skoddet's library 51 articles Export

	Structural artifacts in protein-ligand X-ray structures: implications for the development of docking scoring functions. [My Copy] Journal of medicinal chemistry, Vol. 52, No. 18. (24 September 2009), pp. 5673-5684. by Chresten R. Søndergaard, Alison Elizabeth E. Garrett, Tommy Carstensen, Gianluca Pollastri, Jens Erik E. Nielsen posted to scoring by skoddet on 2009-11-06 11:34:27 as along with 1 person massivemayhem
	Effects of Water Model and Simulation Box Size on Protein Diffusional Motions [My Copy] The Journal of Physical Chemistry B, Vol. 111, No. 41. (1 October 2007), pp. 11870-11872. by Kazuhiro Takemura, Akio Kitao posted to md by skoddet on 2009-08-07 01:02:37 as along with 2 people and 2 groups flbarroso sobolevnrm Nielsen group baker-group
	Free energies of chemical reactions in solution and in enzymes with ab initio quantum mechanics/molecular mechanics methods. [My Copy] Annual review of physical chemistry, Vol. 59, No. 1. (2008), pp. 573-601. by H. Hu, W. Yang posted to catalysis by skoddet on 2009-07-27 14:15:33 as along with 1 person flbarroso
	QM/MM methods for biomolecular systems. [My Copy] Angewandte Chemie (International ed. in English), Vol. 48, No. 7. (2009), pp. 1198-1229. by H. M. Senn, W. Thiel posted to catalysis by skoddet on 2009-07-27 14:15:11 as along with 1 person and 1 group jmccammon McCammon
	Analysing the pH-dependent properties of proteins using pKa calculations [My Copy] Journal of Molecular Graphics and Modelling, Vol. 25, No. 5. (January 2007), pp. 691-699. by Jens E. Nielsen posted to pka by skoddet on 2009-02-24 10:55:53 as along with 1 person and 2 groups sobolevnrm Nielsen group baker-group
	Selecton: a server for detecting evolutionary forces at a single amino-acid site [My Copy] Bioinformatics, Vol. 21, No. 9. (1 May 2005), pp. 2101-2103. by Adi Doron-Faigenboim, Adi Stern, Eran Bacharach, Tal Pupko posted to hiv by skoddet on 2009-01-27 23:21:47 as
	Evolution of HIV resistance during treatment interruption in experienced patients and after restarting a new therapy. [My Copy] J Clin Virol, Vol. 34, No. 4. (December 2005), pp. 277-287. by M. Balduin, S. Sierra, M. P. Däumer, et al.J. K. Rockstroh, M. Oette, G. Fätkenheuer, B. Kupfer, N. Beerenwinkel, D. Hoffmann, J. Selbig, H. J. Pfister, R. Kaiser posted to directed_evolution hiv by skoddet on 2009-01-27 23:18:12 as along with 1 person and 1 group gokhan Nielsen group
	Diversification and Specialization of HIV Protease Function During In Vitro Evolution [My Copy] Molecular Biology and Evolution, Vol. 23, No. 4. (April 2006), pp. 764-772. by Taryn L. Oloughlin, Dina N. Greene, Ichiro Matsumura posted to directed_evolution hiv by skoddet on 2009-01-27 22:17:52 as along with 1 person and 1 group mijogiffin Nielsen group
	A Theoretical Validation of the Substrate Depletion Approach to Determining Kinetic Parameters [My Copy] Drug Metab Dispos, Vol. 34, No. 9. (1 September 2006), pp. 1433-1435. by Abhinav Nath, William M. Atkins posted to catalysis by skoddet on 2009-01-23 11:49:21 as along with 1 person and 1 group cgeneraux Nielsen group
	Rapid whole-genome mutational profiling using next-generation sequencing technologies. [My Copy] Genome research, Vol. 18, No. 10. (4 October 2008), pp. 1638-1642. by Douglas R. Smith, Aaron R. Quinlan, Heather E. Peckham, et al.Kathryn Makowsky, Wei Tao, Betty Woolf, Lei Shen, William F. Donahue, Nadeem Tusneem, Michael P. Stromberg, Donald A. Stewart, Lu Zhang, Swati S. Ranade, Jason B. Warner, Clarence C. Lee, Brittney E. Coleman, Zheng Zhang, Stephen F. McLaughlin, Joel A. Malek, Jon M. Sorenson, Alan P. Blanchard, Jarrod Chapman, David Hillman, Feng Chen, Daniel S. Rokhsar, Kevin J. McKernan, Thomas W. Jeffries, Gabor T. Marth, Paul M. Richardson posted to directed evolution by skoddet on 2009-01-20 14:45:46 as along with 7 people n00c robsyme druvus yupu jfr jmcq GeeSharpMinor
	Utilizing the Charge Field Effect on Amide 15N Chemical Shifts for Protein Structure Validation [My Copy] The Journal of Physical Chemistry B, Vol. 0, No. 0. (0000) by Reto Bader posted to electrostatics nmr by skoddet on 2008-12-16 23:02:12 as
	An electrostatic network and long-range regulation of Src kinases [My Copy] Protein Sci, Vol. 17, No. 11. (1 November 2008), pp. 1871-1880. by Elif Ozkirimli, Shalini S. Yadav, Todd W. Miller, Carol B. Post posted to electrostatics pka by skoddet on 2008-11-05 17:04:30 as along with 1 person tny
	A Critical Assessment of Docking Programs and Scoring Functions [My Copy] J. Med. Chem., Vol. 49, No. 20. (5 October 2006), pp. 5912-5931. by G. L. Warren, C. W. Andrews, A. M. Capelli, et al.B. Clarke, J. Lalonde, M. H. Lambert, M. Lindvall, N. Nevins, S. F. Semus, S. Senger, G. Tedesco, I. D. Wall, J. M. Woolven, C. E. Peishoff, M. S. Head posted to functions scoring by skoddet on 2008-10-14 14:12:37 as along with 6 people ucbcjbm BragilMassoud aalibes schlauchi daevans superpyrin
	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 to nma by skoddet on 2008-10-09 17:38:18 as along with 6 people and 5 groups sobolevnrm aqeel apaydin ruvido agrossfield barry baker-group Nielsen group structural_bioinformatics McCammon Bioinformatics
	Direct evidence of extensive diversity of HIV-1 in Kinshasa by 1960 [My Copy] Nature, Vol. 455, No. 7213. (2 October 2008), pp. 661-664. by Michael Worobey, Marlea Gemmel, Dirk E. Teuwen, et al.Tamara Haselkorn, Kevin Kunstman, Michael Bunce, Jean-Jacques Muyembe, Jean-Marie M. Kabongo, Raphael M. Kalengayi, Eric Van Marck, Gilbert, Steven M. Wolinsky posted to hiv by skoddet on 2008-10-01 20:57:55 as along with 3 people and 2 groups memerman reyez wsjames Oxford Virology Nielsen group
	Visualizing transient events in amino-terminal autoprocessing of HIV-1 protease [My Copy] Nature, Vol. 455, No. 7213. (2 October 2008), pp. 693-696. by Chun Tang, John M. Louis, Annie Aniana, Jeong-Yong Suh, Marius G. Clore posted to hiv by skoddet on 2008-10-01 20:56:49 as along with 2 people and 1 group cactus raik Nielsen group
	On the relationship between folding and chemical landscapes in enzyme catalysis [My Copy] Proceedings of the National Academy of Sciences, Vol. 105, No. 37. (2008), pp. 13877-13882. by Maite Roca, Benjamin Messer, Donald Hilvert, Arieh Warshel posted to no-tag by skoddet on 2008-09-18 16:55:08 as along with 1 person sunhwan
	Understanding the limits to generalizability of experimental evolutionary models [My Copy] Nature, Vol. 455, No. 7210. (2008), pp. 220-223. by Samantha E. Forde, Robert E. Beardmore, Ivana Gudelj, Sinan S. Arkin, John N. Thompson, Laurence D. Hurst posted to hiv by skoddet on 2008-09-10 21:24:57 as along with 10 people and 1 group qwermish pradiptaray jasonn DanHodson druvus Zephyrus Ema zwang Katje tmmurali Roswell Cancer Crosstalk
	Direct Electrochemical Analyses of a Thermophilic Thioredoxin Reductase: Interplay between Conformational Change and Redox Chemistry [My Copy] Biochemistry, Vol. 47, No. 37. (16 September 2008), pp. 9738-9746. by Michael J. Hamill, Sarah E. Chobot, Hector H. Hernandez, Catherine L. Drennan, Sean J. Elliott posted to electrostatics by skoddet on 2008-09-09 11:55:08 as
	Automated Molecular Simulation Based Binding Affinity Calculator for Ligand-Bound HIV-1 Proteases. [My Copy] Journal of chemical information and modeling (19 August 2008) by S K. Sadiq, David Wright, Simon J. Watson, Stefan J. Zasada, Ileana Stoica, Peter V. Coveney posted to hiv by skoddet on 2008-08-26 21:50:32 as along with 2 people and 1 group ibuch mijogiffin Nielsen group
	Microwave Activation of Enzymatic Catalysis [My Copy] J. Am. Chem. Soc. (10 July 2008) by Douglas D. Young, Jason Nichols, Robert M. Kelly, Alexander Deiters posted to catalysis by skoddet on 2008-07-30 15:40:15 as along with 2 people achinerarias katiehumphry
	An orientation-dependent hydrogen bonding potential improves prediction of specificity and structure for proteins and protein-protein complexes. [My Copy] J Mol Biol, Vol. 326, No. 4. (28 February 2003), pp. 1239-1259. by T. Kortemme, A. V. Morozov, D. Baker posted to protein structure by skoddet on 2008-07-10 16:17:17 as along with 2 people and 1 group lna dgront Nielsen group
	A ?solvated rotamer? approach to modeling water-mediated hydrogen bonds at protein-protein interfaces [My Copy] Proteins: Structure, Function, and Bioinformatics, Vol. 58, No. 4. (2005), pp. 893-904. by Lin Jiang, Brian Kuhlman, Tanja Kortemme, David Baker posted to protein structure by skoddet on 2008-07-10 16:16:12 as along with 4 people oceanwind apaydin jwm msuarezdiez
	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 to structure-prediction by skoddet on 2008-06-20 15:35:39 as along with 8 people and 1 group chemrahul82 onufriev oceanwind lna jwm bicko cjeans hmk Nielsen group
	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 to structure-prediction by skoddet on 2008-06-20 15:34:45 as along with 8 people and 6 groups chemrahul82 onufriev pablocarb bicko barry sangeetha blackbart joergkurtwegner structural_bioinformatics Bioinformatics Molecular-Modelling Drug-Design Cheminformatics insilicodrug
	SNPeffect v2.0: a new step in investigating the molecular phenotypic effects of human non synonymous SNPs. [My Copy] Bioinformatics (29 June 2006) by Joke Reumers, Sebastian Maurer-Stroh, Joost Schymkowitz, Frederic Rousseau posted to structure-prediction by skoddet on 2008-06-20 15:33:38 as along with 4 people and 3 groups chad_davis caporaso massivemayhem cat_worth structural_bioinformatics biomedical-nlp Nielsen group
	Joint annotation of coding and non-coding single nucleotide polymorphisms and mutations in the SNPeffect and PupaSuite databases. [My Copy] Nucleic Acids Res (17 December 2007) by Joke Reumers, Lucia Conde, Ignacio Medina, et al.Sebastian Maurer-Stroh, Joost Van V. Durme, Joaquin Dopazo, Frederic Rousseau, Joost Schymkowitz posted to no-tag by skoddet on 2008-06-20 15:31:29 as along with 3 people and 1 group ssgong daforerog guhjy Nielsen group
	Thermodynamic linkage between the binding of protons and inhibitors to HIV-1 protease [My Copy] Protein Sci, Vol. 8, No. 1. (1 January 1999), pp. 180-195. by J. Trylska, J. Antosiewicz, M. Geller, et al.Cn Hodge, Rm Klabe, Ms Head, Mk Gilson posted to hiv pka by skoddet on 2008-06-20 15:29:53 as along with 1 person and 1 group boris_aguilar Nielsen group
	The role of hydrogen bonding in the enzymatic reaction catalyzed by HIV-1 protease. [My Copy] Protein science : a publication of the Protein Society, Vol. 13, No. 2. (February 2004), pp. 513-528. by J. Trylska, P. Grochowski, J. A. McCammon posted to hiv pka by skoddet on 2008-06-20 15:29:31 as
	Binding pathways of ligands to HIV-1 protease: coarse-grained and atomistic simulations. [My Copy] Chem Biol Drug Des, Vol. 69, No. 1. (January 2007), pp. 5-13. by C. E. Chang, J. Trylska, V. Tozzini, J. A. McCammon posted to hiv by skoddet on 2008-06-20 15:28:57 as along with 1 person and 1 group choonpeng Nielsen group
	Magnetic resonance imaging of pH in vivo using hyperpolarized 13C-labelled bicarbonate [My Copy] Nature (28 May 2008) by Ferdia A. Gallagher, Mikko I. Kettunen, Sam E. Day, et al.De-En Hu, Jan H. Ardenkjær-Larsen, René, Pernille R. Jensen, Magnus Karlsson, Klaes Golman, Mathilde H. Lerche, Kevin M. Brindle posted to pka by skoddet on 2008-06-12 10:09:47 as
	Evolutionary analysis of HIV-1 protease inhibitors: Methods for design of inhibitors that evade resistance. [My Copy] Proteins, Vol. 48, No. 1. (1 July 2002), pp. 63-74. by D. Stoffler, M. F. Sanner, G. M. Morris, A. J. Olson, D. S. Goodsell posted to hiv by skoddet on 2008-06-11 16:52:01 as along with 1 group Nielsen group
	Molecular Analysis of the HIV-1 Resistance Development: Enzymatic Activities, Crystal Structures, and Thermodynamics of Nelfinavir-resistant HIV Protease Mutants [My Copy] Journal of Molecular Biology, Vol. 374, No. 4. (7 December 2007), pp. 1005-1016. by Milan Kozísek, Jenelle Bray, Pavlína Rezácová, et al.Klára Sasková, Jirí Brynda, Jana Pokorná, Fabrizio Mammano, Lubomír Rulísek, Jan Konvalinka posted to hiv by skoddet on 2008-06-11 16:50:39 as along with 1 person and 1 group joseph_x_zhou Nielsen group
	Site-directed mutagenesis of the hinge peptide from the hemagglutinin protein: enhancement of the pH-responsive conformational change [My Copy] Protein Engineering, Design and Selection, Vol. 21, No. 6. (1 June 2008), pp. 395-404. by Monica Casali, Scott Banta, Carlo Zambonelli, Zaki Megeed, Martin L. Yarmush posted to pka by skoddet on 2008-05-16 15:22:40 as
	Mapping Local Protein Electrostatics by EPR of pH-Sensitive Thiol-Specific Nitroxide [My Copy] Biochemistry, Vol. 47, No. 20. (20 May 2008), pp. 5626-5637. by Maxim A. Voinov, Andres Ruuge, Vladimir A. Reznikov, Igor A. Grigor’ev, Alex I. Smirnov posted to nmr pka_values by skoddet on 2008-05-13 11:04:17 as along with 1 person and 2 groups sobolevnrm baker-group Nielsen group
	Comparative study of the prereactive protein kinase A Michaelis complex with Kemptide substrate [My Copy] Journal of Computer-Aided Molecular Design, Vol. 21, No. 10. (15 October 2007), pp. 603-615. by Manuel Montenegro, Mireia Garcia-Viloca, Àngels González-Lafont, José Lluch posted to md pka by skoddet on 2008-05-09 13:25:05 as
	Microsecond Molecular Dynamics Simulation Shows Effect of Slow Loop Dynamics on Backbone Amide Order Parameters of Proteins† [My Copy] The Journal of Physical Chemistry B, Vol. 112, No. 19. (1 May 2008), pp. 6155-6158. by Paul Maragakis, Kresten Lindorff-Larsen, Michael P. Eastwood, et al.Ron O. Dror, John L. Klepeis, Isaiah T. Arkin, Morten O. Jensen, Huafeng Xu, Nikola Trbovic, Richard A. Friesner, Arthur G. Palmer, David E. Shaw posted to md by skoddet on 2008-05-08 16:02:47 as along with 3 people and 1 group pavanghatty allmensch LamBras Nielsen group
	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 to no-tag by skoddet on 2008-04-28 20:24:21 as along with 4 people and 1 group flbarroso scampos sobolevnrm sunhwan baker-group
	Molecular Dynamics Simulation of the Escherichia coli NikR Protein: Equilibrium Conformational Fluctuations Reveal Interdomain Allosteric Communication Pathways [My Copy] Journal of Molecular Biology, Vol. 378, No. 5. (16 May 2008), pp. 1155-1173. by Michael J. Bradley, Peter T. Chivers, Nathan A. Baker posted to md by skoddet on 2008-04-27 13:46:29 as along with 2 people and 2 groups sobolevnrm barry baker-group structural_bioinformatics
	Correspondences between low-energy modes in enzymes: Dynamics-based alignment of enzymatic functional families [My Copy] Protein Sci, Vol. 17, No. 5. (1 May 2008), pp. 918-929. by Andrea Zen, Vincenzo Carnevale, Arthur M. Lesk, Cristian Micheletti posted to nma by skoddet on 2008-04-26 09:04:42 as along with 2 people and 1 group edvin tny Nielsen group
	A buried lysine that titrates with a normal pKa : Role of conformational flexibility at the protein-water interface as a determinant of pKa values [My Copy] Protein Sci, Vol. 17, No. 5. (1 May 2008), pp. 833-845. by Michael J. Harms, Jamie L. Schlessman, Michael S. Chimenti, Gloria R. Sue, Ana Damjanovic, Garcia-Moreno posted to electrostatics pka by skoddet on 2008-04-25 21:22:56 as along with 3 people and 2 groups zfekete sobolevnrm RamuAnandakrishnan baker-group Nielsen group
	Electrostatic Fields Near the Active Site of Human Aldose Reductase: 1. New Inhibitors and Vibrational Stark Effect Measurements [My Copy] Biochemistry (19 January 2008) by L. J. Webb, S. G. Boxer posted to electrostatics by skoddet on 2008-04-11 10:57:25 as along with 1 person higueruelo
	Local knowledge helps determine protein structures [My Copy] Proceedings of the National Academy of Sciences, Vol. 105, No. 12. (25 March 2008), pp. 4533-4534. by Michael R. Gryk, Jeffrey C. Hoch posted to nmr structure-prediction by skoddet on 2008-04-11 10:51:06 as
	Consistent blind protein structure generation from NMR chemical shift data [My Copy] Proceedings of the National Academy of Sciences, Vol. 105, No. 12. (25 March 2008), pp. 4685-4690. by Yang Shen, Oliver Lange, Frank Delaglio, et al.Paolo Rossi, James M. Aramini, Gaohua Liu, Alexander Eletsky, Yibing Wu, Kiran K. Singarapu, Alexander Lemak, Alexandr Ignatchenko, Cheryl H. Arrowsmith, Thomas Szyperski, Gaetano T. Montelione, David Baker, Ad Bax posted to nmr prediction structure by skoddet on 2008-04-11 10:50:48 as along with 7 people and 1 group siggi84 babakap dgront zwang biehl sunhwan apaydin Nielsen group
	A finite element framework for computation of protein normal modes and mechanical response [My Copy] Proteins: Structure, Function, and Bioinformatics, Vol. 9999, No. 9999. (2007), NA. by Mark Bathe posted to nma by skoddet on 2008-04-11 10:44:14 as along with 2 people and 1 group choonpeng RamuAnandakrishnan Nielsen group
	A knowledge-based forcefield for protein-protein interface design. [My Copy] Proteins, Vol. 70, No. 4. (March 2008), pp. 1540-1550. by L. A. Clark, H. W. van Vlijmen posted to design protein by skoddet on 2008-04-11 10:44:01 as along with 1 group Nielsen group
	Classifying protein kinase structures guides use of ligand-selectivity profiles to predict inactive conformations: Structure of lck/imatinib complex. [My Copy] Proteins (1 October 2007) by Marc D D. Jacobs, Paul R R. Caron, Brian J J. Hare posted to kinases by skoddet on 2008-04-11 10:43:42 as along with 2 people hryk bicko
	Efficient comprehensive scoring of docked protein complexes using probabilistic support vector machines [My Copy] Proteins: Structure, Function, and Bioinformatics, Vol. 70, No. 4. (2008), pp. 1367-1378. by Oliver Martin, Dietmar Schomburg posted to no-tag by skoddet on 2008-04-11 10:43:28 as
	Solvent effects in the slow dynamics of proteins [My Copy] Proteins: Structure, Function, and Bioinformatics, Vol. 70, No. 4. (2008), pp. 1235-1242. by Konrad Hinsen, Gerald R. Kneller posted to no-tag by skoddet on 2008-04-11 10:43:11 as along with 2 people choonpeng saravan
	PDB improvement starts with data deposition [3] [My Copy] Science, Vol. 317, No. 5835. (2007), pp. 195-196. by R. P. Joosten, G. Vriend posted to no-tag by skoddet on 2008-04-09 10:39:09 as

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