thermaneutist McCammon jmccammon superpyrin sschurer baker-group sobolevnrm
	CHARMM: The biomolecular simulation program [My Copy] Journal of Computational Chemistry, Vol. 30, No. 10. (30 July 2009), pp. 1545-1614. by B. R. Brooks, C. L. Brooks, A. D. Mackerell, et al.L. Nilsson, R. J. Petrella, B. Roux, Y. Won, G. Archontis, C. Bartels, S. Boresch, A. Caflisch, L. Caves, Q. Cui, A. R. Dinner, M. Feig, S. Fischer, J. Gao, M. Hodoscek, W. Im, K. Kuczera, T. Lazaridis, J. Ma, V. Ovchinnikov, E. Paci, R. W. Pastor, C. B. Post, J. Z. Pu, M. Schaefer, B. Tidor, R. M. Venable, H. L. Woodcock, X. Wu, W. Yang, D. M. York, M. Karplus posted by 12 people ckmyo dgront rodrigofaccioli mmuecke medic0747 flbarroso jrperillaj xavierprat saravan baker-group sobolevnrm dimka
	Side-chain recognition and gating in the ribosome exit tunnel [My Copy] Proceedings of the National Academy of Sciences, Vol. 105, No. 43. (28 October 2008), pp. 16549-16554. by Paula M. Petrone, Christopher D. Snow, Del Lucent, Vijay S. Pande posted by 5 people carlosjavierna baker-group sobolevnrm McCammon barry
	Cloud computing [My Copy] Bioinformatics, Vol. 25, No. 12. (15 June 2009), 1475. by Alex Bateman, Matt Wood posted by 29 people agomez 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
	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
	Molecular dynamics study of the effect of cholesterol on the properties of lipid monolayers at low surface tensions [My Copy] Phys. Chem. Chem. Phys., Vol. 11, No. 12. (2009), pp. 1916-1922. by Cameron Laing, Svetlana Baoukina, Peter D. Tieleman posted by 5 people dimka patvarilly baker-group sobolevnrm flbarroso
	Bad Seeds Sprout Perilous Dynamics: Stochastic Thermostat Induced Trajectory Synchronization in Biomolecules [My Copy] Journal of Chemical Theory and Computation, Vol. 5, No. 6. (9 June 2009), pp. 1624-1631. by Daniel J. Sindhikara, Seonah Kim, Arthur F. Voter, Adrian E. Roitberg posted by 5 people McCammon jmccammon edws baker-group sobolevnrm
	Aminoglycoside Association Pathways with the 30S Ribosomal Subunit [My Copy] The Journal of Physical Chemistry B, Vol. 0, No. 0. (0000) by Maciej Długosz, Joanna Trylska posted by 4 people McCammon jmccammon baker-group sobolevnrm
	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 46 people lmichan iskanbasal agomez danilov chriswillmott freesci artaban421 benoitvalley reflist singhsh 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
	Achieving energy conservation in Poisson–Boltzmann molecular dynamics: Accuracy and precision with finite-difference algorithms [My Copy] Chemical Physics Letters, Vol. 468, No. 4-6. (22 January 2009), pp. 112-118. by J. Wang, Q. Cai, Z. Li, H. Zhao, R. Luo posted by 4 people baker-group sobolevnrm McCammon jmccammon
	HOLLOW: Generating Accurate Representations of Channel and Interior Surfaces in Molecular Structures [My Copy] BMC Structural Biology, Vol. 8 (14 November 2008), 49. by Bosco K. Ho, Franz Gruswitz2 posted by 4 people baker-group sobolevnrm McCammon jmccammon
	Poisson–Boltzmann model analysis of binding mRNA cap analogues to the translation initiation factor eIF4E [My Copy] Biophysical Chemistry, Vol. 140, No. 1-3. (March 2009), pp. 16-23. by O. Szklarczyk, J. Zuberek, J. Antosiewicz posted by 4 people baker-group sobolevnrm McCammon jmccammon
	Isotropic periodic sum of electrostatic interactions for polar systems [My Copy] The Journal of Chemical Physics, Vol. 131, No. 2. (2009), 024107. by Xiongwu Wu, Bernard R. Brooks posted by 3 people mikaellund agrossfield dlimmer
	Nothing about protein structure classification makes sense except in the light of evolution [My Copy] Current Opinion in Structural Biology, Vol. 19, No. 3. (24 June 2009), pp. 329-334. by Ruben E. Valas, Song Yang, Philip E. Bourne posted by 17 people dfdong mkotlyar skywalkerus02 dgront nyyu robfsouza apaydin structural_bioinformatics barry coela R.E.A.D Zephyrus baker-group sobolevnrm zwang friendpine paulschlesinger
	The Membrane Potential and its Representation by a Constant Electric Field in Computer Simulations. [My Copy] Biophysical journal (18 July 2008) by Benoit Roux posted by 7 people baker-group sobolevnrm agrossfield paulschlesinger McCammon abebe dimka
	The role of lipid composition for insertion and stabilization of amino acids in membranes [My Copy] The Journal of Chemical Physics, Vol. 130, No. 18. (2009), 185101. by Anna C. V. Johansson, Erik Lindahl posted by 4 people agrossfield baker-group sobolevnrm paulschlesinger
	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
	Orientation and Peptide−Lipid Interactions of Alamethicin Incorporated in Phospholipid Membranes: Polarized Infrared and Spin-Label EPR Spectroscopy [My Copy] Biochemistry, Vol. 0, No. 0. (0000) by Derek Marsh posted by 4 people baker-group sobolevnrm agrossfield paulschlesinger
	Multiscale Modeling of Form and Function [My Copy] Science, Vol. 324, No. 5924. (10 April 2009), pp. 208-212. by Adam J. Engler, Patrick O. Humbert, Bernhard Wehrle-Haller, Valerie M. Weaver posted by 7 people paulymer edws structural_bioinformatics McCammon barry baker-group sobolevnrm
	Free Energy and Kinetics of Conformational Transitions from Voronoi Tessellated Milestoning with Restraining Potentials [My Copy] Journal of Chemical Theory and Computation, Vol. 5, No. 10. (13 October 2009), pp. 2589-2594. by Luca Maragliano, Eric Vanden-Eijnden, Benoît Roux posted by 4 people McCammon jmccammon anuragsethi sobolevnrm
	Three-dimensional “Mercedes-Benz” model for water [My Copy] The Journal of Chemical Physics, Vol. 131, No. 5. (2009), 054505. by Cristiano L. Dias, Tapio A. Nissila, Martin Grant, Mikko Karttunen posted by 3 people softsimu sobolevnrm dlimmer
	Many-Body Polarization Effects and the Membrane Dipole Potential [My Copy] Journal of the American Chemical Society, Vol. 0, No. 0. (0000) by Edward Harder, Alexander D. Mackerell, Benoît Roux posted by 4 people baker-group sobolevnrm kafuitay carlosjavierna
	Transition networks for modeling the kinetics of conformational change in macromolecules [My Copy] Current Opinion in Structural Biology In Theory and simulation / Macromolecular assemblages, Vol. 18, No. 2. (April 2008), pp. 154-162. by F NOE,, S FISCHER, posted by 10 people ckmyo Diego_Prada aqeel barry sobolevnrm structural_bioinformatics baker-group paulschlesinger McCammon toerst
	Drug discovery using chemical systems biology: identification of the protein-ligand binding network to explain the side effects of CETP inhibitors. [My Copy] PLoS computational biology, Vol. 5, No. 5. (15 May 2009), e1000387. by Li Xie, Jerry Li, Lei Xie, Philip E. Bourne posted by 7 people ubcg08l flbarroso McCammon jmccammon reyez barry dolchan
	Current performance gains from utilizing the GPU or the ASIC MDGRAPE-3 within an enhanced Poisson Boltzmann approach. [My Copy] Journal of computational chemistry, Vol. 30, No. 14. (15 November 2009), pp. 2351-2357. by Tetsu Narumi, Kenji Yasuoka, Makoto Taiji, Siegfried Höfinger posted by 3 people sobolevnrm ihaque RamuAnandakrishnan
	Protein model refinement using an optimized physics-based all-atom force field [My Copy] Proceedings of the National Academy of Sciences, Vol. 105, No. 24. (17 June 2008), pp. 8268-8273. by Anna Jagielska, Liliana Wroblewska, Jeffrey Skolnick posted by 7 people krapnik RamuAnandakrishnan jmccammon barry structural_bioinformatics McCammon zwang
	Predicting new molecular targets for known drugs. [My Copy] Nature In Nature, Vol. 462, No. 7270. (12 November 2009), pp. 175-181. by Michael J. Keiser, Vincent Setola, John J. Irwin, et al.Christian Laggner, Atheir I. Abbas, Sandra J. Hufeisen, Niels H. Jensen, Michael B. Kuijer, Roberto C. Matos, Thuy B. Tran, Ryan Whaley, Richard A. Glennon, Jérôme Hert, Kelan L. Thomas, Douglas D. Edwards, Brian K. Shoichet, Bryan L. Roth posted by 24 people agomez guhjy hmx fernan renatomilani McCammon barry flbarroso venancio okapi Journal picks ahmetbakan zufar pablocarb zwang TRHvidsten phoenixzxl qshao Yanno mnishimu tmmurali sjcockell seb1 abhishek_tiwari
	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
	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
	Nonspecific DNA-Protein Interaction: Why Proteins Can Diffuse along DNA [My Copy] Physical Review Letters, Vol. 102, No. 22. (2009), 228101. by Vincent Dahirel, Fabien Paillusson, Marie Jardat, Maria Barbi, Jean M. Victor posted by 8 people zeldin kumar_physics flbarroso sobolevnrm edws jjray spm82 scratchmandoo
	Approximate normal mode analysis based on vibrational subsystem analysis with high accuracy and efficiency [My Copy] The Journal of Chemical Physics, Vol. 130, No. 19. (2009), 194111. by Jeffrey Hafner, Wenjun Zheng posted by 2 people dlimmer agrossfield
	Optimal estimators and asymptotic variances for nonequilibrium path-ensemble averages [My Copy] The Journal of Chemical Physics, Vol. 131, No. 13. (2009), 134110. by David D. L. Minh, John D. Chodera posted by 2 people dlimmer agrossfield
	Generalized Langevin models of molecular dynamics simulations with applications to ion channels [My Copy] The Journal of Chemical Physics, Vol. 131, No. 13. (2009), 134102. by Dan Gordon, Vikram Krishnamurthy, Shin H. Chung posted by 2 people dlimmer agrossfield
	An optimized replica exchange molecular dynamics method [My Copy] The Journal of Chemical Physics, Vol. 130, No. 7. (2009) by Hiqmet Kamberaj, Arjan van der Vaart posted by 2 people dlimmer agrossfield