franklu310's Top Recommendations

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	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 51 people trishul 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
	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
	Incorporating protein conformational flexibility into the calculation of pH-dependent protein properties. [My Copy] Biophysical journal, Vol. 72, No. 5. (May 1997), pp. 2075-2093. by E. G. Alexov, M. R. Gunner posted by 3 people flbarroso sim82 RamuAnandakrishnan
	A Self-Consistent, Microenvironment Modulated Screened Coulomb Potential Approximation to Calculate pH-Dependent Electrostatic Effects in Proteins [My Copy] Biophys. J., Vol. 77, No. 1. (1 July 1999), pp. 3-22. by Ernest L. Mehler, Frank Guarnieri posted by 2 people sim82 RamuAnandakrishnan
	Optimizing pK<SUB><FONT SIZE='-1'>A</FONT></SUB> computation in proteins with pH adapted conformations [My Copy] Proteins: Structure, Function, and Bioinformatics, Vol. 9999, No. 9999. (2007), NA. by Gernot Kieseritzky, Ernst-Walter Knapp posted by 5 people sim82 sobolevnrm baker-group RamuAnandakrishnan boris_aguilar
	Tunneling Electroresistance Effect in Ferroelectric Tunnel Junctions at the Nanoscale [My Copy] Nano Letters, Vol. 9, No. 10. (14 October 2009), pp. 3539-3543. by A. Gruverman, D. Wu, H. Lu, et al.Y. Wang, H. W. Jang, C. M. Folkman, Zhuravlev, D. Felker, M. Rzchowski, C. B. Eom, E. Y. Tsymbal posted by 1 person findroot
	Dynamic Nanoinscribing for Continuous and Seamless Metal and Polymer Nanogratings [My Copy] Nano Letters, Vol. 0, No. 0. (0000) by Se H. Ahn, L. Jay Guo posted by 1 person findroot
	Deformation Measurements on Thin Clay Tactoids [My Copy] Small, Vol. 5, No. 16. (2009), pp. 1816-1820. by Daniel A. Kunz, Eva Max, Richard Weinkamer, Thomas Lunkenbein, Josef Breu, Andreas Fery posted by 1 person findroot
	Controllable Patterning and CVD Growth of Isolated Carbon Nanotubes with Direct Parallel Writing of Catalyst Using Dip-Pen Nanolithography [My Copy] Small, Vol. 9999, No. 9999. (2009), NA. by Irma Kuljanishvili, Dmitriy A. Dikin, Sergey Rozhok, Scott Mayle, Venkat Chandrasekhar posted by 1 person findroot
	After Hard Drives—What Comes Next? [My Copy] Magnetics, IEEE Transactions on, Vol. 45, No. 10. (22 September 2009), pp. 3406-3413. by M. H. Kryder, Chang S. Kim posted by 1 person findroot
	Self-Aligned Nanolithography in a Nanogap [My Copy] Nano Letters, Vol. 9, No. 6. (10 June 2009), pp. 2234-2238. by Yung-Chen Lin, Jingwei Bai, Yu Huang posted by 1 person findroot
	Imaging the Evolution of Nanoscale Photocurrent Collection and Transport Networks during Annealing of Polythiophene/Fullerene Solar Cells [My Copy] Nano Letters, Vol. 9, No. 8. (12 August 2009), pp. 2946-2952. by Liam S. C. Pingree, Obadiah G. Reid, David S. Ginger posted by 1 person findroot
	Mass Sensing Based on Deterministic and Stochastic Responses of Elastically Coupled Nanocantilevers [My Copy] Nano Letters, Vol. 0, No. 0. (0000) by Eduardo Gil-Santos, Daniel Ramos, Anirban Jana, Montserrat Calleja, Arvind Raman, Javier Tamayo posted by 2 people findroot akhuettel
	Electrical Connectivity in Single-Walled Carbon Nanotube Networks [My Copy] Nano Letters, Vol. 0, No. 0. (0000) by Peter N. Nirmalraj, Philip E. Lyons, Sukanta De, Jonathan N. Coleman, John J. Boland posted by 2 people findroot akhuettel
	Polysilicon MEMS accelerometers exposed to shocks: numerical–experimental investigation [My Copy] Journal of Micromechanics and Microengineering, Vol. 19, No. 3. (2009), 035023. by Aldo Ghisi, Stanislaw Kalicinski, Stefano Mariani, Ingrid D. Wolf, Alberto Corigliano posted by 1 person findroot
	Ultrahigh-density phase-change data storage without the use of heating [My Copy] Nature Nanotechnology, Vol. advance online publication (13 September 2009) by Ara Jo, Wonchul Joo, Won-Hyeog Jin, Hyojin Nam, Jin K. Kim posted by 1 person findroot
	Silicon nitride cantilever array integrated with silicon heaters and piezoelectric detectors for probe-based data storage [My Copy] Sensors and Actuators A: Physical, Vol. 134, No. 2. (15 March 2007), pp. 329-333. by H. Nam, Y. Kim, C. Lee, et al.W. Jin, S. Jang, I. Cho, J. Bu, W. Choi, S. Choi posted by 1 person findroot
	Development of magnetic levitated stage for wide area movements [My Copy] Electrical Machines and Systems, 2007. ICEMS. International Conference on In Electrical Machines and Systems, 2007. ICEMS. International Conference on (2007), pp. 1486-1491. by Jeong-Woo Jeon, M. Caraiani, Yong-Joo Kim, Hyeon-Seok Oh, Sung-Shin Kim posted by 1 person findroot
	High-precision control of magnetic levitation system [My Copy] Industrial Electronics Society, 2005. IECON 2005. 31st Annual Conference of IEEE In Industrial Electronics Society, 2005. IECON 2005. 31st Annual Conference of IEEE (2005), 6 pp.. by Jeong-Woo Jeon, Mitica Caraiani, Ki-Chang Lee, et al.Don-Ha Hwang, Joo-Hoon Lee, Yong-Joo Kim, Taek-Kun Nam, Sung-Shin Kim posted by 1 person findroot
	Inside Cover: Writing Self-Erasing Images using Metastable Nanoparticle “Inks” (Angew. Chem. Int. Ed. 38/2009) [My Copy] Angewandte Chemie International Edition, Vol. 48, No. 38. (07 September 2009), pp. 6924-6924. by Rafal Klajn, Paul J Wesson, Kyle J Bishop, Bartosz A Grzybowski posted by 1 person findroot
	Large-Area Roll-to-Roll and Roll-to-Plate Nanoimprint Lithography: A Step toward High-Throughput Application of Continuous Nanoimprinting [My Copy] ACS Nano, Vol. 3, No. 8. (25 August 2009), pp. 2304-2310. by Se H. Ahn, L. Jay Guo posted by 2 people findroot tbenanti
	Parametric Nanomechanical Amplification at Very High Frequency [My Copy] Nano Letters, Vol. 9, No. 9. (9 September 2009), pp. 3116-3123. by R. B. Karabalin, X. L. Feng, M. L. Roukes posted by 2 people findroot akhuettel
	Free-Standing Epitaxial Graphene [My Copy] Nano Letters, Vol. 9, No. 9. (9 September 2009), pp. 3100-3105. by Shriram Shivaraman, Robert A. Barton, Xun Yu, et al.Jonathan Alden, Lihong Herman, M. V. S. Chandrashekhar, Jiwoong Park, Paul L. McEuen, Jeevak M. Parpia, Harold G. Craighead, Michael G. Spencer posted by 2 people findroot kas
	Quantum Dot Light-Emitting Devices with Electroluminescence Tunable over the Entire Visible Spectrum [My Copy] Nano Letters, Vol. 9, No. 7. (8 July 2009), pp. 2532-2536. by Polina O. Anikeeva, Jonathan E. Halpert, Moungi G. Bawendi, Vladimir Bulović posted by 3 people findroot tbenanti julienburgin
	High Local Concentration: A Fundamental Strategy of Life [My Copy] Journal of Molecular Biology (31 October 2009) by Stefan Oehler, Benno Müller-Hill posted by 3 people Orengo Group Journal Picks bdessailly RamuAnandakrishnan
	Coarse Point Charge Models For Proteins From Smoothed Molecular Electrostatic Potentials [My Copy] Journal of Chemical Theory and Computation, Vol. 0, No. 0. (0000) by Laurence Leherte, Daniel P. Vercauteren posted by 2 people middledomain RamuAnandakrishnan
	Correct virial formulation in the isotropic periodic sum method [My Copy] The Journal of Chemical Physics, Vol. 131, No. 16. (2009), 164103. by Iordan H. Hristov, Reginald Paul, Stephen J. Paddison posted by 1 person RamuAnandakrishnan
	Efficient nonbonded interactions for molecular dynamics on a graphics processing unit [My Copy] Journal of Computational Chemistry, Vol. 9999, No. 9999. (2009), NA. by Peter Eastman, Vijay S. Pande posted by 2 people klexa RamuAnandakrishnan
	RNA secondary structure prediction by centroids in a Boltzmann weighted ensemble [My Copy] RNA, Vol. 11, No. 8. (August 2005), pp. 1157-1166. by Y. E. Ding, Chi Y. U. Chan, Charles E. Lawrence posted by 1 person RamuAnandakrishnan
	An image-based reaction field method for electrostatic interactions in molecular dynamics simulations of aqueous solutions [My Copy] The Journal of Chemical Physics, Vol. 131, No. 15. (2009), 154103. by Yuchun Lin, Andrij Baumketner, Shaozhong Deng, Zhenli Xu, Donald Jacobs, Wei Cai posted by 3 people agrossfield dlimmer RamuAnandakrishnan
	Conserving energy during molecular dynamics simulations of water, proteins, and proteins in water [My Copy] Journal of Computational Chemistry, Vol. 11, No. 10. (1990), pp. 1169-1180. by Douglas B. Kitchen, Fumio Hirata, John D. Westbrook, Ronald Levy, David Kofke, Martin Yarmush posted by 1 person RamuAnandakrishnan
	Scaling of Multimillion-Atom Biological Molecular Dynamics Simulation on a Petascale Supercomputer [My Copy] Journal of Chemical Theory and Computation, Vol. 0, No. 0. (0000) by Roland Schulz, Benjamin Lindner, Loukas Petridis, Jeremy C. Smith posted by 2 people r2s2 RamuAnandakrishnan
	Dynamics and function of compact nucleosome arrays. [My Copy] Nature structural & molecular biology, Vol. 16, No. 9. (September 2009), pp. 938-944. by Michael G. Poirier, Eugene Oh, Hannah S. Tims, Jonathan Widom posted by 2 people sebastien_vigneau RamuAnandakrishnan
	Universal Solvation Model Based on the Generalized Born Approximation with Asymmetric Descreening [My Copy] Journal of Chemical Theory and Computation, Vol. 5, No. 9. (8 September 2009), pp. 2447-2464. by Aleksandr V. Marenich, Christopher J. Cramer, Donald G. Truhlar posted by 3 people sobolevnrm RamuAnandakrishnan acpan
	Nucleosome positioning as a determinant of exon recognition [My Copy] Nature Structural & Molecular Biology, Vol. 16, No. 9. (16 August 2009), pp. 996-1001. by Hagen Tilgner, Christoforos Nikolaou, Sonja Althammer, et al.Michael Sammeth, Miguel Beato, Juan Valcarcel, Roderic Guigo posted by 5 people inesdesantiago sebastien_vigneau fenghezi RamuAnandakrishnan aalibes
	Analyses on hydrophobicity and attractiveness of all-atom distance-dependent potentials [My Copy] Protein Science, Vol. 9999, No. 9999. (2009), NA. by Matsuyuki Shirota, Takashi Ishida, Kengo Kinoshita posted by 1 person RamuAnandakrishnan
	Evaluating the Performance of the ff99SB Force Field Based on NMR Scalar Coupling Data [My Copy] Vol. 97, No. 3. (5 August 2009), pp. 853-856. by Lauren Wickstrom, Asim Okur, Carlos Simmerling posted by 1 person RamuAnandakrishnan
	R/BHC: fast Bayesian hierarchical clustering for microarray data [My Copy] BMC Bioinformatics, Vol. 10, No. 1. (6 August 2009), 242. by Richard Savage, Katherine Heller, Yang Xu, et al.Zoubin Ghahramani, William Truman, Murray Grant, Katherine Denby, David Wild posted by 12 people ptrobajo meanerelk nuin rdiaz guhjy Bioinformatics lwaldron rschulz phoenixzxl barriot RamuAnandakrishnan erexhepa
	Improving detection of differentially expressed gene sets by applying cluster enrichment analysis to Gene Ontology [My Copy] BMC Bioinformatics, Vol. 10, No. 1. (5 August 2009), 240. by Tao Xu, JianLei Gu, Yan Zhou, LinFang Du posted by 10 people dipenps rdiaz tonamswish guhjy lwaldron dswan RamuAnandakrishnan barriot kshameer renatomilani
	Stabilization of protein structure by interaction of [alpha]-helix dipole with a charged side chain [My Copy] Nature, Vol. 335, No. 6192. (20 October 1988), pp. 740-743. by Dasa S[breve]ali, Mark Bycroft, Alan R. Fersht posted by 1 person RamuAnandakrishnan
	The conserved, buried aspartic acid in oxidized Escherichia coli thioredoxin has a pKa of 7.5. Its titration produces a related shift in global stability [My Copy] Biochemistry, Vol. 30, No. 30. (1 July 1991), pp. 7603-7609. by Knut Langsetmo, James A. Fuchs, Clare Woodward posted by 1 person RamuAnandakrishnan
	Linkage of thioredoxin stability to titration of ionizable groups with perturbed pKa [My Copy] Biochemistry, Vol. 30, No. 30. (1 July 1991), pp. 7609-7614. by Knut Langsetmo, James A. Fuchs, Clare Woodward, Kim A. Sharp posted by 1 person RamuAnandakrishnan
	Nucleosomal fluctuations govern the transcription dynamics of RNA polymerase II. [My Copy] Science (New York, N.Y.), Vol. 325, No. 5940. (31 July 2009), pp. 626-628. by Courtney Hodges, Lacramioara Bintu, Lucyna Lubkowska, Mikhail Kashlev, Carlos Bustamante posted by 10 people sebastien_vigneau Koch_Lab skoch3 emptyhb jbhiatt pkner absterga leliavski TRHvidsten RamuAnandakrishnan
	CLEAN: CLustering Enrichment ANalysis [My Copy] BMC Bioinformatics, Vol. 10, No. 1. (29 July 2009), 234. by Johannes Freudenberg, Vineet Joshi, Zhen Hu, Mario Medvedovic posted by 10 people zufar brianb nuin rdiaz dswan guhjy frohike RamuAnandakrishnan barriot renatomilani
	Molecular dynamics simulation exploration of cooperative migration mechanism of calcium ions in sarcoplasmic reticulum Ca<SUP><FONT SIZE='-1'>2+</FONT></SUP>-ATPase [My Copy] Journal of Computational Chemistry, Vol. 30, No. 13. (2009), pp. 2136-2145. by Yongqi Huang, Huifang Li, Yuxiang Bu posted by 1 person RamuAnandakrishnan
	The conserved, buried aspartic acid in oxidized Escherichia coli thioredoxin has a pKa of 7.5. Its titration produces a related shift in global stability. [My Copy] Biochemistry, Vol. 30, No. 30. (30 July 1991), pp. 7603-7609. by K. Langsetmo, J. A. Fuchs, C. Woodward posted by 1 person RamuAnandakrishnan
	Protein folding roller coaster, one molecule at a time [My Copy] Proceedings of the National Academy of Sciences, Vol. 106, No. 29. (21 July 2009), pp. 11823-11824. by Eugene Shakhnovich posted by 2 people RamuAnandakrishnan 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
	Error statistics of hidden Markov model and hidden Boltzmann model results [My Copy] BMC Bioinformatics, Vol. 10, No. 1. (2009), 212. by Lee Newberg posted by 3 people rdiaz erexhepa RamuAnandakrishnan
	Kinking Occurs during Molecular Dynamics Simulations of Small DNA Minicircles [My Copy] Vol. 14, No. 10. (1 October 2006), pp. 1527-1534. by Filip Lankaa, Richard Lavery, John H. Maddocks posted by 1 person RamuAnandakrishnan
	An <I>N</I> log <I>N</I> approximation based on the natural organization of biomolecules for speeding up the computation of long range interactions [My Copy] Journal of Computational Chemistry, Vol. 9999, No. 9999. (2009), NA. by Ramu Anandakrishnan, Alexey V. Onufriev posted by 2 people sobolevnrm RamuAnandakrishnan
	Fourier transform convolution integrals applied to generalized Born molecular volume [My Copy] Journal of Computational Chemistry, Vol. 9999, No. 9999. (2009), NA. by Thierry Schüpbach, Vincent Zoete, Brice Tsakam-Sotché, Olivier Michielin posted by 1 person 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
	Algorithmic design of self-assembling structures [My Copy] Proceedings of the National Academy of Sciences, Vol. 106, No. 24. (16 June 2009), pp. 9570-9575. by Henry Cohn, Abhinav Kumar posted by 4 people ajholanda Scis0000002 RamuAnandakrishnan mstumpf
	Integrated Assessment of Genomic Correlates of Protein Evolutionary Rate [My Copy] PLoS Comput Biol, Vol. 5, No. 6. (12 June 2009), e1000413. by Yu Xia, Eric A. Franzosa, Mark B. Gerstein posted by 10 people aprasad chica biomcgary gjuggler Journal picks kiekyon michaelbarton djkt RamuAnandakrishnan bpcusack
	Converging concepts of protein folding in vitro and in vivo [My Copy] Nature Structural & Molecular Biology, Vol. 16, No. 6. (03 June 2009), pp. 574-581. by F. Ulrich Hartl, Manajit Hayer-Hartl posted by 7 people bratwurst skywalkerus02 siggi84 scampos melo_mcr reyez RamuAnandakrishnan
	Assessment of biomolecular force fields for molecular dynamics simulations in a protein crystal [My Copy] Journal of Computational Chemistry, Vol. 9999, No. 9999. (2009), NA. by Zhongqiao Hu, Jianwen Jiang posted by 1 person RamuAnandakrishnan
	Energetic coupling between DNA bending and base pair opening [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 85, No. 19. (October 1988), pp. 7231-7235. by J. Ramstein, R. Lavery posted by 1 person RamuAnandakrishnan
	pH-Dependent Mechanism of Nitric Oxide Release in Nitrophorins 2 and 4 [My Copy] The Journal of Physical Chemistry B, Vol. 113, No. 4. (29 January 2009), pp. 1192-1201. by Jason M. Swails, Yilin Meng, Ann F. Walker, Marcelo A. Marti, Dario A. Estrin, Adrian E. Roitberg posted by 1 person RamuAnandakrishnan
	Native secondary structure topology has near minimum contact energy among all possible geometrically constrained topologies [My Copy] Proteins: Structure, Function, and Bioinformatics, Vol. 9999, No. 9999. (2009), NA. by Weitao Sun, Jing He posted by 3 people Orengo Group Journal Picks AliC RamuAnandakrishnan
	Single-molecule force spectroscopy reveals a highly compliant helical folding for the 30-nm chromatin fiber [My Copy] Nature Structural & Molecular Biology, Vol. 16, No. 5. (19 April 2009), pp. 534-540. by Maarten Kruithof, Fan-Tso Chien, Andrew Routh, Colin Logie, Daniela Rhodes, John van Noort posted by 2 people ramalldf RamuAnandakrishnan
	Dynamic folding pathway models of the villin headpiece subdomain (HP-36) structure [My Copy] Journal of Computational Chemistry, Vol. 9999, No. 9999. (2009), NA. by In-Ho Lee, Seung-Yeon Kim, Jooyoung Lee posted by 1 person RamuAnandakrishnan
	Free energy simulations reveal a double mutant avian H5N1 virus hemagglutinin with altered receptor binding specificity [My Copy] Journal of Computational Chemistry, Vol. 30, No. 11. (27 August 2009), pp. 1654-1663. by Payel Das, Jingyuan Li, Ajay K. Royyuru, Ruhong Zhou posted by 4 people RamuAnandakrishnan oceanwind idoerg zwang
	The universal distribution of evolutionary rates of genes and distinct characteristics of eukaryotic genes of different apparent ages [My Copy] Proceedings of the National Academy of Sciences (7 April 2009) by Yuri I. Wolf, Pavel S. Novichkov, Georgy P. Karev, Eugene V. Koonin, David J. Lipman posted by 6 people RamuAnandakrishnan deanmalmgren jjray gjuggler FAB-lab rvosa
	Assignment of polar states for protein amino acid residues using an interaction cluster decomposition algorithm and its application to high resolution protein structure modeling [My Copy] Proteins: Structure, Function, and Bioinformatics, Vol. 66, No. 4. (2007), pp. 824-837. by Xin Li, Matthew P. Jacobson, Kai Zhu, Suwen Zhao, Richard A. Friesner posted by 1 person RamuAnandakrishnan
	Automated site preparation in physics-based rescoring of receptor ligand complexes. [My Copy] Proteins, Vol. 77, No. 1. (October 2009), pp. 52-61. by Chaya S. Rapp, Cheryl Schonbrun, Matthew P. Jacobson, Chakrapani Kalyanaraman, Niu Huang posted by 5 people oteri klexa McCammon jmccammon RamuAnandakrishnan
	Unorthodox uses of Bennett's acceptance ratio method [My Copy] Journal of Computational Chemistry, Vol. 9999, No. 9999. (2009), NA. by Gerhard König, Stefan Bruckner, Stefan Boresch posted by 3 people ssomani agrossfield RamuAnandakrishnan
	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
	Correcting mesh-based force calculations to conserve both energy and momentum in molecular dynamics simulations [My Copy] Journal of Computational Physics, Vol. 225, No. 1. (01 July 2007), pp. 1-5. by R. Skeel, D. Hardy, J. Phillips posted by 2 people RamuAnandakrishnan dmitry_s_yershov
	CUSA and CUDE: GPU-Accelerated Methods for Estimating Solvent Accessible Surface Area and Desolvation [My Copy] Journal of Computational Biology, Vol. 16, No. 4. (2009), pp. 523-537. by David Dynerman, Erick Butzlaff, Julie C. Mitchell posted by 3 people baker-group sobolevnrm RamuAnandakrishnan
	ProtSA: a web application for calculating sequence specific protein solvent accessibilities in the unfolded ensemble [My Copy] BMC Bioinformatics, Vol. 10 (08 April 2009), 104. by Jorge, Javier Sancho posted by 2 people biehl RamuAnandakrishnan
	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. (2009), pp. 2351-2357. by Tetsu Narumi, Kenji Yasuoka, Makoto Taiji, Siegfried Höfinger posted by 2 people ihaque RamuAnandakrishnan
	Accelerating Density Functional Calculations with Graphics Processing Unit [My Copy] Journal of Chemical Theory and Computation, Vol. 4, No. 8. (1 August 2008), pp. 1230-1236. by Koji Yasuda posted by 1 person RamuAnandakrishnan
	Quantum Chemistry on Graphical Processing Units. 1. Strategies for Two-Electron Integral Evaluation [My Copy] Journal of Chemical Theory and Computation, Vol. 4, No. 2. (1 February 2008), pp. 222-231. by Ivan S. Ufimtsev, Todd J. Martinez posted by 2 people ihaque RamuAnandakrishnan
	Graphical Processing Units for Quantum Chemistry [My Copy] Computing in Science and Engineering In Computing in Science & Engineering, Vol. 10, No. 6. (2008), pp. 26-34. by Ivan S. Ufimtsev, Todd J. Martínez posted by 2 people mmeteo RamuAnandakrishnan
	Quantum Chemistry on Graphical Processing Units. 2. Direct Self-Consistent-Field Implementation [My Copy] Journal of Chemical Theory and Computation, Vol. 5, No. 4. (14 April 2009), pp. 1004-1015. by Ivan S. Ufimtsev, Todd J. Martinez posted by 3 people Fortran charris5 RamuAnandakrishnan
	Optimizing Energy Potential for Protein Fold Recognition with Parametric Evaluation Function [My Copy] Journal of Computational Biology, Vol. 16, No. 3. (2009), pp. 427-442. by Junfeng Gu, Honglin Li, Hualiang Jiang, Xicheng Wang posted by 1 person RamuAnandakrishnan
	Cross-Ontological Analytics: Combining Associative and Hierarchical Relations in the Gene Ontologies to Assess Gene Product Similarity [My Copy] Computational Science – ICCS 2006 (2006), pp. 871-878. by C. Posse, A. Sanfilippo, B. Gopalan, R. Riensche, N. Beagley, B. Baddeley posted by 1 person RamuAnandakrishnan
	Combining Hierarchical and Associative Gene Ontology Relations With Textual Evidence in Estimating Gene and Gene Product Similarity [My Copy] NanoBioscience, IEEE Transactions on In NanoBioscience, IEEE Transactions on, Vol. 6, No. 1. (2007), pp. 51-59. by A. Sanfilippo, C. Posse, B. Gopalan, et al.R. Riensche, N. Beagley, B. Baddeley, S. Tratz, M. Gregory posted by 1 person RamuAnandakrishnan
	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
	Parallel implementation of molecular dynamics simulation for short-ranged interaction [My Copy] Computer Physics Communications, Vol. 170, No. 2. (01 August 2005), pp. 175-185. by J. Wu, Y. Hsu, Y. Lee posted by 1 person RamuAnandakrishnan
	Performance of fast multipole methods for calculating electrostatic interactions in biomacromolecular simulations [My Copy] Journal of Computational Chemistry, Vol. 15, No. 1. (1994), pp. 28-43. by Jiro Shimada, Hiroki Kaneko, Toshikazu Takada posted by 1 person RamuAnandakrishnan
	Zinc binding in proteins and solution: A simple but accurate nonbonded representation [My Copy] Proteins: Structure, Function, and Genetics, Vol. 23, No. 1. (1995), pp. 12-31. by Roland H. Stote, Martin Karplus posted by 1 person RamuAnandakrishnan
	Visualizing breathing motion of internal cavities in concert with ligand migration in myoglobin [My Copy] Proceedings of the National Academy of Sciences, Vol. 106, No. 8. (24 February 2009), pp. 2612-2616. by Ayana Tomita, Tokushi Sato, Kouhei Ichiyanagi, et al.Shunsuke Nozawa, Hirohiko Ichikawa, Matthieu Chollet, Fumihiro Kawai, Sam-Yong Park, Takayuki Tsuduki, Takahisa Yamato, Shin-Ya Koshihara, Shin-Ichi Adachi posted by 2 people hsekiguc RamuAnandakrishnan
	Assessment of standard force field models against high-quality <I>ab initio</I> potential curves for prototypes of pi-pi, CH/pi, and SH/pi interactions [My Copy] Journal of Computational Chemistry, Vol. 30, No. 14. (2009), pp. 2187-2193. by C. David Sherrill, Bobby G. Sumpter, Mutasem O. Sinnokrot, et al.Michael S. Marshall, Edward G. Hohenstein, Ross C. Walker, Ian R. Gould posted by 3 people Structural Biology Group TorVergata oteri RamuAnandakrishnan
	Statistical potentials extracted from protein structures: how accurate are they? [My Copy] Journal of molecular biology, Vol. 257, No. 2. (29 March 1996), pp. 457-469. by P. D. Thomas, K. A. Dill posted by 2 people RamuAnandakrishnan ashaytan
	Is Genetic Evolution Predictable? [My Copy] Science, Vol. 323, No. 5915. (6 February 2009), pp. 746-751. by David L. Stern, Virginie Orgogozo posted by 14 people emptyhb Scis0000002 anphony provero kshundyak balabu pkonings R.E.A.D Zephyrus jjray kaniko RamuAnandakrishnan zwang phoenixzxl
	High-resolution dynamic mapping of histone-DNA interactions in a nucleosome [My Copy] Nat Struct Mol Biol, Vol. 16, No. 2. (February 2009), pp. 124-129. by Michael A. Hall, Alla Shundrovsky, Lu Bai, Robert M. Fulbright, John T. Lis, Michelle D. Wang posted by 2 people RamuAnandakrishnan aalibes
	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 15 people oteri anuragsethi kevinchannon flbarroso r2s2 iantunbridge ihaque baker-group sobolevnrm ruvido massivemayhem structural_bioinformatics McCammon barry RamuAnandakrishnan
	GOrilla: a tool for discovery and visualization of enriched GO terms in ranked gene lists. [My Copy] BMC bioinformatics, Vol. 10 (03 February 2009), 48. by Eran Eden, Roy Navon, Israel Steinfeld, Doron Lipson, Zohar Yakhini posted by 10 people NaCTeM Effie guhjy RamuAnandakrishnan kshameer renatomilani grahamc cmzmasek paszkows jmeppley
	A general modular framework for gene set enrichment analysis [My Copy] BMC Bioinformatics, Vol. 10, No. 1. (03 February 2009), 47. by Marit Ackermann, Korbinian Strimmer posted by 19 people ptrobajo zufar srp33 vingron dipenps shikin arjun_citeulike guhjy pk506 aviad_work thomaskelder ydhwang rdiaz kshameer renatomilani Bioinformatics dswan cmzmasek RamuAnandakrishnan
	Approximate atomic surfaces from linear combinations of pairwise overlaps (LCPO) [My Copy] Journal of Computational Chemistry, Vol. 20, No. 2. (1999), pp. 217-230. by Jörg Weiser, Peter S. Shenkin, W. Clark Still posted by 2 people RamuAnandakrishnan mijam
	Divergent Evolution of Duplicate Genes Leads to Genetic Incompatibilities Within A. thaliana [My Copy] Science, Vol. 323, No. 5914. (30 January 2009), pp. 623-626. by David Bikard, Dhaval Patel, Claire Le Mette, et al.Veronica Giorgi, Christine Camilleri, Malcolm J. Bennett, Olivier Loudet posted by 8 people fenghezi rjlawren gjuggler bpcusack dinnes djkt RamuAnandakrishnan dbikard
	Duplicate genes increase expression diversity in closely related species and allopolyploids. [My Copy] Proceedings of the National Academy of Sciences of the United States of America (23 January 2009) by Misook Ha, Eun-Deok D. Kim, Z Jeffrey J. Chen posted by 4 people xianjun maximilianh RamuAnandakrishnan bpcusack
	Algorithms for computing the volume and other integral properties of solids. II. A family of algorithms based on representation conversion and cellular approximation [My Copy] Commun. ACM, Vol. 25, No. 9. (1982), pp. 642-650. by Yong T. Lee, Aristides A. G. Requicha posted by 3 people RamuAnandakrishnan Structural Biology Group TorVergata oteri
	Simulating protein folding initiation sites using an alpha-carbon-only knowledge-based force field [My Copy] Proteins: Structure, Function, and Bioinformatics, Vol. 9999, No. 9999. (2009), NA. by Patrick M. Buck, Christopher Bystroff posted by 1 person RamuAnandakrishnan
	Determination of the effective dielectric constant from the accurate solution of the Poisson equation [My Copy] Journal of Computational Chemistry, Vol. 23, No. 13. (2002), pp. 1254-1265. by Vladislav Vasilyev posted by 1 person RamuAnandakrishnan
	Modeling salt-mediated electrostatics of macromolecules: The discrete surface charge optimization algorithm and its application to the nucleosome [My Copy] Biopolymers, Vol. 58, No. 1. (2001), pp. 106-115. by Daniel A. Beard, Tamar Schlick posted by 1 person RamuAnandakrishnan
	A new FFT-based algorithm to compute Born radii in the generalized Born theory of biomolecule solvation [My Copy] Journal of Computational Physics, Vol. 227, No. 24. (20 December 2008), pp. 10162-10177. by W. Cai, Z. Xu, A. Baumketner posted by 2 people onufriev RamuAnandakrishnan
	Effect of Electrostatic Force Truncation on Interfacial and Transport Properties of Water [My Copy] The Journal of Physical Chemistry, Vol. 100, No. 42. (1 January 1996), pp. 17011-17020. by Scott E. Feller, Richard W. Pastor, Atipat Rojnuckarin, Stephen Bogusz, Bernard R. Brooks posted by 1 person RamuAnandakrishnan