Tag alanine [58 articles] Export

Recent papers classified by the tag alanine.

	Calculation of free-energy differences by confinement simulations. Application to peptide conformers. [My Copy] The journal of physical chemistry. B, Vol. 113, No. 29. (23 July 2009), pp. 9728-9740. by M. Cecchini, S. V. Krivov, M. Spichty, M. Karplus posted to molecular_dynamics_simulations alanine by jjurban on 2009-11-03 13:46:21 as
	Unravelling the conformational dynamics of the aqueous alanine dipeptide with first-principle molecular dynamics. [My Copy] The journal of physical chemistry. B, Vol. 113, No. 30. (30 July 2009), pp. 10059-10062. by M-P P. Gaigeot posted to molecular_dynamics_simulations alanine by jjurban on 2009-11-03 13:46:21 as
	Relationship between local structure and stability in hen egg white lysozyme mutant with alanine substituted for glycine. [My Copy] Protein engineering, Vol. 13, No. 10. (October 2000), pp. 691-695. by K. Masumoto, T. Ueda, H. Motoshima, T. Imoto posted to mutation masumot00pdf lysozyme glycine dihedral angles alanine by paulschlesinger on 2009-10-27 23:28:45 as
	Probing the role of the conserved beta-II turn Pro-76/Gly-77 of mitochondrial cytochrome c. [My Copy] Biochemistry and cell biology = Biochimie et biologie cellulaire, Vol. 85, No. 3. (June 2007), pp. 366-374. by Karen M. Black, Carmichael J. Wallace posted to modulation dihedral cytochrome c black07pdf angle alanine by paulschlesinger on 2009-10-27 23:00:40 as
	Diverse Roles of Glycine Residues Conserved in Photoactive Yellow Proteins☆ [My Copy] Biophysical Journal, Vol. 94, No. 9. (01 May 2008), pp. 3620-3628. by Yasushi Imamoto, Sanae Tatsumi, Miki Harigai, Yoichi Yamazaki, Hironari Kamikubo, Mikio Kataoka posted to omamo08pdf mutation glycine conserved alanine by paulschlesinger on 2009-10-27 22:14:01 as
	Water and Alanine: From Puddles(32) to Ponds(49) [My Copy] The Journal of Physical Chemistry B, Vol. 113, No. 43. (29 October 2009), pp. 14413-14420. by Jonathan M. Mullin, Mark S. Gordon posted to alanine ala by carlosjavierna on 2009-10-23 01:30:29 as along with 2 people and 1 group qshao whitead Jiang Research Group
	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
	Conformational entropy of alanine versus glycine in protein denatured states [My Copy] Proceedings of the National Academy of Sciences, Vol. 104, No. 8. (20 February 2007), pp. 2661-2666. by Kathryn A. Scott, Darwin O. V. Alonso, Satoshi Sato, Alan R. Fersht, Valerie Daggett posted to hexapeptide glycine free-energy conformational_entropy alanine by Diego_Prada on 2009-09-17 12:38:50 as
	Conformational changes in polypeptides and proteins [My Copy] International Journal of Quantum Chemistry, Vol. 9999, No. 9999. (2009), NA. by Alexander V. Yakubovich, Andrey V. Solov'yov, Walter Greiner posted to ala alanine conformational-change molecular-dynamics-simulations por-conseguir proteins by carlosjavierna on 2009-08-05 17:19:29 as
	Conformation dependence of the C<SUP><FONT SIZE='-1'>alpha</FONT></SUP>D<SUP><FONT SIZE='-1'>alpha</FONT></SUP> stretch mode in peptides. II. Explicitly hydrated alanine peptide structures [My Copy] Biopolymers, Vol. 91, No. 9. (2009), pp. 791-800. by Noemi G. Mirkin, Samuel Krimm posted to ala alanine por-conseguir by carlosjavierna on 2009-08-05 06:22:37 as
	A conserved NA+ binding site of the sodium-coupled neutral amino acid transporter 2 (SNAT2) [My Copy] J. Biol. Chem. (9 July 2009), M109.038422. by Zhou Zhang, Thomas Albers, Heather L. Fiumera, Armanda Gameiro, Christof Grewer posted to ala alanine mutagenesis thr threonine by carlosjavierna on 2009-07-16 00:06:42 as
	Molecular Dynamics Investigations on the Effect of d Amino Acid Substitution in a Triple-Helix Structure and the Stability of Collagen [My Copy] The Journal of Physical Chemistry B, Vol. 113, No. 26. (2 July 2009), pp. 8983-8992. by V. Punitha, Sundar S. Raman, R. Parthasarathi, et al.V. Subramanian, J. Raghava Rao, Balachandran U. Nair, T. Ramasami posted to ala alanine amber amino-acid amino-acids helix molecular-dynamics molecular-dynamics-simulations by carlosjavierna on 2009-07-13 06:05:04 as
	Mutations That Increase DNA Binding by the Processivity Factor of Herpes Simplex Virus Affect Virus Production and DNA Replication Fidelity [My Copy] J. Virol., Vol. 83, No. 15. (1 August 2009), pp. 7573-7580. by Changying Jiang, Gloria Komazin-Meredith, Wang Tian, Donald M. Coen, Charles B. C. Hwang posted to ala alanine arg arginine gln glutamine mutagenesis mutation by carlosjavierna on 2009-07-12 16:07:37 as
	Identification of Spectroscopic Patterns of CH···O H-Bonds in Proteins [My Copy] The Journal of Physical Chemistry B, Vol. 0, No. 0. (0000) by Steve Scheiner posted to ala alanine gly glycine hydrogen-bonds proteins by carlosjavierna on 2009-07-12 15:17:16 as
	Solvation and Hydrogen Bonding in Alanine- and Glycine-Containing Dipeptides Probed Using Solution- and Solid-State NMR Spectroscopy [My Copy] Journal of the American Chemical Society, Vol. 131, No. 27. (15 July 2009), pp. 9579-9589. by Manasi P. Bhate, Jaie C. Woodard, Manish A. Mehta posted to ala alanine dipeptide gly glycine hydrogen-bonds solvation by carlosjavierna on 2009-07-11 20:34:08 as along with 2 people and 1 group yzlab qaiser_fatmi Chang group
	An A257V mutation in the Bacillus subtilis response regulator Spo0A prevents regulated expression of promoters with low consensus binding sites [My Copy] J. Bacteriol. (6 July 2009), JB.00590-09. by Steve D. Seredick, Barbara M. Seredick, David Baker, George B. Spiegelman posted to ala alanine binding-site binding-sites molecular-recognition mutagenesis val valine by carlosjavierna on 2009-07-08 17:54:52 as
	Mutation of tyrosine 190 to alanine eliminates the inactivation of cytochrome P450 2B1 by peroxynitrite. [My Copy] Chemical research in toxicology, Vol. 16, No. 2. (February 2003), pp. 129-136. by H. L. Lin, U. M. Kent, H. Zhang, L. Waskell, P. F. Hollenberg posted to alanine cytochrome mutation p450 peroxynitrite tyrosine by fisherp on 2009-07-08 17:20:41 as
	Structure of the Alanine Hydration Shell as Probed by NMR Chemical Shifts and Indirect Spin−Spin Coupling [My Copy] The Journal of Physical Chemistry B, Vol. 113, No. 44. (5 November 2009), pp. 14698-14707. by Martin Dračínský, Jakub Kaminský, Petr Bouř posted to alanine experiment nmr structure water by whitead to the group Jiang Research Group on 2009-07-07 20:13:25 as along with 4 people ehesan kubikuk thegoose carlosjavierna
	Unravelling the Conformational Dynamics of the Aqueous Alanine Dipeptide with First-Principle Molecular Dynamics [My Copy] The Journal of Physical Chemistry B, Vol. 113, No. 30. (30 July 2009), pp. 10059-10062. by M. P. Gaigeot posted to alanine cpmd by whitead to the group Jiang Research Group on 2009-07-06 21:11:09 as along with 3 people and 1 group loison jmccammon carlosjavierna McCammon
	l-Alanyl-l-alanine Conformational Changes Induced by pH As Monitored by the Raman Optical Activity Spectra [My Copy] The Journal of Physical Chemistry A, Vol. 113, No. 27. (9 July 2009), pp. 7760-7768. by Jiří Šebek, Josef Kapitán, Jaroslav Šebestík, Vladimír Baumruk, Petr Bouř posted to ala alanine conformational conformational-change by carlosjavierna on 2009-07-06 02:04:14 as
	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
	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
	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
	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
	The Active Form of Human Aryl Hydrocarbon Receptor (AHR) Repressor Lacks Exon 8, and Its Pro185 and Ala185 Variants Repress both AHR and Hypoxia-Inducible Factor [My Copy] Mol. Cell. Biol., Vol. 29, No. 13. (1 July 2009), pp. 3465-3477. by Sibel I. Karchner, Matthew J. Jenny, Ann M. Tarrant, et al.Brad R. Evans, Hyo J. Kang, Insoo Bae, David H. Sherr, Mark E. Hahn posted to ala alanine pro proline by carlosjavierna on 2009-06-15 17:47:48 as
	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
	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
	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
	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
	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
	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
	First-Principles Free-Energy Analysis of Helix Stability: The Origin of the Low Entropy in π Helices [My Copy] The Journal of Physical Chemistry B, Vol. 112, No. 13. (1 April 2008), pp. 4109-4112. by Lars Ismer, Joel Ireta, Jorg Neugebauer posted to 3_10 alanine alpha dft pi simulation by Vadikus on 2009-05-07 04:41:45 as
	Chapter 1 Stability and Design of α-Helical Peptides [My Copy] In Molecular Biology of Protein Folding, Part A, Vol. 83 (2008), pp. 1-52. by A. Doig posted to 3_10 acid alanine alpha amino dihedrals helix by Vadikus on 2009-05-06 16:52:12 as
	Helix Forming Tendency of Valine Substituted Poly-Alanine: A Molecular Dynamics Investigation [My Copy] The Journal of Physical Chemistry B, Vol. 112, No. 30. (1 July 2008), pp. 9100-9104. by Sundar S. Raman, R. Vijayaraj, R. Parthasarathi, V. Subramanian posted to 3_10 alanine alpha helix simulation read by Vadikus on 2009-05-04 04:03:39 as
	Studying the structural properties of polyalanine and polyglutamine peptides [My Copy] Journal of Molecular Modeling, Vol. 13, No. 11. (November 2007), pp. 1141-1150. by Balazs Leitgeb, Adam Kerenyi, Ferenc Bogar, Gabor Paragi, Botond Penke, Gabor Rakhely posted to 3_10 alanine alpha bad dihedrals simulation read by Vadikus on 2009-05-04 03:21:36 as
	Comparison of a QM/MM force field and molecular mechanics force fields in simulations of alanine and glycine ldquodipeptidesrdquo (Ace-Ala-Nme and Ace-Gly-Nme) in water in relation to the problem of modeling the unfolded peptide backbone in solution [My Copy] Proteins: Structure, Function, and Bioinformatics, Vol. 50, No. 3. (15 February 2003), pp. 451-463. by Hao Hu, Marcus Elstner, Jan Hermans posted to alanine amber charmm comparison dipeptide forcefield gromos plot protein ramachandran by paddydu on 2009-02-25 17:22:05 as along with 3 people Diego_Prada flbarroso allmensch
	Reaction coordinates of biomolecular isomerization. [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 97, No. 11. (23 May 2000), pp. 5877-5882. by P. G. Bolhuis, C. Dellago, D. Chandler posted to alanine dipeptide folding path protein sampling transition by paddydu on 2009-02-25 17:17:40 as along with 3 people stephenbond doktornoe Diego_Prada
	4D 1H−13C NMR Spectroscopy for Assignments of Alanine Methyls in Large and Complex Protein Structures [My Copy] Journal of the American Chemical Society, Vol. 131, No. 4. (4 February 2009), pp. 1364-1365. by Devon Sheppard, Chenyun Guo, Vitali Tugarinov posted to ala alanine by carlosjavierna on 2009-02-04 19:31:04 as along with 1 person mkrishna
	Molecular dynamics simulations of alanine rich beta-sheet oligomers: Insight into amyloid formation [My Copy] Protein Science, Vol. 11, No. 10. (1 October 2002), pp. 2335-2350. by Buyong Ma, Ruth Nussinov posted to alanine amyloid mds simulations by chiufanlee on 2008-11-12 14:32:47 as along with 1 person Diego_Prada
	The equivalent potential of water molecules for electronic structure of alanine [My Copy] Molecular Physics, Vol. 106, No. 11. (2008), pp. 1427-1439. by Shu Yan, Haoping Zheng, Tian Zhang posted to alanine by middledomain on 2008-09-09 21:23:42 as
	Temperature and Pressure Dependence of Alanine Dipeptide Studied by Multibaric−Multithermal Molecular Dynamics Simulations [My Copy] J. Phys. Chem. B (30 August 2008) by Hisashi Okumura, Yuko Okamoto posted to alanine dinamics dipeptide simulation by paulschlesinger on 2008-09-04 00:59:56 as
	l-Alanine hydrochloride monohydrate [My Copy] Acta Crystallographica Section E: Structure Reports Online, Vol. 64, No. 5. (01 May 2008), pp. 806-806. by K. Yamada, A. Sato, T. Shimizu, T. Yamazaki, S. Yokoyama posted to alanine amino_acids crystal_structure by andreasauerwein on 2008-08-22 10:09:26 as
	A comparison of the CHARMM, AMBER and ECEPP potentials for peptides. II. Phi-psi maps for N-acetyl alanine N'-methyl amide: comparisons, contrasts and simple experimental tests. [My Copy] Journal of biomolecular structure & dynamics, Vol. 7, No. 3. (December 1989), pp. 421-453. by I. K. Roterman, M. H. Lambert, K. D. Gibson, H. A. Scheraga posted to chapt_cmn alanine amino dialanine plos by Diego_Prada on 2008-08-03 18:21:35 as
	Modeling the Microhydration of Protonated Alanine [My Copy] J. Phys. Chem. B (23 July 2008) by Catherine Michaux, Johan Wouters, Eric A. Perpète, Denis Jacquemin posted to alanine by middledomain on 2008-07-23 16:48:56 as
	Resolution Enhancement in Multiple-Quantum MAS NMR Spectroscopy [My Copy] Journal of Magnetic Resonance, Vol. 133, No. 1. (July 1998), pp. 61-69. by Ingo Schnell, Adonis Lupulescu, Siegfried Hafner, Dan E. Demco, Hans W. Spiess posted to 1h_ssnmr alanine amino_acids cshift homonuclear_dipolar_recoupling by andreasauerwein on 2008-07-15 11:26:40 as
	NMR chemical shifts in amino acids: effects of environments in the condensed phase [My Copy] Solid State Communications, Vol. 131, No. 1. (July 2004), pp. 15-19. by Young-Gui Yoon, Bernd G. Pfrommer, Steven G. Louie, Andrew Canning posted to alanine amino_acids glycine h_cshift by andreasauerwein on 2008-07-10 15:05:44 as

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ala	14
alpha	12
simulation	12
experiment	9
3_10	7
dipeptide	7
nmr	7
beta	6
glycine	6
carnosine	5
dihedrals	5
3k	4
amino_acids	4
glutamine	4
mutation	4
spectroscopy	4
astrocyte	3
cd	3
cd_spectrum	3
helix	3
lactate	3
mutagenesis	3
por-conseguir	3
raman	3
amber	2
amino	2
aspartate	2
cell_culture	2
conformational-change	2
cpmd	2
crystal_structure	2
cv	2
cytochrome	2
dft	2
dihedral	2
exercise	2
glutamate	2
glutamine_synthetase	2
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mice	2
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publications	2
read	2
structure	2
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valine	2
water	2
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31p	1
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aconitase	1
adp	1
aib	1
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aminooxyacetic_acid	1
amp	1
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brainstem	1
c	1
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glia	1
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gromos	1
hexapeptide	1
hypoglossus	1
isoleucine	1
mass_spectrometry	1
masumot00pdf	1
mds	1
molecular-dynamics	1
mp2	1
neuron-glia_interaction	1
omamo08pdf	1
pag	1
peroxynitrite	1
plos	1
position	1
pre-btzinger_complex	1
ramachandran	1
sampling	1
simulations	1
temperature	1
transition	1
weight	1

Tag alanine [58 articles] Export

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