krapnik's library 136 articles Export

	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 to no-tag by krapnik on 2009-11-18 09:44:16 as along with 14 people and 2 groups ucbcjbm flbarroso mikaellund baaden jwm bicko chad_davis dullhunk dgront drastic ruvido Evangelia higueruelo timg Radiation_Damage Stressosome
	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 to no-tag by krapnik on 2009-11-18 09:43:58 as along with 18 people and 3 groups rabio ucbcjbm paddydu flbarroso thaliana jwm vavi bicko KyuhoLee marcius eweaver tny nickolay dgront rsantana mirzazadeh insectopalo barry BioinfoCIPF SGU-CIPF structural_bioinformatics
	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 to no-tag by krapnik on 2009-11-18 09:43:18 as along with 18 people and 3 groups csrocha nickolay mmuecke flbarroso charris5 pavanghatty tahereh62 lna jwm ttjoseph xdeupi tovrstra bilab RamuAnandakrishnan IrinaMoreira adilson_mohr mikaellund gisle Radiation_Damage Stressosome LabCompMed
	Scalable molecular dynamics with NAMD [My Copy] Journal of Computational Chemistry, Vol. 26, No. 16. (December 2005), pp. 1781-1802. by James C. Phillips, Rosemary Braun, Wei Wang, et al.James Gumbart, Emad Tajkhorshid, Elizabeth Villa, Christophe Chipot, Robert D. Skeel, Laxmikant Kalé, Klaus Schulten posted to no-tag by krapnik on 2009-11-18 09:43:08 as along with 20 people and 5 groups pjkiley flbarroso yxue r2s2 grondina rpetrenko oteri oceanwind dfgreen vahmurk gisle dimka jwm ttjoseph sangeetha yoel_rf bilab wilsoros sobolevnrm ibuch Radiation_Damage Stressosome Bioinformatics insilicodrug baker-group
	Basic local alignment search tool. [My Copy] Journal of molecular biology, Vol. 215, No. 3. (5 October 1990), pp. 403-410. by S. F. Altschul, W. Gish, W. Miller, E. W. Myers, D. J. Lipman posted to no-tag by krapnik on 2009-11-18 09:43:01 as along with 77 people and 6 groups VGreiff richter80 azazello rshe mtaschuk sjcockell niallhaslam djohnson thegoose humburg timhubbard pachorip n00c maria_hauser rpetrenko parnell yylin esyoun APRegier idoerg Neeperando robert85 thegoose2 daforerog mcbla coela alessandroparini bertelsen Blackbeard florisbuijzen laurabailey treangen pwais mmartin tharris dmp camster davidng evaf dragonrez jwm jmeppley Ayest RMGraze ea yas balajis alexg indigoviolet moborg arcticrasta dullhunk dgront caporaso michC myui BioNica CitoJam rabio timflutre lusk cjeans incovoma beatrizfernandez wenhan jtomasch GustavoLacerda sgoetz siebertm ichbins81 jofiel Thaverkamp shung marti ashaytan benwei granujilla C. elegans / WormBase dbk-lab EisenLab T_lab biomedical-nlp Microbial-Ecology
	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 to no-tag by krapnik on 2009-11-18 09:42:38 as along with 45 people and 5 groups trishul barmak7282 viktor21614 badi ucbcjbm TLVincent maria_hauser Martin8223 tomjad Diego_Prada flbarroso Taguan oceanwind dsmueller fisherp semin MarcoAlvarez kumar_physics LamBras RamuAnandakrishnan nlapalu reyez nigham lillekatt thaliana dimka kuhn jwm vavi bicko itmeson dgront caporaso condon aengisch debatebob massivemayhem gisle girschick selrac tji higueruelo boris_aguilar sebk timg References for 3DSim paper Radiation_Damage Stressosome biomedical-nlp beta
	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 to no-tag by krapnik on 2009-11-18 09:42:34 as along with 20 people and 2 groups arifor r2s2 janneb dsmueller oteri choonpeng sebk dimka jwm ttjoseph bilab rabio Dinler tji softsimu ashaytan robertvacha sunnytov Diego_Prada A_Coletta_Thesis Radiation_Damage Stressosome
	Entropy in protein folding and in protein—protein interactions [My Copy] Current Opinion in Structural Biology, Vol. 7, No. 2. (April 1997), pp. 215-221. by G. Brady posted to protein_structure_database protein_protein_interactions protein_folding estimates entropy conformational_entropy by krapnik on 2009-10-06 13:04:04 as along with 1 person flbarroso
	Calculation of the nonlinear optical properties of molecules [My Copy] Journal of Computational Chemistry, Vol. 11, No. 1. (1990), pp. 82-87. by Henry A. Kurtz, James J. P. Stewart, Kenneth M. Dieter posted to polarizability nonlinear_optical_properties hyperpolarizabilities dipole_moment by krapnik on 2009-10-01 07:58:36 as
	Additivity methods in molecular polarizability [My Copy] Journal of the American Chemical Society, Vol. 112, No. 23. (1 November 1990), pp. 8533-8542. by Kenneth J. Miller posted to polarizability by krapnik on 2009-10-01 07:24:02 as along with 1 person mightmightys
	Allosteric and Signaling Pathways in Proteins [My Copy] Annual Review of Biophysics, Vol. 39, No. 1. (2010) by Rama Ranganathan posted to protein by krapnik on 2009-09-20 09:16:43 as
	Structureâneurotoxicity relationships of amyloid Î²-protein oligomers [My Copy] Proceedings of the National Academy of Sciences, Vol. 106, No. 35. (1 September 2009), pp. 14745-14750. by Kenjiro Ono, Margaret M. Condron, David B. Teplow posted to structure_activity relative_toxicity analysis amyloid by krapnik on 2009-09-19 15:16:07 as along with 3 people aip carlosjavierna chiufanlee
	AmberTools 1.2 User Manual [My Copy] posted to no-tag by krapnik on 2009-09-02 16:15:03 as along with 1 person and 1 group oteri Structural Biology Group TorVergata
	Effect of Temperature on the Structure and Phase Behavior of Water Confined by Hydrophobic, Hydrophilic, and Heterogeneous Surfaces† [My Copy] The Journal of Physical Chemistry B, Vol. 0, No. 0. (0000) by Nicolas Giovambattista, Peter J. Rossky, Pablo G. Debenedetti posted to hydrophilicity hydrophobicity interactions thermostability water by krapnik on 2009-07-28 17:34:58 as
	Hydrophobicity of protein surfaces: Separating geometry from chemistry [My Copy] Proceedings of the National Academy of Sciences, Vol. 105, No. 7. (19 February 2008), pp. 2274-2279. by Nicolas Giovambattista, Carlos F. Lopez, Peter J. Rossky, Pablo G. Debenedetti posted to hydrophilicity hydrophobicity interactions md water by krapnik on 2009-07-28 17:29:49 as along with 3 people and 1 group qshao mijam sobolevnrm baker-group
	Dominant forces in protein folding [My Copy] Biochemistry, Vol. 29, No. 31. (1 August 1990), pp. 7133-7155. by Ken A. Dill posted to dispersion electrostatic entropy folding hydrophobicity interactions by krapnik on 2009-07-28 15:01:59 as along with 3 people flbarroso chiufanlee mlg
	GCN4 protein, a positive transcription factor in yeast, binds general control promoters at all 5' TGACTC 3' sequences [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 83, No. 22. (November 1986), pp. 8516-8520. by K. Arndt, G. R. Fink posted to coiled-coil gcn4 transcription_factor by krapnik on 2009-07-27 15:57:13 as along with 1 person hplatero
	Covalent Trimers of the Internal N-terminal Trimeric Coiled-coil of gp41 and Antibodies Directed against Them Are Potent Inhibitors of HIV Envelope-mediated Cell Fusion [My Copy] J. Biol. Chem., Vol. 278, No. 22. (23 May 2003), pp. 20278-20285. by John M. Louis, Issa Nesheiwat, Lengchee Chang, G. Marius Clore, Carole A. Bewley posted to coiled-coil hiv by krapnik on 2009-07-27 15:50:37 as
	Thermodynamics of Buried Water Clusters at a Protein−Ligand Binding Interface [My Copy] The Journal of Physical Chemistry B, Vol. 110, No. 3. (1 January 2006), pp. 1464-1475. by Zheng Li, Themis Lazaridis posted to protein-ligand water by krapnik on 2009-07-27 11:45:18 as along with 1 person jteyra
	Hydration Thermodynamic Properties of Amino Acid Analogues: A Systematic Comparison of Biomolecular Force Fields and Water Models [My Copy] The Journal of Physical Chemistry B, Vol. 110, No. 35. (1 September 2006), pp. 17616-17626. by Berk Hess, Nico F. A. van der Vegt posted to force-field water by krapnik on 2009-07-27 11:36:06 as along with 6 people and 1 group softsimu arnaucordomi flbarroso Diego_Prada Marine ashaytan Molecular dynamics in MSU
	Solvation free energies of amino acid side chain analogs for common molecular mechanics water models [My Copy] The Journal of Chemical Physics, Vol. 122, No. 13. (2005), 134508. by Michael R. Shirts, Vijay S. Pande posted to acid amino mm water by krapnik on 2009-07-27 11:35:13 as
	Water-mediated interactions between hydrophobic and ionic species in cylindrical nanopores [My Copy] The Journal of Chemical Physics, Vol. 130, No. 9. (2009), 094502. by S. Vaitheeswaran, G. Reddy, D. Thirumalai posted to nano water by krapnik on 2009-07-27 11:34:13 as along with 2 people vitroid dlimmer
	Potential energy functions for atomic-level simulations of water and organic and biomolecular systems [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 102, No. 19. (10 May 2005), pp. 6665-6670. by William L. Jorgensen, Julian Tirado-Rives posted to force-field potential water by krapnik on 2009-07-27 11:33:11 as along with 3 people r2s2 flbarroso choonpeng
	Interfacial free energy and the hydrophobic effect [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 76, No. 9. (September 1979), pp. 4175-4176. by Charles Tanford posted to free-energy hydrophobicity by krapnik on 2009-07-27 11:23:44 as
	Molecular basis of coiled-coil formation [My Copy] Proceedings of the National Academy of Sciences, Vol. 104, No. 17. (24 April 2007), pp. 7062-7067. by Michel O. Steinmetz, Ilian Jelesarov, William M. Matousek, et al.Srinivas Honnappa, Wolfgang Jahnke, John H. Missimer, Sabine Frank, Andrei T. Alexandrescu, Richard A. Kammerer posted to coiled-coil interactions by krapnik on 2009-07-26 13:34:38 as along with 2 people kgutwin Diego_Prada
	Electrostatic Interactions in Leucine Zippers: Effects on Stability and Specificity of Interaction [My Copy] Journal of Bioactive and Compatible Polymers, Vol. 15, No. 4. (1 July 2000), pp. 334-356. by Kevin P. Mcgrath, Michelle M. Butler, Carla M. Digirolamo, David L. Kaplan, Wendy A. Petka, Thomas M. Laue posted to coiled-coil electrostatic interactions leucine_zipper by krapnik on 2009-07-26 13:13:51 as
	Seeing and Knowing in Structural Biology [My Copy] J. Biol. Chem., Vol. 282, No. 45. (9 November 2007), pp. 32529-32538. by Carolyn Cohen posted to coiled-coil by krapnik on 2009-07-26 13:06:02 as along with 2 people kgutwin paulschlesinger
	CC+: a relational database of coiled-coil structures. [My Copy] Nucleic acids research, Vol. 37, No. Database issue. (1 January 2009), pp. D315-322. by Oliver D. Testa, Efrosini Moutevelis, Derek N. Woolfson posted to coiled-coil database by krapnik on 2009-07-26 13:05:02 as along with 4 people TLVincent Zoltan_Barczikay patrickking kgutwin
	The Effects of the Side Chains of Hydrophobic Aliphatic Amino Acid Residues in an Amphipathic Polypeptide on the Formation of alpha Helix and Its Association [My Copy] J Biochem, Vol. 139, No. 2. (1 February 2006), pp. 271-278. by Toshiaki Takei, Atsuhito Okonogi, Kumiko Tateno, et al.Akiko Kimura, Shuichi Kojima, Kazumori Yazaki, Kin-Ichiro Miura posted to coiled-coil by krapnik on 2009-07-26 13:03:43 as
	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 to no-tag by krapnik on 2009-07-09 11:28:52 as along with 23 people and 2 groups sunnytov softsimu parnell rabio oteri robertvacha rodrigofaccioli pavanghatty janneb ZhangYinhe okapi flbarroso marceavi A_Coletta_Thesis choonpeng Lombardo_7 jwm daevans mmuecke sobolevnrm r2s2 middledomain loison Structural Biology Group TorVergata baker-group
	Implementation of the SCC-DFTB Method for Hybrid QM/MM Simulations within the Amber Molecular Dynamics Package. [My Copy] J Phys Chem A (24 May 2007) by Gustavo D. Seabra, Ross C. Walker, Marcus Elstner, David A. Case, Adrian E. Roitberg posted to no-tag by krapnik on 2009-07-09 09:48:57 as along with 3 people and 1 group charris5 vahmurk xdeupi LabCompMed
	A dictionary for protein side-chain entropies from NMR order parameters. [My Copy] Journal of the American Chemical Society, Vol. 131, No. 21. (3 June 2009), pp. 7226-7227. by D. W. Li, R. Brüschweiler posted to conformation entropy nmr protein simulation by krapnik on 2009-07-09 07:06:26 as along with 3 people kintoki anna_yershova carlosjavierna
	Hydrocarbon Bond Dissociation Energies [My Copy] Annual Review of Physical Chemistry, Vol. 33, No. 1. (1982), pp. 493-532. by D. F. Mcmillen, D. M. Golden posted to bond cysteine experimental thermostability by krapnik on 2009-05-26 07:39:29 as
	Potential functions for hydrogen bonds in protein structure prediction and design. [My Copy] Adv Protein Chem, Vol. 72 (2005), pp. 1-38. by A. V. Morozov, T. Kortemme posted to no-tag by krapnik on 2009-05-14 15:54:04 as along with 1 person jwm
	Dispersion Interactions Govern the Strong Thermal Stability of a Protein [My Copy] Chemistry - A European Journal, Vol. 13, No. 32. (2007), pp. 9022-9027. by Jiří Vondrášek, Tomáš Kubař, Jenney, et al.Michael W. Adams, Milan Kožíšek, Jiří Černý, Vladimír Sklenář, Pavel Hobza posted to no-tag by krapnik on 2009-04-15 17:36:08 as
	Comparative study of generalized Born models: protein dynamics. [My Copy] Proc Natl Acad Sci U S A, Vol. 102, No. 19. (10 May 2005), pp. 6760-6764. by H. Fan, A. E. Mark, J. Zhu, B. Honig posted to dielectric_constant force-field solvatation validation by krapnik on 2009-04-07 14:07:06 as along with 1 person ttjoseph
	An Orientation-dependent Hydrogen Bonding Potential Improves Prediction of Specificity and Structure for Proteins and Protein-Protein Complexes [My Copy] Journal of Molecular Biology, Vol. 326, No. 4. (28 February 2003), pp. 1239-1259. by Tanja Kortemme, Alexandre V. Morozov, David Baker posted to no-tag by krapnik on 2009-03-31 15:41:34 as along with 3 people Elena_Zubova hmk mirzazadeh
	Potential energy functions for protein design. [My Copy] Curr Opin Struct Biol (24 March 2007) by F Edward E. Boas, Pehr B B. Harbury posted to no-tag by krapnik on 2009-03-25 12:37:38 as along with 5 people kgutwin msuarezdiez BragilMassoud aalibes onufriev
	In quest of an empirical potential for protein structure prediction. [My Copy] Current opinion in structural biology, Vol. 16, No. 2. (6 April 2006), pp. 166-171. by J. Skolnick posted to no-tag by krapnik on 2009-03-25 12:37:27 as along with 4 people flbarroso BragilMassoud nigham bilab
	Macromolecular Modeling with Rosetta [My Copy] Annual Review of Biochemistry, Vol. 77, No. 1. (2008), pp. 363-382. by Rhiju Das, David Baker posted to conformation software by krapnik on 2009-03-25 12:10:52 as along with 9 people bmduggan choonpeng mijam kgutwin carlk phoenixzxl flbarroso saunders gisle
	Close agreement between the orientation dependence of hydrogen bonds observed in protein structures and quantum mechanical calculations [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 101, No. 18. (4 May 2004), pp. 6946-6951. by Alexandre V. Morozov, Tanja Kortemme, Kiril Tsemekhman, David Baker posted to quantum_chemical statistical_potential by krapnik on 2009-03-25 11:36:28 as along with 3 people j3xucite lna dgront
	Origin of the neighboring residue effect on peptide backbone conformation. [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 101, No. 30. (27 July 2004), pp. 10967-10972. by F. Avbelj, R. L. Baldwin posted to no-tag by krapnik on 2009-03-22 19:39:32 as
	Role of electrostatic screening in determining protein main chain conformational preferences. [My Copy] Biochemistry, Vol. 34, No. 3. (24 January 1995), pp. 755-764. by F. Avbelj, J. Moult posted to no-tag by krapnik on 2009-03-22 19:10:34 as
	A review about nothing: Are apolar cavities in proteins really empty? [My Copy] Protein Science, Vol. 18, No. 3. (2009), pp. 494-502. by Brian W. Matthews, Lijun Liu posted to cleft by krapnik on 2009-03-05 11:20:47 as along with 2 people franklu310 viktor21614
	Representative Amino Acid Side Chain Interactions in Proteins. A Comparison of Highly Accurate Correlated ab Initio Quantum Chemical and Empirical Potential Procedures [My Copy] Journal of Chemical Theory and Computation, Vol. 5, No. 4. (2009), pp. 982-992. by Karel Berka, Roman Laskowski, Kevin E. Riley, Pavel Hobza, Jiří Vondrášek posted to amber force-field function interactions potential protein quantum_chemical residue-residue side-chain validation by krapnik on 2009-03-05 11:02:22 as along with 1 person carlosjavierna
	Redox Properties of Mesophilic and Hyperthermophilic Rubredoxins as a Function of Pressure and Temperature† [My Copy] Biochemistry, Vol. 38, No. 24. (1 June 1999), pp. 7874-7880. by Gilles, Eugene T. Smith posted to dielectric_constant experimental protein solvatation validation by krapnik on 2009-02-26 15:47:44 as
	Biophysical Journal - The Dependence of All-Atom Statistical Potentials on Structural Training Database [My Copy] Biophysical Journal, Vol. 86, No. 6. (1 June 2004), pp. 3349-3358. by Chi Zhang, Song Liu, Hongyi Zhou, Yaoqi Zhou posted to no-tag by krapnik on 2009-02-22 13:06:03 as
	Development of Novel Statistical Potentials Describing Cation−π Interactions in Proteins and Comparison with Semiempirical and Quantum Chemistry Approaches [My Copy] Journal of Chemical Information and Modeling, Vol. 46, No. 2. (1 March 2006), pp. 884-893. by Dimitri Gilis, Christophe Biot, Eric Buisine, Yves Dehouck, Marianne Rooman posted to force-field quantum_chemical statistical_potential validation by krapnik on 2009-02-22 12:53:51 as
	A distance-dependent atomic knowledge-based potential for improved protein structure selection [My Copy] Proteins: Structure, Function, and Genetics, Vol. 44, No. 3. (2001), pp. 223-232. by Hui Lu, Jeffrey Skolnick posted to no-tag by krapnik on 2009-02-22 09:53:14 as
	Residue contact-count potentials are as effective as residue-residue contact-type potentials for ranking protein decoys. [My Copy] BMC structural biology, Vol. 8 (08 December 2008), 53. by Dan M. Bolser, Ioannis Filippis, Henning Stehr, Jose Duarte, Michael Lappe posted to no-tag by krapnik on 2009-02-21 22:55:24 as along with 3 people tcschen RamuAnandakrishnan chad_davis

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protein	52
potential	37
folding	27
interactions	26
residue-residue	26
coarse-graining	19
modeling	18
force-field	15
water	15
conformation	14
statistical_potential	14
validation	12
analysis	11
free-energy	10
side-chain	8
coiled-coil	7
prediction	7
solvatation	7
amyloid	6
membrane	6
hydrophobicity	4
quantum_chemical	4
simulation	4
zpve	4
alzheimer	3
cleft	3
entropy	3
gpcr	3
melatonin	3
protein-ligand	3
receptor	3
software	3
thermostability	3
united-atom	3
acid	2
amber	2
benzene	2
cysteine	2
dielectric_constant	2
dispersion	2
electrostatic	2
experimental	2
function	2
guanidinium	2
hydrophilicity	2
mutation	2
pocket	2
polarizability	2
ramachandran	2
united-residue	2
vizualization	2
alignment	1
amino	1
arachidonic	1
bond	1
coding	1
conformational_entropy	1
database	1
dft	1
dipole_moment	1
dna_computation	1
estimates	1
etoh	1
gcn4	1
hf	1
hiv	1
hyperpolarizabilities	1
lattice_model	1
leucine_zipper	1
lipids	1
math	1
md	1
mean-force	1
meoh	1
mm	1
motion	1
mp2	1
nano	1
nmr	1
nonlinear_optical_properties	1
pathway	1
prion	1
proline	1
protein_folding	1
protein_protein_interactions	1
protein_structure_database	1
pymol	1
relative_toxicity	1
secondary-structure	1
structure_activity	1
threading	1
transcription_factor	1

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