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	Conformational preferences of amino acids in globular proteins [My Copy] Biochemistry, Vol. 17, No. 20. (1 October 1978), pp. 4277-4285. by Michael Levitt posted to propensity amino alpha alanine acid by Vadikus on 2009-11-12 19:51:35 as
	Structural Basis of Amino Acid α Helix Propensity [My Copy] Science, Vol. 260, No. 5114. (1993), pp. 1637-1640. by Michael Blaber, Xue J. Zhang, Brian W. Matthews posted to propensity experiment alpha alanine by Vadikus on 2009-11-12 19:48:04 as
	Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes [My Copy] Journal of Computational Physics, Vol. 23, No. 3. (March 1977), pp. 327-341. by J. Ryckaert, G. Ciccotti, H. Berendsen posted to simulation shake by Vadikus on 2009-11-08 22:50:03 as along with 8 people dimka rpetrenko choonpeng gcottone stephenbond bmduggan A_Coletta_Thesis ashaytan
	Langevin stabilization of molecular dynamics [My Copy] The Journal of Chemical Physics, Vol. 114, No. 5. (2001), pp. 2090-2098. by Jesús A. Izaguirre, Daniel P. Catarello, Justin M. Wozniak, Robert D. Skeel posted to simulation langevin by Vadikus on 2009-11-08 22:44:09 as along with 1 person pavanghatty
	Synchronization of trajectories in canonical molecular-dynamics simulations: Observation, explanation, and exploitation [My Copy] The Journal of Chemical Physics, Vol. 120, No. 14. (2004), pp. 6363-6374. by Blas P. Uberuaga, Marian Anghel, Arthur F. Voter posted to simulation by Vadikus on 2009-11-08 22:37:10 as
	A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations [My Copy] Journal of Computational Chemistry, Vol. 24, No. 16. (December 2003), pp. 1999-2012. by Yong Duan, Chun Wu, Shibasish Chowdhury, et al.Mathew C. Lee, Guoming Xiong, Wei Zhang, Rong Yang, Piotr Cieplak, Ray Luo, Taisung Lee, James Caldwell, Junmei Wang, Peter Kollman posted to simulation ff03 by Vadikus on 2009-11-08 21:50:12 as along with 6 people and 1 group flbarroso ashaytan Lombardo_7 A_Coletta_Thesis xdeupi schlauchi LabCompMed
	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 to simulation gb born by Vadikus on 2009-11-08 21:39:03 as along with 5 people oteri flbarroso Lombardo_7 ttjoseph RamuAnandakrishnan
	Parametrized Models of Aqueous Free Energies of Solvation Based on Pairwise Descreening of Solute Atomic Charges from a Dielectric Medium [My Copy] The Journal of Physical Chemistry, Vol. 100, No. 51. (1 January 1996), pp. 19824-19839. by Gregory D. Hawkins, Christopher J. Cramer, Donald G. Truhlar posted to simulation gb born by Vadikus on 2009-11-08 21:33:59 as
	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 to helicity dssp by Vadikus on 2009-10-22 04:33:02 as along with 33 people dfdong barmak7282 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
	Entropy, Order Parameters, and Complexity [My Copy] by James Sethna posted to no-tag by Vadikus on 2009-10-19 17:50:01 as
	Validation of an All-Atom Protein Force Field: From Dipeptides to Larger Peptides [My Copy] The Journal of Physical Chemistry B, Vol. 107, No. 46. (1 November 2003), pp. 12555-12557. by S. Gnanakaran, Angel E. Garcia posted to simulation peptide ff alpha alanine by Vadikus on 2009-09-17 22:21:03 as along with 1 person diasc
	Folding of Polypeptide Chains in Proteins: A Proposed Mechanism for Folding [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 68, No. 9. (September 1971), pp. 2293-2297. by Peter N. Lewis, Frank A. Momany, Harold A. Scheraga posted to secondary_structure alpha_carbon alpha by Vadikus on 2009-09-17 21:11:14 as
	Identification of structural motifs from protein coordinate data: Secondary structure and first-level supersecondary structure [My Copy] Proteins: Structure, Function, and Genetics, Vol. 3, No. 2. (1988), pp. 71-84. by Frederic M. Richards, Craig E. Kundrot posted to secondary_structure prediction alpha_carbon alpha by Vadikus on 2009-09-17 20:56:01 as along with 1 person and 2 groups ana structural_bioinformatics Bioinformatics
	Protein secondary structure analyses from circular dichroism spectroscopy: Methods and reference databases [My Copy] Biopolymers, Vol. 89, No. 5. (2008), pp. 392-400. by Lee Whitmore, B. A. Wallace posted to experiment cd_spectrum cd by Vadikus on 2009-09-10 21:36:04 as
	Using circular dichroism spectra to estimate protein secondary structure [My Copy] Nature Protocols, Vol. 1, No. 6. (25 January 2007), pp. 2876-2890. by Norma J. Greenfield posted to experiment cd_spectrum cd by Vadikus on 2009-09-10 21:35:27 as
	Elasticity of alpha-Helical Coiled Coils [My Copy] Physical Review Letters, Vol. 97, No. 24. (2006), 248101. by Charles W. Wolgemuth, Sean X. Sun posted to simulation persistence helix-coil helix by Vadikus on 2009-09-02 15:58:12 as
	Effect of flexibility and cis residues in single-molecule FRET studies of polyproline [My Copy] Proceedings of the National Academy of Sciences, Vol. 104, No. 48. (27 November 2007), pp. 18964-18969. by Robert B. Best, Kusai A. Merchant, Irina V. Gopich, Benjamin Schuler, Ad Bax, William A. Eaton posted to simulation pro persistence experiment by Vadikus on 2009-09-02 15:33:32 as along with 1 person coreyrountree
	A multi-timescale strength model of alpha-helical protein domains [My Copy] Journal of Physics: Condensed Matter, Vol. 21, No. 3. (2009), 035111. by Theodor Ackbarow, Sinan Keten, Markus J. Buehler posted to timescale tensile_deformation simulation alpha by Vadikus on 2009-09-02 15:27:02 as
	Strength limit of entropic elasticity in beta-sheet protein domains [My Copy] Physical Review E (Statistical, Nonlinear, and Soft Matter Physics), Vol. 78, No. 6. (2008), 061913. by Sinan Keten, Markus J. Buehler posted to persistence peptide experiment beta_sheet by Vadikus on 2009-09-02 15:22:48 as
	Leveraging Single Protein Polymers To Measure Flexural Rigidity† [My Copy] The Journal of Physical Chemistry B, Vol. 113, No. 12. (26 March 2009), pp. 3837-3844. by Joost van Mameren, Karen C. Vermeulen, Fred Gittes, Christoph F. Schmidt posted to persistence peptide experiment by Vadikus on 2009-09-02 15:17:56 as
	Adaptively biased molecular dynamics for free energy calculations [My Copy] The Journal of Chemical Physics, Vol. 128, No. 13. (2008), 134101. by Volodymyr Babin, Christopher Roland, Celeste Sagui posted to no-tag by Vadikus on 2009-07-30 17:19:36 as along with 2 people loison dmobley
	Conformational Properties of a Peptide Model for Unfolded α-Helices† [My Copy] Biochemistry, Vol. 47, No. 10. (1 March 2008), pp. 3216-3224. by Angela M. Firestine, Veronique M. Chellgren, Shelly J. Rucker, Terrence E. Lester, Trevor P. Creamer posted to alanine alpha cd cd_spectrum experiment propensity spectroscopy by Vadikus on 2009-06-29 17:30:13 as
	Theoretical calculations of infrared absorption, vibrational circular dichroism, and two-dimensional vibrational spectra of acetylproline in liquids water and chloroform [My Copy] The Journal of Chemical Physics, Vol. 121, No. 4. (2004), pp. 1849-1865. by Seungsoo Hahn, Hochan Lee, Minhaeng Cho posted to 3_10 cd cd_spectrum dihedrals ff99 irspectroscopy pro simulation by Vadikus on 2009-06-28 22:13:32 as
	Structure of N-Acetylproline Amide in Liquid Water: Experimentally Measured and Numerically Simulated Infrared and Vibrational Circular Dichroism Spectra† [My Copy] The Journal of Physical Chemistry B, Vol. 110, No. 38. (1 September 2006), 18834. by Kyung-Koo Lee, Seungsoo Hahn, Kwang-Im Oh, et al.Jin S. Choi, Cheonik Joo, Hochan Lee, Hogyu Han, Minhaeng Cho posted to cd cd_spectrum irspectroscopy pro spectroscopy spectrum_summation by Vadikus on 2009-06-28 22:03:01 as
	Conformations of N-Acetyl-l-Prolinamide by Two-Dimensional Infrared Spectroscopy† [My Copy] The Journal of Physical Chemistry B, Vol. 110, No. 40. (1 October 2006), pp. 19891-19905. by Soohwan Sul, Denis Karaiskaj, Ying Jiang, Nien-Hui Ge posted to experiment irspectroscopy pro spectroscopy by Vadikus on 2009-06-28 21:51:00 as
	Conformations of Alanine-Based Peptides in Water Probed by FTIR, Raman, Vibrational Circular Dichroism, Electronic Circular Dichroism, and NMR Spectroscopy† [My Copy] Biochemistry, Vol. 46, No. 6. (1 February 2007), pp. 1587-1596. by Reinhard Schweitzer-Stenner, Thomas Measey, Lazaros Kakalis, et al.Frank Jordan, Silvia Pizzanelli, Claudia Forte, Kai Griebenow posted to alanine cd cd_spectrum irspectroscopy nmr raman spectroscopy experiment by Vadikus on 2009-06-28 21:43:37 as
	Carbon-deuterium vibrational probes of peptide conformation: Alanine dipeptide and glycine dipeptide [My Copy] The Journal of Chemical Physics, Vol. 130, No. 12. (2009), 125103. by C. S. Miller, E. A. Ploetz, M. E. Cremeens, S. A. Corcelli posted to alanine dihedrals dipeptide simulation by Vadikus on 2009-06-28 21:19:49 as
	DichroCalc--circular and linear dichroism online [My Copy] Bioinformatics, Vol. 25, No. 4. (15 February 2009), pp. 539-540. by Benjamin M. Bulheller, Jonathan D. Hirst posted to cd_spectrum prediction spectroscopy by Vadikus on 2009-06-28 20:36:22 as
	Solvent-dependent conformational distributions of some dipeptides [My Copy] Journal of the American Chemical Society, Vol. 102, No. 15. (1 July 1980), pp. 4855-4863. by Vincent Madison, Kenneth D. Kopple posted to cd cd_spectrum pro spectroscopy experiment by Vadikus on 2009-06-28 14:21:43 as
	Classical and quantum mechanical/molecular mechanical molecular dynamics simulations of alanine dipeptide in water: Comparisons with IR and vibrational circular dichroism spectra [My Copy] The Journal of Chemical Physics, Vol. 128, No. 10. (2008), 105106. by Kijeong Kwac, Kyung K. Lee, Jae B. Han, Kwang I. Oh, Minhaeng Cho posted to alanine cd cd_spectrum dihedrals ff03 simulation spectroscopy experiment by Vadikus on 2009-06-28 14:09:05 as
	Natural Circular Dichroism Spectra of Alanine and Valine Films in Vacuum Ultraviolet Region [My Copy] Journal of the Physical Society of Japan, Vol. 78, No. 1. (2009) by Fusae Kaneko, Kazutoshi Y. Watanabe, Masahito Tanaka, Kazumichi Nakagawa posted to cd cd_spectrum dft simulation val alanine experiment by Vadikus on 2009-06-28 13:57:52 as
	Comparison of Quantitative Conformer Analyses by Nuclear Magnetic Resonance and Raman Optical Activity Spectra for Model Dipeptides [My Copy] The Journal of Physical Chemistry A, Vol. 112, No. 37. (18 September 2008), pp. 8633-8640. by Miloš Buděšínský, Petr Daněček, Lucie Bednárová, Josef Kapitán, Vladimír Baumruk, Petr Bouř posted to alanine dft dihedrals dipeptide ff99 raman raman_simulation by Vadikus on 2009-06-28 13:19:55 as
	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 to ff99sb by Vadikus on 2009-06-28 05:49:00 as along with 10 people arnaucordomi bmduggan baaden lna allmensch choonpeng kazemi barry GermanErlenkamp RamuAnandakrishnan
	Energy Landscapes Associated with the Self-Aggregation of an Alanine-Based Oligopeptide (AAKA)4 [My Copy] The Journal of Physical Chemistry B, Vol. 113, No. 17. (30 April 2009), pp. 6054-6061. by Soonmin Jang, Jian-Min Yuan, Jungho Shin, Thomas J. Measey, Reinhard Schweitzer-Stenner, Feng-Yin Li posted to aaka alanine betta cv hbond remd temperature water_solution by Vadikus on 2009-05-22 21:50:27 as
	Experimental molecular dynamics of an alanine-based helical peptide determined by spin label electron spin resonance [My Copy] Biochemistry, Vol. 32, No. 31. (1 August 1993), pp. 8014-8021. by Siobhan M. Miick, Karen M. Casteel, Glenn L. Millhauser posted to 3k alanine alpha experiment nmr by Vadikus on 2009-05-20 18:23:40 as
	Estimating the relative populations of 310-helix and α-helix in Ala-rich peptides: a hydrogen exchange and high field NMR study1 [My Copy] Journal of Molecular Biology, Vol. 267, No. 4. (11 April 1997), pp. 963-974. by Glenn L. Millhauser, Chris J. Stenland, Paul Hanson, Kimberly A. Bolin, Frank J. van de Ven posted to 3_10 3k alanine alpha experiment nmr by Vadikus on 2009-05-20 18:14:21 as
	Computer Simulation Studies of Finite Temperature Conformational Equilibrium in Alanine-Based Peptides [My Copy] The Journal of Physical Chemistry B, Vol. 103, No. 10. (1 March 1999), pp. 1752-1766. by S. Samuelson, G. J. Martyna posted to 3k alanine simulation by Vadikus on 2009-05-20 18:08:23 as
	Nitroxide Side-Chain Dynamics in a Spin-Labeled Helix-Forming Peptide Revealed by High-Frequency (139.5-GHz) EPR Spectroscopy [My Copy] Journal of Magnetic Resonance, Vol. 139, No. 2. (1999) by M. Bennati, G. J. Gerfen, G. V. Martinez, R. G. Griffin, D. J. Singel, G. L. Millhauser posted to 3k alpha anisotropic dynamics epr experiment frequency high motion peptide side-chain by Vadikus on 2009-05-20 17:47:27 as
	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 to 3k alanine alpha simulation by Vadikus on 2009-05-19 19:04:54 as along with 3 people jjurban flbarroso onufriev
	Molecular dynamics guided study of salt bridge length dependence in both fluorinated and non-fluorinated parallel dimeric coiled-coils [My Copy] Proteins: Structure, Function, and Bioinformatics, Vol. 9999, No. 9999. (2008), NA. by Scott S. Pendley, Yihua B. Yu, Thomas E. Cheatham posted to alpha amino ff99sb helix helix-coil long_run molecular simulation water_solution by Vadikus on 2009-05-18 17:22:21 as along with 2 people and 1 group oteri Lombardo_7 LOX-1 Receptor
	Optimal temperature ladders in replica exchange simulations [My Copy] Chemical Physics Letters, Vol. 473, No. 1-3. (29 April 2009), pp. 193-195. by Robert Denschlag, Martin Lingenheil, Paul Tavan posted to remd temperature by Vadikus on 2009-05-12 22:49:12 as
	Structural Transitions in the Polyalanine α-Helix under Uniaxial Strain [My Copy] Journal of the American Chemical Society, Vol. 127, No. 49. (1 December 2005), pp. 17241-17244. by Joel Ireta, Jorg Neugebauer, Matthias Scheffler, Arturo Rojo, Marcelo Galvan posted to 3_10 alanine alpha cv pi simulation by Vadikus on 2009-05-12 16:21:37 as
	Hydrogen bonding in globular proteins [My Copy] Progress in Biophysics and Molecular Biology, Vol. 44, No. 2. (1984), pp. 97-179. by E. Baker posted to 3_10 alpha hbond helix pi by Vadikus on 2009-05-08 13:03:37 as
	Evaluation of coarse grained models for hydrogen bonds in proteins. [My Copy] J Comput Chem (13 February 2007) by David De Sancho, Antonio Rey posted to acid amino cv hbond method statistics by Vadikus on 2009-05-08 13:00:34 as along with 3 people dgront choonpeng mijam
	α-Helix folding in the presence of structural constraints [My Copy] Proceedings of the National Academy of Sciences, Vol. 105, No. 28. (15 July 2008), pp. 9588-9593. by Janne A. Ihalainen, Beatrice Paoli, Stefanie Muff, et al.Ellen H. Backus, Jens Bredenbeck, Andrew G. Woolley, Amedeo Caflisch, Peter Hamm posted to alanine alpha experiment by Vadikus on 2009-05-08 12:55:46 as
	Helix geometry in proteins [My Copy] Journal of Molecular Biology, Vol. 201, No. 3. (05 June 1988), pp. 601-619. by D. Barlow, J. Thornton posted to 3_10 alpha dihedrals statistics by Vadikus on 2009-05-08 12:43:11 as
	The helix-coil transition in heterogeneous peptides with specific side-chain interactions: Theory and comparison with CD spectral data [My Copy] Biopolymers, Vol. 31, No. 13. (1991), pp. 1605-1614. by Paul J. Gans, Pingchiang C. Lyu, Mark C. Manning, Robert W. Woody, Neville R. Kallenbach posted to acid alpha amino helix-coil position by Vadikus on 2009-05-07 20:00:13 as
	Stabilizing Helical Polyalanine Peptides with Negative Polarity or Charge: Capping with Cysteine [My Copy] The Journal of Physical Chemistry B, Vol. 112, No. 18. (1 May 2008), pp. 5702-5709. by Silvya Oommachen, Jianhua Ren, Michael C. Mccallum posted to 3_10 alanine alpha gromass simulation by Vadikus on 2009-05-07 19:54:01 as
	pi-Turns: types, systematics and the context of their occurrence in protein structures [My Copy] BMC Structural Biology, Vol. 8 (22 September 2008), 39. by Bhaskar Dasgupta, Pinak Chakrabarti posted to biophysics dihedrals helicity pi by Vadikus on 2009-05-07 19:34:26 as along with 1 person bd4g
	Conformational Manifold of α-Aminoisobutyric Acid (Aib) Containing Alanine-Based Tripeptides in Aqueous Solution Explored by Vibrational Spectroscopy, Electronic Circular Dichroism Spectroscopy, and Molecular Dynamics Simulations [My Copy] Journal of the American Chemical Society, Vol. 129, No. 43. (1 October 2007), pp. 13095-13109. by Reinhard Schweitzer-Stenner, Widalys Gonzales, Gregory T. Bourne, Jianwen A. Feng, Garland R. Marshall posted to aib alanine experiment raman simulation spectroscopy by Vadikus on 2009-05-07 05:11:04 as

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biophysics	1
shake	1
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