dfgreen's Top Recommendations

These recommendations were last updated 45 minutes ago.

	The Protein Data Bank [My Copy] Nucl. Acids Res., Vol. 28, No. 1. (1 January 2000), pp. 235-242. by Helen M. Berman, John Westbrook, Zukang Feng, et al.Gary Gilliland, T. N. Bhat, Helge Weissig, Ilya N. Shindyalov, Philip E. Bourne posted by 50 people krapnik barmak7282 viktor21614 badi ucbcjbm TLVincent maria_hauser Martin8223 tomjad Diego_Prada flbarroso Taguan oceanwind dsmueller fisherp semin MarcoAlvarez kumar_physics References for 3DSim paper LamBras RamuAnandakrishnan nlapalu reyez nigham lillekatt thaliana dimka kuhn jwm vavi bicko itmeson dgront caporaso condon aengisch debatebob massivemayhem gisle girschick selrac Radiation_Damage Stressosome biomedical-nlp beta tji higueruelo boris_aguilar sebk timg
	The Amber biomolecular simulation programs. [My Copy] Journal of computational chemistry, Vol. 26, No. 16. (December 2005), pp. 1668-1688. by David A. Case, Thomas E. Cheatham, Tom Darden, et al.Holger Gohlke, Ray Luo, Kenneth M. Merz, Alexey Onufriev, Carlos Simmerling, Bing Wang, Robert J. Woods posted by 22 people krapnik csrocha nickolay mmuecke flbarroso charris5 pavanghatty tahereh62 lna jwm ttjoseph xdeupi tovrstra bilab Radiation_Damage Stressosome LabCompMed RamuAnandakrishnan IrinaMoreira adilson_mohr mikaellund gisle
	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
	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
	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
	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
	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
	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
	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
	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
	Principles of docking: An overview of search algorithms and a guide to scoring functions. [My Copy] Proteins, Vol. 47, No. 4. (1 June 2002), pp. 409-443. by Inbal Halperin, Buyong Ma, Haim Wolfson, Ruth Nussinov posted by 30 people rabio ucbcjbm flbarroso csrocha Structural Biology Group TorVergata oteri timg dgruiz cantupaz apaydin bicko chad_davis yongzhao ttjoseph nickolay ima sangeetha dgront blackbart gane5h mmuecke kazemi bpagano massivemayhem cjeans Bioinformatics TSRI_MGL insilicodrug Evangelia nigham
	Molecular dynamics and protein function. [My Copy] Proc Natl Acad Sci U S A, Vol. 102, No. 19. (10 May 2005), pp. 6679-6685. by M. Karplus, J. Kuriyan posted by 6 people flbarroso onufriev apaydin bilab allmensch RamuAnandakrishnan
	Implicit Solvent Electrostatics in Biomolecular Simulation [My Copy] New Algorithms for Macromolecular Simulation (2006), pp. 263-295. by Nathan Baker, Donald Bashford, David Case posted by 7 people flbarroso Scis0000002 dmitry_s_yershov stephenbond sunhwan onufriev qwermish
	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
	Very fast empirical prediction and rationalization of protein pK<SUB><FONT SIZE='-1'>a</FONT></SUB> values [My Copy] Proteins: Structure, Function, and Bioinformatics, Vol. 61, No. 4. (1 December 2005), pp. 704-721. by Hui Li, Andrew D. Robertson, Jan H. Jensen posted by 11 people flbarroso Martin8223 franklu310 RamuAnandakrishnan gisle bicko sim82 barry Bioinformatics sunhwan mschofie
	Continuum Electrostatic Energies of Macromolecules in Aqueous Solutions [My Copy] The Journal of Physical Chemistry A, Vol. 101, No. 43. (1 October 1997), pp. 8098-8106. by Marco Scarsi, Joannis Apostolakis, Amedeo Caflisch posted by 4 people flbarroso dmitry_s_yershov onufriev RamuAnandakrishnan
	Ten thousand interactions for the molecular biologist [My Copy] Nature Biotechnology, Vol. 22, No. 10. (06 October 2004), pp. 1317-1321. by Patrick Aloy, Robert B. Russell posted by 17 people krapnik ucbcjbm flbarroso mikaellund baaden jwm bicko chad_davis dullhunk dgront drastic ruvido Radiation_Damage Stressosome Evangelia higueruelo timg
	Benchmarking pKa Prediction Methods for Residues in Proteins [My Copy] Journal of Chemical Theory and Computation, Vol. 4, No. 6. (1 June 2008), pp. 951-966. by Courtney L. Stanton, Kendall N. Houk posted by 6 people scampos flbarroso franklu310 onufriev sobolevnrm baker-group
	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
	Free energy landscape of protein folding in water: Explicit vs. implicit solvent [My Copy] Proteins: Structure, Function, and Genetics, Vol. 53, No. 2. (2003), pp. 148-161. by Ruhong Zhou posted by 6 people chemrahul82 flbarroso choonpeng RamuAnandakrishnan onufriev msuarezdiez
	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
	Electrostatics calculations: latest methodological advances. [My Copy] Current opinion in structural biology, Vol. 16, No. 2. (13 April 2006), pp. 142-151. by Patrice Koehl posted by 8 people oteri r2s2 flbarroso LamBras BragilMassoud qwermish RamuAnandakrishnan jteyra
	Charge asymmetries in hydration of polar solutes. [My Copy] The journal of physical chemistry. B, Vol. 112, No. 8. (28 February 2008), pp. 2405-2414. by D. L. Mobley, A. E. Barber, C. J. Fennell, K. A. Dill posted by 6 people flbarroso sobolevnrm baker-group onufriev dmobley middledomain
	Pathways to a protein folding intermediate observed in a 1-microsecond simulation in aqueous solution. [My Copy] Science (New York, N.Y.), Vol. 282, No. 5389. (23 October 1998), pp. 740-744. by Y. Duan, P. A. Kollman posted by 7 people flbarroso doktornoe Diego_Prada j3xucite allmensch RamuAnandakrishnan choonpeng
	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
	Solvent reaction field potential inside an uncharged globular protein: A bridge between implicit and explicit solvent models? [My Copy] The Journal of Chemical Physics, Vol. 127, No. 15. (2007) by David S. Cerutti, Nathan A. Baker, Andrew J. Mccammon posted by 4 people flbarroso sobolevnrm baker-group onufriev
	Classical electrostatics in biology and chemistry. [My Copy] Science (New York, N.Y.), Vol. 268, No. 5214. (26 May 1995), pp. 1144-1149. by B. Honig, A. Nicholls posted by 5 people onufriev dmitry_s_yershov stephenbond flbarroso apostola
	Progress in Modeling of Protein Structures and Interactions [My Copy] Science, Vol. 310, No. 5748. (28 October 2005), pp. 638-642. by Ora Schueler-Furman, Chu Wang, Phil Bradley, Kira Misura, David Baker posted by 22 people krapnik rabio ucbcjbm paddydu flbarroso thaliana jwm vavi bicko KyuhoLee marcius eweaver tny nickolay dgront rsantana mirzazadeh insectopalo BioinfoCIPF SGU-CIPF barry structural_bioinformatics
	A reappraisal of what we have learnt during three decades of computer simulations on water [My Copy] Journal of Molecular Liquids In Molecular Liquids. Water at the New Millenium, Vol. 101, No. 1-3. (November 2002), pp. 219-260. by Bertrand Guillot posted by 6 people pavanghatty flbarroso loison ruvido softsimu onufriev
	Macromolecular Modeling with Rosetta [My Copy] Annual Review of Biochemistry, Vol. 77, No. 1. (2008), pp. 363-382. by Rhiju Das, David Baker posted by 10 people bmduggan choonpeng mijam kgutwin carlk phoenixzxl krapnik flbarroso saunders gisle
	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
	Protein families and their evolution-a structural perspective. [My Copy] Annu Rev Biochem, Vol. 74 (2005), pp. 867-900. by C. A. Orengo, J. M. Thornton posted by 25 people ucbcjbm flbarroso kumar_physics yuslinaz ssgong ana barry tjimenez jwm chad_davis Einat Schmidtc marcius sriram_s ezotenko redelings medic0747 structural_bioinformatics Radiation_Damage Stressosome Bioinformatics BioinfoCIPF SGU-CIPF nigham sim82
	D<FONT SIZE='-2'>OCKGROUND</FONT> system of databases for protein recognition studies: Unbound structures for docking [My Copy] Proteins: Structure, Function, and Bioinformatics, Vol. 9999, No. 9999. (2007), NA. by Ying Gao, Dominique Douguet, Andrey Tovchigrechko, Ilya A. Vakser posted by 6 people flbarroso marti bicko chad_davis RamuAnandakrishnan timg
	An implicit membrane generalized born theory for the study of structure, stability, and interactions of membrane proteins. [My Copy] Biophysical journal, Vol. 85, No. 5. (November 2003), pp. 2900-2918. by W. Im, M. Feig, C. L. Brooks posted by 3 people flbarroso onufriev dimka
	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
	On the pH dependence of protein stability. [My Copy] Journal of molecular biology, Vol. 231, No. 2. (20 May 1993), pp. 459-474. by A. S. Yang, B. Honig posted by 5 people onufriev scampos flbarroso cat_worth structural_bioinformatics
	Ten-microsecond MD simulation of a fast-folding WW domain [My Copy] Biophys. J. (13 March 2008), biophysj.108.131565. by Peter L. Freddolino, Feng Liu, Martin H. Gruebele, Klaus Schulten posted by 9 people r2s2 flbarroso doktornoe RamuAnandakrishnan paulschlesinger skoch3 Koch_Lab samjlord biehl
	SCOWLP: a web-based database for detailed characterization and visualization of protein interfaces. [My Copy] BMC Bioinformatics, Vol. 7, No. 1. (2 March 2006) by Joan Teyra, Andreas Doms, Michael Schroeder, M Teresa T. Pisabarro posted by 12 people timg flbarroso HawkinsJohnC higueruelo jwm bicko chad_davis choonpeng Radiation_Damage Stressosome jteyra Lombardo_7
	Electric fields at the active site of an enzyme: direct comparison of experiment with theory. [My Copy] Science (New York, N.Y.), Vol. 313, No. 5784. (14 July 2006), pp. 200-204. by Ian T. Suydam, Christopher D. Snow, Vijay S. Pande, Steven G. Boxer posted by 6 people onufriev charris5 flbarroso mikaellund jbchang kjell
	A graph-theory algorithm for rapid protein side-chain prediction. [My Copy] Protein Sci, Vol. 12, No. 9. (September 2003), pp. 2001-2014. by A. A. Canutescu, A. A. Shelenkov, R. L. Dunbrack posted by 12 people oceanwind mcbla karbak nigham bicko blackbart bluvsh1 rsantana mijam jwm carlk newton1234
	Integrated Modeling Program, Applied Chemical Theory (IMPACT). [My Copy] Journal of computational chemistry, Vol. 26, No. 16. (December 2005), pp. 1752-1780. by Jay L. Banks, Hege S. Beard, Yixiang Cao, et al.Art E. Cho, Wolfgang Damm, Ramy Farid, Anthony K. Felts, Thomas A. Halgren, Daniel T. Mainz, Jon R. Maple, Robert Murphy, Dean M. Philipp, Matthew P. Repasky, Linda Y. Zhang, Bruce J. Berne, Richard A. Friesner, Emilio Gallicchio, Ronald M. Levy posted by 3 people oteri flbarroso onufriev
	Converging free energy estimates: MM-PB(GB)SA studies on the protein-protein complex Ras-Raf. [My Copy] Journal of computational chemistry, Vol. 25, No. 2. (30 January 2004), pp. 238-250. by H. Gohlke, D. A. Case posted by 4 people flbarroso bmduggan onufriev lillekatt
	Conformational changes associated with protein-protein interactions [My Copy] Current Opinion in Structural Biology, Vol. 14, No. 1. (February 2004), pp. 104-109. by Chern-Sing Goh, Duncan Milburn, Mark Gerstein posted by 6 people flbarroso LamBras boris_aguilar apaydin bicko nigham
	Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features [My Copy] Biopolymers, Vol. 22, No. 12. (December 1983), pp. 2577-2637. by Wolfgang Kabsch, Christian Sander posted by 33 people barmak7282 Vadikus j3xucite scampos TLVincent maria_hauser pablocarb rpetrenko carlosjavierna mijam wqia007 dsmueller niallhaslam saunders jwm sebk Diego_Prada pjcite kaarsinogen lna chad_davis wouterboomsma penka ffranca dgront choonpeng rabio gisle medic0747 martainn chgjb mschofie marti
	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
	Improving the Continuum Dielectric Approach to Calculating pKas of Ionizable Groups in Proteins [My Copy] J. Phys. Chem., Vol. 100, No. 43. (24 October 1996), pp. 17373-17387. by E. Demchuk, R. C. Wade posted by 3 people flbarroso sim82 RamuAnandakrishnan
	Electrostatics of Ligand Binding: Parametrization of the Generalized Born Model and Comparison with the Poisson−Boltzmann Approach [My Copy] The Journal of Physical Chemistry B, Vol. 110, No. 18. (1 May 2006), pp. 9304-9313. by Hao-Yang Liu, Xiaoqin Zou posted by 3 people nickolay flbarroso onufriev
	Areas, Volumes, Packing, and Protein Structure [My Copy] Annual Review of Biophysics and Bioengineering, Vol. 6, No. 1. (1977), pp. 151-176. by F. M. Richards posted by 5 people scampos flbarroso Lombardo_7 sobolevnrm baker-group
	MCCE2: Improving protein p<I>K</I><SUB><FONT SIZE='-1'>a</FONT></SUB> calculations with extensive side chain rotamer sampling [My Copy] Journal of Computational Chemistry, Vol. 30, No. 14. (2009), pp. 2231-2247. by Yifan Song, Junjun Mao, M. R. Gunner posted by 5 people girayenkavi flbarroso baker-group sobolevnrm RamuAnandakrishnan
	Electrostatic Properties of Protein-Protein Complexes [My Copy] Biophysical Journal, Vol. 91, No. 5. (01 September 2006), pp. 1724-1736. by P. Kundrotas, E. Alexov posted by 2 people flbarroso RamuAnandakrishnan
	Molecular determinants of the p<I>K</I><SUB><FONT SIZE='-1'>a</FONT></SUB> values of Asp and Glu residues in staphylococcal nuclease [My Copy] Proteins: Structure, Function, and Bioinformatics, Vol. 9999, No. 9999. (2009), NA. by Carlos A. Castañeda, Carolyn A. Fitch, Ananya Majumdar, Victor Khangulov, Jamie L. Schlessman, Bertrand E. García-Moreno posted by 3 people flbarroso RamuAnandakrishnan sobolevnrm
	Structural origins of pH and ionic strength effects on protein stability. Acid denaturation of sperm whale apomyoglobin. [My Copy] Journal of molecular biology, Vol. 237, No. 5. (15 April 1994), pp. 602-614. by A. S. Yang, B. Honig posted by 4 people flbarroso cat_worth structural_bioinformatics onufriev
	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
	The generalized Born/volume integral implicit solvent model: Estimation of the free energy of hydration using London dispersion instead of atomic surface area [My Copy] Journal of Computational Chemistry, Vol. 9999, No. 9999. (2008), NA. by Paul Labute posted by 8 people onufriev sobolevnrm baker-group RamuAnandakrishnan middledomain sunhwan dmobley GermanErlenkamp
	CATH--a hierarchic classification of protein domain structures. [My Copy] Structure (London, England : 1993), Vol. 5, No. 8. (15 August 1997), pp. 1093-1108. by C. A. Orengo, A. D. Michie, S. Jones, D. T. Jones, M. B. Swindells, J. M. Thornton posted by 19 people ucbcjbm flbarroso kumar_physics semin sebk tjimenez dimka jwm chad_davis Einat caporaso structural_bioinformatics Radiation_Damage Stressosome biomedical-nlp massivemayhem sim82 jteyra gulkur
	Importance of accurate charges in molecular docking: Quantum mechanical/molecular mechanical (QM/MM) approach [My Copy] Journal of Computational Chemistry, Vol. 26, No. 9. (2005), pp. 915-931. by Art E. Cho, Victor Guallar, Bruce J. Berne, Richard Friesner posted by 5 people mijam flbarroso boris_aguilar qaiser_fatmi Chang group
	Accurate solution of multi-region continuum biomolecule electrostatic problems using the linearized Poisson-Boltzmann equation with curved boundary elements. [My Copy] Journal of computational chemistry, Vol. 30, No. 1. (15 January 2009), pp. 132-153. by M. D. Altman, J. P. Bardhan, J. K. White, B. Tidor posted by 2 people flbarroso RamuAnandakrishnan
	Multiscale methods for macromolecular simulations [My Copy] Current Opinion in Structural Biology, Vol. 18, No. 5. (October 2008), pp. 630-640. by P. Sherwood, B. Brooks, M. Sansom posted by 8 people jonathancooper xavierprat flbarroso carlk aqeel choonpeng McCammon jmccammon
	Structural systems biology: modelling protein interactions. [My Copy] Nature reviews. Molecular cell biology, Vol. 7, No. 3. (March 2006), pp. 188-197. by Patrick Aloy, Robert B. Russell posted by 28 people flbarroso timg chica Scis0000002 ubcg08l ana aalibes bicko xico dgront drastic choonpeng henschel ruvido massivemayhem cat_worth fishtank iris_2001 gvuister lpfernandes structural_bioinformatics Bioinformatics WetBiology Evangelia andreas_foersch higueruelo chad_davis jteyra
	Solvation forces on biomolecular structures: A comparison of explicit solvent and Poisson-Boltzmann models [My Copy] Journal of Computational Chemistry, Vol. 25, No. 13. (2004), pp. 1623-1629. by Jason Wagoner, Nathan A. Baker posted by 3 people flbarroso onufriev qwermish
	Proton Binding to Proteins: pKa Calculations with Explicit and Implicit Solvent Models [My Copy] Journal of the American Chemical Society, Vol. 126, No. 13. (1 April 2004), pp. 4167-4180. by Thomas Simonson, Jens Carlsson, David A. Case posted by 7 people fralium flbarroso 6rheology sobolevnrm baker-group RamuAnandakrishnan dmobley
	Critical importance of length-scale dependence in implicit modeling of hydrophobic interactions. [My Copy] Journal of the American Chemical Society, Vol. 129, No. 9. (7 March 2007), pp. 2444-2445. by J. Chen, C. L. Brooks posted by 2 people flbarroso onufriev
	Calculation of absolute protein-ligand binding free energy using distributed replica sampling. [My Copy] The Journal of chemical physics, Vol. 129, No. 15. (21 October 2008) by T. Rodinger, P. L. Howell, R. Pomès posted by 3 people flbarroso onufriev kentsis
	Can a continuum solvent model reproduce the free energy landscape of a beta -hairpin folding in water? [My Copy] Proceedings of the National Academy of Sciences, Vol. 99, No. 20. (1 October 2002), pp. 12777-12782. by Ruhong Zhou, Bruce J. Berne posted by 2 people flbarroso onufriev
	Comparison of multiple Amber force fields and development of improved protein backbone parameters. [My Copy] Proteins, Vol. 65, No. 3. (15 November 2006), pp. 712-725. by Viktor Hornak, Robert Abel, Asim Okur, Bentley Strockbine, Adrian Roitberg, Carlos Simmerling posted by 11 people arnaucordomi Vadikus bmduggan baaden lna allmensch choonpeng kazemi barry GermanErlenkamp RamuAnandakrishnan
	Protein-ligand docking: Current status and future challenges. [My Copy] Proteins (21 July 2006) by Sérgio Filipe F. Sousa, Pedro Alexandrino A. Fernandes, Maria João J. Ramos posted by 13 people flbarroso ramensky BragilMassoud yongzhao peprovy kazemi sergio_fms carlescorbi TSRI_MGL robert boris_aguilar qaiser_fatmi Chang group
	Generalized born models of macromolecular solvation effects. [My Copy] Annual review of physical chemistry, Vol. 51, No. 1. (2000), pp. 129-152. by D. Bashford, D. A. Case posted by 5 people oteri ras flbarroso dgront RamuAnandakrishnan
	The protein folding problem: when will it be solved? [My Copy] Curr Opin Struct Biol (13 June 2007) by Ken A A. Dill, S Banu B. Ozkan, Thomas R R. Weikl, John D D. Chodera, Vincent A A. Voelz posted by 9 people flbarroso onufriev wouterboomsma cat_worth cactus Jporci cdeane kalicuta sebk
	FACTS: Fast analytical continuum treatment of solvation. [My Copy] Journal of computational chemistry, Vol. 29, No. 5. (15 April 2008), pp. 701-715. by U. Haberthür, A. Caflisch posted by 3 people flbarroso onufriev apostola
	Comparative Study of Generalized Born Models: Born Radii and Peptide Folding [My Copy] The Journal of Physical Chemistry B, Vol. 109, No. 7. (1 February 2005), pp. 3008-3022. by Jiang Zhu, Emil Alexov, Barry Honig posted by 4 people jjurban flbarroso Vadikus onufriev
	Application of the frozen atom approximation to the GB/SA continuum model for solvation free energy. [My Copy] Journal of computational chemistry, Vol. 23, No. 2. (30 January 2002), pp. 214-221. by O. Guvench, J. Weiser, P. Shenkin, I. Kolossváry, W. C. Still posted by 2 people flbarroso onufriev
	A simple physical model for binding energy hot spots in proteinâprotein complexes [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 99, No. 22. (29 October 2002), pp. 14116-14121. by Tanja Kortemme, David Baker posted by 10 people chemrahul82 onufriev oceanwind lna jwm bicko cjeans hmk skoddet Nielsen group
	Deciphering Protein–Protein Interactions. Part I. Experimental Techniques and Databases [My Copy] PLoS Comput Biol, Vol. 3, No. 3. (30 March 2007), e42. by Benjamin A. Shoemaker, Anna R. Panchenko posted by 13 people colmryan chica flbarroso kiekyon semin giovenko Yanno IbnBio zwang Evangelia carlk higueruelo ethkim
	Theory and applications of the generalized born solvation model in macromolecular simulations [My Copy] Biopolymers, Vol. 56, No. 4. (4 December 2000), pp. 275-291. by Vickie Tsui, David A. Case posted by 6 people Vadikus oteri flbarroso Lombardo_7 ttjoseph RamuAnandakrishnan
	Prediction of protein side-chain rotamers from a backbone-dependent rotamer library: a new homology modeling tool [My Copy] Journal of Molecular Biology, Vol. 267, No. 5. (18 April 1997), pp. 1268-1282. by M. Bower posted by 8 people carlosjavierna kaarsinogen nknii blackbart TCR_Signaling mijam jwm carlk
	A hierarchy of timescales in protein dynamics is linked to enzyme catalysis [My Copy] Nature (18 November 2007) by Katherine A. Henzler-Wildman, Ming Lei, Vu Thai, Jordan S. Kerns, Martin Karplus, Dorothee Kern posted by 11 people Diego_Prada ruvido tmmurali allmensch cactus sobolevnrm jlh64 baker-group RamuAnandakrishnan dmobley chenway
	Molecular dynamics simulations of biomolecules: long-range electrostatic effects. [My Copy] Annu Rev Biophys Biomol Struct, Vol. 28 (1999), pp. 155-179. by C. Sagui, T. A. Darden posted by 9 people Scis0000002 babakap onufriev lillekatt ttjoseph dgront RamuAnandakrishnan AndreaColetta r2s2
	Bayesian statistical analysis of protein side-chain rotamer preferences. [My Copy] Protein Sci, Vol. 6, No. 8. (August 1997), pp. 1661-1681. by R. L. Dunbrack, F. E. Cohen posted by 15 people MuraLab karbak nknii j3xucite dgront blackbart kazemi rsantana hmk TCR_Signaling LamBras mijam jwm phoenixzxl zwang
	Flexible protein-protein docking [My Copy] Current Opinion in Structural Biology In Theory and simulation/Macromolecular assemblages - Joel Janin and Michael Levitt/Edward H Egelman and Andrew GW Leslie, Vol. 16, No. 2. (April 2006), pp. 194-200. by Alexandre M. J. J. Bonvin posted by 15 people timg flbarroso oteri laurabailey dgruiz aqeel bicko yongzhao ima sangeetha gloria Bioinformatics TSRI_MGL insilicodrug higueruelo
	High-resolution protein-protein docking [My Copy] Current Opinion in Structural Biology In Theory and simulation/Macromolecular assemblages - Joel Janin and Michael Levitt/Edward H Egelman and Andrew GW Leslie, Vol. 16, No. 2. (April 2006), pp. 183-193. by Jeffrey J. Gray posted by 8 people flbarroso aqeel jwm ima bluvsh1 ruvido cjeans higueruelo
	Improved side-chain modeling for protein-protein docking. [My Copy] Protein Sci, Vol. 14, No. 5. (May 2005), pp. 1328-1339. by C. Wang, O. Schueler-Furman, D. Baker posted by 15 people dgront csrocha barry aqeel jwm bicko yongzhao blackbart bluvsh1 hmk selrac structural_bioinformatics Bioinformatics TSRI_MGL Evangelia
	Large-Scale Molecular Dynamics Simulations of Self-Assembling Systems [My Copy] Science, Vol. 321, No. 5890. (8 August 2008), pp. 798-800. by Michael L. Klein, Wataru Shinoda posted by 8 people flbarroso cjryan abebe skumagai zwang pbartlett dgront middledomain
	Molecular dynamics simulations of biomolecules. [My Copy] Nat Struct Biol, Vol. 9, No. 9. (September 2002), pp. 646-652. by M. Karplus, J. A. McCammon posted by 9 people saravan yxue onufriev adilson_mohr yalexeev baaden aqeel RamuAnandakrishnan LamBras
	Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome [My Copy] Science, Vol. 326, No. 5950. (9 October 2009), pp. 289-293. by Erez Lieberman-Aiden, Nynke L. van Berkum, Louise Williams, et al.Maxim Imakaev, Tobias Ragoczy, Agnes Telling, Ido Amit, Bryan R. Lajoie, Peter J. Sabo, Michael O. Dorschner, Richard Sandstrom, Bradley Bernstein, M. A. Bender, Mark Groudine, Andreas Gnirke, John Stamatoyannopoulos, Leonid A. Mirny, Eric S. Lander, Job Dekker posted by 35 people pmcarlton alhufton psique qayub chvlyl TorstenWaldminghaus kintoki Garamonfok inesdesantiago NickFurnham DrRichardBadge roys rdiaz daveGerrard colinveal frohike nrk891 zwang timflutre afenley kshameer JLab BergmanLab polivares mgatmedsci diamantis flbarroso jdoconnell fenghezi daforerog bpcusack gjuggler Journal picks gdb gbloeb
	HOW WELL CAN SIMULATION PREDICT PROTEIN FOLDING KINETICS AND THERMODYNAMICS? [My Copy] Annual Review of Biophysics and Biomolecular Structure, Vol. 34, No. 1. (29 October 2005), pp. 43-69. by Christopher D. Snow, Eric J. Sorin, Young M. Rhee, Vijay S. Pande posted by 10 people amphibina flbarroso Diego_Prada doktornoe dgront blackbart allmensch saunders evanse toerst
	Combining docking and molecular dynamic simulations in drug design. [My Copy] Med Res Rev (6 June 2006) by Hernán Alonso, Andrey A A. Bliznyuk, Jill E E. Gready posted by 11 people karinaecomp flbarroso hryk Structural Biology Group TorVergata oteri A_Coletta_Thesis aqeel yongzhao kazemi TSRI_MGL LamBras
	Structure validation by Calpha geometry: &phis;,psi and Cbeta deviation [My Copy] Proteins: Structure, Function, and Genetics, Vol. 50, No. 3. (15 February 2003), pp. 437-450. by Simon C. Lovell, Ian W. Davis, W. Bryan Arendall, et al.Paul I. W. de Bakker, J. Michael Word, Michael G. Prisant, Jane S. Richardson, David C. Richardson posted by 12 people Diego_Prada bmduggan aqeel jwm robert dgront xiaobeizhao martainn Radiation_Damage Stressosome mijam pavanghatty
	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
	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 20 people saravan Diego_Prada xdeupi viktor21614 ruvido barry pavanghatty chad_davis allmensch choonpeng rsantana cjeans sobolevnrm baker-group wilbur mijam kjell phoenixzxl higueruelo GeeSharpMinor
	Dielectric relaxation in proteins: the computational perspective. [My Copy] Photosynthesis research (29 April 2008) by Thomas Simonson posted by 5 people flbarroso chiufanlee dimka sobolevnrm baker-group
	Linking folding with aggregation in Alzheimer's beta-amyloid peptides [My Copy] Proceedings of the National Academy of Sciences, Vol. 104, No. 43. (23 October 2007), pp. 16880-16885. by Jana Khandogin, Charles L. Brooks posted by 5 people scampos Diego_Prada onufriev sobolevnrm baker-group
	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
	Recent advances in the development and application of implicit solvent models in biomolecule simulations [My Copy] Current Opinion in Structural Biology, Vol. 14, No. 2. (April 2004), pp. 217-224. by M. Feig posted by 9 people flbarroso LamBras apostola ttjoseph marcius gane5h BioinfoCIPF SGU-CIPF RamuAnandakrishnan
	Multiple grid methods for classical molecular dynamics [My Copy] Journal of Computational Chemistry, Vol. 23, No. 6. (2002), pp. 673-684. by Robert D. Skeel, Ismail Tezcan, David J. Hardy posted by 4 people dmitry_s_yershov stephenbond RamuAnandakrishnan r2s2
	Cations as hydrogen bond donors: a view of electrostatic interactions in DNA. [My Copy] Annu Rev Biophys Biomol Struct, Vol. 32 (2003), pp. 27-45. by J. A. Subirana, M. Soler-Lopez posted by 2 people flbarroso Elena_Zubova
	Computational Alanine Scanning of Protein-Protein Interfaces [My Copy] Sci. STKE, Vol. 2004, No. 219. (10 February 2004), pl2. by Tanja Kortemme, David E. Kim, David Baker posted by 15 people chemrahul82 onufriev pablocarb bicko barry sangeetha blackbart joergkurtwegner structural_bioinformatics Bioinformatics Molecular-Modelling Drug-Design Cheminformatics insilicodrug skoddet
	Theory of protein folding. [My Copy] Current opinion in structural biology, Vol. 14, No. 1. (February 2004), pp. 70-75. by José Nelson N. Onuchic, Peter G. Wolynes posted by 7 people siggi84 flbarroso dgront choonpeng rabio allmensch Diego_Prada
	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
	A new test set for validating predictions of protein-ligand interaction. [My Copy] Proteins, Vol. 49, No. 4. (1 December 2002), pp. 457-471. by J. W. Nissink, C. Murray, M. Hartshorn, M. L. Verdonk, J. C. Cole, R. Taylor posted by 6 people flbarroso BragilMassoud yongzhao blackbart ramensky TSRI_MGL
	An electrostatic basis for the stability of thermophilic proteins. [My Copy] Proteins, Vol. 57, No. 1. (1 October 2004), pp. 128-141. by B. N. Dominy, H. Minoux, C. L. Brooks posted by 5 people flbarroso mikaellund jwm Radiation_Damage Stressosome