jjurban's library 183 articles Export

	Alanine: Then There Was Water [My Copy] The Journal of Physical Chemistry B, Vol. 113, No. 25. (25 June 2009), pp. 8657-8669. by Jonathan M. Mullin, Mark S. Gordon posted to no-tag by jjurban on 2009-11-03 19:42:37 as
	Isosteres of peptides: boron analogs as dipolar forms of alpha-amino acids - a theoretical study [My Copy] Journal of Physical Organic Chemistry, Vol. 20, No. 2. (2007), pp. 151-160. by Alpeshkumar K. Malde, Santosh A. Khedkar, Evans C. Coutinho posted to no-tag by jjurban on 2009-11-03 19:34:59 as
	Role of Water in Structural Changes of Poly(AVGVP) and Poly(GVGVP) Studied by FTIR and Raman Spectroscopy and ab Initio Calculations [My Copy] Biomacromolecules, Vol. 6, No. 2. (1 March 2005), pp. 697-706. by Pavel Schmidt, Jiri Dybal, Jose C. Rodriguez-Cabello, Virginia Reboto posted to no-tag by jjurban on 2009-11-03 19:32:24 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 no-tag by jjurban on 2009-11-03 19:31:05 as along with 3 people flbarroso Vadikus onufriev
	Theoretical Study on Tertiary Structural Elements of β-peptides: Nanotubes Formed from Parallel-Sheet-Derived Assemblies of β-Peptides [My Copy] Journal of the American Chemical Society, Vol. 128, No. 15. (1 April 2006), pp. 5158-5167. by Tamas Beke, Imre G. Csizmadia, Andras Perczel posted to no-tag by jjurban on 2009-11-03 19:17:46 as
	Use of Constrained Synthetic Amino Acids in β-Helix Proteins for Conformational Control [My Copy] The Journal of Physical Chemistry B, Vol. 111, No. 12. (1 March 2007), pp. 3236-3242. by David Zanuy, Ana I. Jimenez, Carlos Cativiela, Ruth Nussinov, Carlos Aleman posted to no-tag by jjurban on 2009-11-03 19:16:26 as
	Conformation Dependence of the CαDα Stretch Mode in Peptides. 1. Isolated Alanine Peptide Structures [My Copy] The Journal of Physical Chemistry A, Vol. 111, No. 24. (1 June 2007), pp. 5300-5303. by Noemi G. Mirkin, Samuel Krimm posted to no-tag by jjurban on 2009-11-03 19:15:36 as
	Secondary structure binding motifs of the jet cooled tetrapeptide model Ac-Leu-Val-Tyr(Me)-NHMe [My Copy] Phys. Chem. Chem. Phys., Vol. 9, No. 32. (2007), pp. 4592-4597. by H. Fricke, G. Schafer, T. Schrader, M. Gerhards posted to no-tag by jjurban on 2009-11-03 19:14:42 as
	Site specificity of the <SUP><FONT SIZE='-1'>alpha</FONT></SUP>C&bond;H bond dissociation energy for a naturally occurring beta-hairpin peptide - An <I>ab initio</I> study [My Copy] Journal of Computational Chemistry, Vol. 30, No. 3. (2009), pp. 407-414. by Wan-Chun Cheng, Soonmin Jang, Chen-Chang Wu, Ren-Jie Lin, Hsiu-Feng Lu, Feng-Yin Li posted to density_functional_theory by jjurban on 2009-11-03 18:58:55 as
	Computing conformational free energy by deactivated morphing. [My Copy] Journal of Chemical Physics, Vol. 129, No. 13. (2008) by Sanghyun Park, Albert Y. Lau, Benoî;t Roux posted to relationship macromolecules linear free file-import-09-11-03 energy constants conformational biomolecules arbitrary analysis by jjurban on 2009-11-03 17:02:22 as
	Simple estimation of absolute free energies for biomolecules [My Copy] The Journal of Chemical Physics, Vol. 124, No. 10. (2006), 104105. by F. Marty Ytreberg, Daniel M. Zuckerman posted to dipeptide conformational_equilibrium by jjurban on 2009-11-03 16:47:22 as along with 1 person dmobley
	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
	Ab initio molecular dynamics study of proton transfer in a polyglycine analog of the ion channel gramicidin A. [My Copy] Biophysical journal, Vol. 71, No. 3. (September 1996), pp. 1172-1178. by D. E. Sagnella, K. Laasonen, M. L. Klein posted to parrinello molecular dynamics car by jjurban on 2009-11-03 04:43:22 as
	Alanine polypeptide structural fingerprints at room temperature: what can be gained from non-harmonic Car-Parrinello molecular dynamics simulations. [My Copy] The journal of physical chemistry. A, Vol. 112, No. 51. (25 December 2008), pp. 13507-13517. by M-P P. Gaigeot posted to parrinello molecular dynamics car by jjurban on 2009-11-03 04:43:22 as
	A genetic algorithm with conformational memories for structure prediction of polypeptides. [My Copy] Journal of biomolecular structure & dynamics, Vol. 21, No. 1. (August 2003), pp. 65-87. by Ramón Garduño-Juárez, Luis B. Morales posted to polyglycine by jjurban on 2009-11-03 04:11:59 as
	Calculation of the entropy and free energy by the hypothetical scanning Monte Carlo method: application to peptides. [My Copy] The Journal of chemical physics, Vol. 122, No. 5. (1 February 2005) by Srinath Cheluvaraja, Hagai Meirovitch posted to polyglycine by jjurban on 2009-11-03 04:11:59 as
	An efficient fragment-based approach for predicting the ground-state energies and structures of large molecules. [My Copy] Journal of the American Chemical Society, Vol. 127, No. 19. (18 May 2005), pp. 7215-7226. by Shuhua Li, Wei Li, Tao Fang posted to polyglycine by jjurban on 2009-11-03 04:11:59 as
	Enol-to-keto tautomerism of peptide groups. [My Copy] The journal of physical chemistry. B, Vol. 110, No. 9. (9 March 2006), pp. 4443-4450. by Katsumasa Kamiya, Mauro Boero, Kenji Shiraishi, Atsushi Oshiyama posted to polyglycine by jjurban on 2009-11-03 04:11:59 as
	Role of backbone-solvent interactions in determining conformational equilibria of intrinsically disordered proteins. [My Copy] Journal of the American Chemical Society, Vol. 130, No. 23. (11 June 2008), pp. 7380-7392. by Hoang T. Tran, Albert Mao, Rohit V. Pappu posted to polyglycine by jjurban on 2009-11-03 04:11:59 as
	Methods for calculating the absolute entropy and free energy of biological systems based on ideas from polymer physics. [My Copy] Journal of molecular recognition : JMR (31 July 2009) by Hagai Meirovitch posted to polyglycine by jjurban on 2009-11-03 04:11:59 as
	Conformationally homogeneous cyclic tetrapeptides: useful new three-dimensional scaffolds. [My Copy] Journal of the American Chemical Society, Vol. 125, No. 3. (22 January 2003), pp. 640-641. by Matthew P. Glenn, Michael J. Kelso, Joel D. Tyndall, David P. Fairlie posted to no-tag by jjurban on 2009-11-03 03:04:55 as
	Computational screening of branched cyclic peptide motifs as potential enzyme mimetics. [My Copy] Journal of peptide science : an official publication of the European Peptide Society, Vol. 9, No. 3. (March 2003), pp. 145-155. by Athanassios Stavrakoudis, Sevasti Makropoulou, Vassilios Tsikaris, Maria Sakarellos-Daitsiotis, Constantinos Sakarellos, Ioannis N. Demetropoulos posted to no-tag by jjurban on 2009-11-03 03:04:55 as
	Do benzodiazepines mimic reverse-turn structures? [My Copy] Journal of Computer-Aided Molecular Design, Vol. 20, No. 5. (May 2006), pp. 321-331. by Hata, Masayuki, Marshall, R. Garland posted to no-tag by jjurban on 2009-11-03 03:04:55 as along with 1 person higueruelo
	Synthesis and conformational studies of peptidomimetics containing a new bifunctional diketopiperazine scaffold acting as a beta-hairpin inducer. [My Copy] The Journal of organic chemistry, Vol. 73, No. 2. (18 January 2008), pp. 652-660. by Ana Sofia S. Ressurreição, Andrea Bordessa, Monica Civera, Laura Belvisi, Cesare Gennari, Umberto Piarulli posted to no-tag by jjurban on 2009-11-03 02:51:16 as
	Modeling of the intestinal peptide transporter hPepT1 and analysis of its transport capacities by docking and pharmacophore mapping. [My Copy] ChemMedChem, Vol. 3, No. 12. (December 2008), pp. 1913-1921. by Alessandro Pedretti, Laura De Luca, Cristina Marconi, Gianpaolo Negrisoli, Giancarlo Aldini, Giulio Vistoli posted to no-tag by jjurban on 2009-11-03 02:51:16 as
	Atomistic Insights into the Inhibition of Cysteine Proteases: First QM/MM Calculations Clarifying the Stereoselectivity of Epoxide-Based Inhibitors [My Copy] The Journal of Physical Chemistry B, Vol. 112, No. 37. (18 September 2008), pp. 11798-11808. by Milena Mladenovic, Kay Ansorg, Reinhold F. Fink, Walter Thiel, Tanja Schirmeister, Bernd Engels posted to no-tag by jjurban on 2009-11-02 22:17:10 as
	Coevolutionary analysis of resistance-evading peptidomimetic inhibitors of HIV-1 protease. [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 96, No. 4. (16 February 1999), pp. 1369-1374. by C. D. Rosin, R. K. Belew, G. M. Morris, A. J. Olson, D. S. Goodsell posted to inhibitor drug by jjurban on 2009-11-02 22:03:46 as
	Molecular recognition of macrocyclic peptidomimetic inhibitors by HIV-1 protease. [My Copy] Biochemistry, Vol. 38, No. 25. (22 June 1999), pp. 7978-7988. by J. L. Martin, J. Begun, A. Schindeler, et al.W. A. Wickramasinghe, D. Alewood, P. F. Alewood, D. A. Bergman, R. I. Brinkworth, G. Abbenante, D. R. March, R. C. Reid, D. P. Fairlie posted to inhibitor drug by jjurban on 2009-11-02 22:03:45 as
	A peptide inhibitor of HIV-1 protease using alpha, beta- dehydro residues: a structure based computer model. [My Copy] Indian journal of biochemistry & biophysics, Vol. 38, No. 1-2. (r 2001), pp. 90-95. by M. I. Siddiqui, S. Kataria, V. Ahuja, G. S. Rao posted to inhibitor drug by jjurban on 2009-11-02 22:03:45 as
	Free energy component analysis for drug design: a case study of HIV-1 protease-inhibitor binding. [My Copy] Journal of medicinal chemistry, Vol. 44, No. 25. (6 December 2001), pp. 4325-4338. by P. Kalra, T. V. Reddy, B. Jayaram posted to inhibitor drug by jjurban on 2009-11-02 22:03:45 as
	Computational study of the catalytic domain of human neutrophil collagenase. specific role of the S3 and S'3 subsites in the interaction with a phosphonate inhibitor. [My Copy] Journal of computer-aided molecular design, Vol. 16, No. 3. (March 2002), pp. 213-225. by Massimiliano Aschi, Danilo Roccatano, Alfredo Di Nola, et al.Carlo Gallina, Enrico Gavuzzo, Giorgio Pochetti, Michael Pieper, Harald Tschesche, Fernando Mazza posted to inhibitor drug by jjurban on 2009-11-02 22:03:45 as
	Design and synthesis of o-trifluoromethylbiphenyl substituted 2-amino-nicotinonitriles as inhibitors of farnesyltransferase. [My Copy] Bioorganic & medicinal chemistry letters, Vol. 15, No. 1. (3 January 2005), pp. 153-158. by Gary T. Wang, Xilu Wang, Weibo Wang, et al.Lisa A. Hasvold, Gerry Sullivan, Charles W. Hutchins, Steve O'Conner, Robert Gentiles, Thomas Sowin, Jerry Cohen, Wen-Zhen Z. Gu, Haiying Zhang, Saul H. Rosenberg, Hing L. Sham posted to inhibitor drug by jjurban on 2009-11-02 22:03:45 as
	Protein farnesyltransferase: flexible docking studies on inhibitors using computational modeling. [My Copy] Journal of computer-aided molecular design, Vol. 19, No. 12. (December 2005), pp. 871-885. by Wayne C. Guida, Andrew D. Hamilton, Justin W. Crotty, Saïd M. Sebti posted to inhibitor drug by jjurban on 2009-11-02 22:03:45 as
	Design, synthesis, and evaluation of 3C protease inhibitors as anti-enterovirus 71 agents. [My Copy] Bioorganic & medicinal chemistry, Vol. 16, No. 15. (1 August 2008), pp. 7388-7398. by Chih-Jung J. Kuo, Jiun-Jie J. Shie, Jim-Min M. Fang, et al.Guei-Rung R. Yen, John T-A T. Hsu, Hun-Ge G. Liu, Sung-Nain N. Tseng, Shih-Cheng C. Chang, Ching-Yin Y. Lee, Shin-Ru R. Shih, Po-Huang H. Liang posted to inhibitor drug by jjurban on 2009-11-02 22:03:45 as
	Design of peptidomimetic inhibitors of aspartic protease of HIV-1 containing -Phe Psi Pro- core and displaying favourable ADME-related properties. [My Copy] Journal of molecular graphics & modelling, Vol. 27, No. 3. (October 2008), pp. 376-387. by Vladimir Frecer, Federico Berti, Fabio Benedetti, Stanislav Miertus posted to inhibitor drug by jjurban on 2009-11-02 22:03:45 as
	Thermodynamic and computational studies on the binding of p53-derived peptides and peptidomimetic inhibitors to HDM2. [My Copy] Chembiochem : a European journal of chemical biology, Vol. 10, No. 8. (25 May 2009), pp. 1360-1368. by Anja Grässlin, Celine Amoreira, Kim K. Baldridge, John A. Robinson posted to inhibitor drug by jjurban on 2009-11-02 22:03:45 as
	Probing Membrane Insertion Activity of Antimicrobial Polymers via Coarse-Grain Molecular Dynamics [My Copy] Journal of Chemical Theory and Computation, Vol. 2, No. 3. (1 May 2006), pp. 649-655. by Carlos F. Lopez, Steven O. Nielsen, Goundla Srinivas, William F. DeGrado, Michael L. Klein posted to coarse_grain antimicrobial_compounds by jjurban on 2009-11-02 21:38:42 as along with 1 person loison
	Computational Design of Heterochiral Peptides against a Helical Target. [My Copy] J Am Chem Soc, Vol. 128, No. 3. (25 January 2006), pp. 809-816. by Vikas Nanda, William F. DeGrado posted to no-tag by jjurban on 2009-11-02 20:03:29 as along with 1 person shuns
	Foldamers as versatile frameworks for the design and evolution of function. [My Copy] Nat Chem Biol, Vol. 3, No. 5. (May 2007), pp. 252-262. by C. M. Goodman, S. Choi, S. Shandler, W. F. DeGrado posted to no-tag by jjurban on 2009-11-02 20:03:29 as along with 4 people dsekaran apaydin chgjb jwm
	Computational Design of Peptides That Target Transmembrane Helices [My Copy] Science, Vol. 315, No. 5820. (30 March 2007), pp. 1817-1822. by Hang Yin, Joanna S. Slusky, Bryan W. Berger, et al.Robin S. Walters, Gaston Vilaire, Rustem I. Litvinov, James D. Lear, Gregory A. Caputo, Joel S. Bennett, William F. DeGrado posted to no-tag by jjurban on 2009-11-02 20:03:29 as along with 7 people paulschlesinger hc5428 chad_davis zwang xxh0541 Evangelia chgjb
	New design of helix bundle peptide-polymer conjugates. [My Copy] Biomacromolecules, Vol. 9, No. 8. (August 2008), pp. 2111-2117. by Jessica Y. Shu, Cen Tan, William F. DeGrado, Ting Xu posted to no-tag by jjurban on 2009-11-02 20:03:29 as
	Computationally designed peptide inhibitors of protein-protein interactions in membranes. [My Copy] Biochemistry, Vol. 47, No. 33. (19 August 2008), pp. 8600-8606. by Gregory A. Caputo, Rustem I. Litvinov, Wei Li, Joel S. Bennett, William F. DeGrado, Hang Yin posted to no-tag by jjurban on 2009-11-02 20:03:29 as
	De novo design and in vivo activity of conformationally restrained antimicrobial arylamide foldamers. [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 106, No. 17. (28 April 2009), pp. 6968-6973. by Sungwook Choi, Andre Isaacs, Dylan Clements, et al.Dahui Liu, Hyemin Kim, Richard W. Scott, Jeffrey D. Winkler, William F. DeGrado posted to no-tag by jjurban on 2009-11-02 20:03:29 as
	Controlling the Conformation of Arylamides: Computational Studies of Intramolecular Hydrogen Bonds between Amides and Ethers or Thioethers [My Copy] Chemistry - A European Journal, Vol. 10, No. 20. (11 October 2004), pp. 5008-5016. by Robert J. Doerksen, Bin Chen, Dahui Liu, Gregory N. Tew, William F. DeGrado, Michael L. Klein posted to no-tag by jjurban on 2009-11-02 20:01:05 as
	Computational de novo design and characterization of a four-helix bundle protein that selectively binds a nonbiological cofactor. [My Copy] Journal of the American Chemical Society, Vol. 127, No. 5. (9 February 2005), pp. 1346-1347. by Frank V. Cochran, Sophia P. Wu, Wei Wang, et al.Vikas Nanda, Jeffery G. Saven, Michael J. Therien, William F. DeGrado posted to no-tag by jjurban on 2009-11-02 20:01:05 as
	Peptidic modulators of protein-protein interactions: progress and challenges in computational design. [My Copy] Biopolymers, Vol. 91, No. 7. (18 July 2009), pp. 505-513. by Mor Rubinstein, Masha Y. Niv posted to no-tag by jjurban on 2009-11-02 19:38:27 as along with 1 person higueruelo
	Hydrazino peptides as foldamers: an extension of the beta-peptide concept. [My Copy] Journal of the American Chemical Society, Vol. 123, No. 2. (17 January 2001), pp. 247-255. by R. Günther, H. J. Hofmann posted to no-tag by jjurban on 2009-11-02 19:35:38 as
	Delta-peptides and delta-amino acids as tools for peptide structure design--a theoretical study. [My Copy] The Journal of organic chemistry, Vol. 69, No. 19. (17 September 2004), pp. 6214-6220. by Carsten Baldauf, Robert Günther, Hans-Jörg J. Hofmann posted to no-tag by jjurban on 2009-11-02 19:35:38 as
	Side-chain control of folding of the homologous alpha-, beta-, and gamma-peptides into "mixed" helices (beta-helices). [My Copy] Biopolymers, Vol. 80, No. 5. (2005), pp. 675-687. by Carsten Baldauf, Robert Günther, Hans-Jörg J. Hofmann posted to no-tag by jjurban on 2009-11-02 19:35:38 as

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peptidomimetic	66
peptide_models	45
nano	21
peptides	19
computational	12
inhibitor	11
drug	11
polyglycine	6
peptoid	5
density_functional_theory	5
experimental	5
review	4
molecular	3
molecular_dynamics_simulations	3
dynamics	3
pseudopeptide	2
parrinello	2
file-import-09-11-01	2
depsipeptides	2
alanine	2
biomimic	2
car	2
electrons	1
biomolecules	1
computational_structure	1
noe	1
de	1
chemotherapy	1
energy	1
arbitrary	1
b3lyp	1
enkephalin	1
liaison	1
la	1
conformational_equilibrium	1
proteins	1
file-import-09-11-03	1
conformational	1
sn	1
modified_peptides	1
proline	1
--	1
free	1
constants	1
enthalpy	1
computational_evaluation	1
bcl-2	1
radiolysis	1
md	1
cell	1
death	1
s-n	1
linear	1
three-electron	1
coarse_grain	1
oxidation	1
antimicrobial_compounds	1
pulse	1
oxydation	1
apoptosis	1
inhibition	1
bonding	1
conformation_analysis	1
trois	1
design	1
analysis	1
pesticide	1
methionine	1
dipeptide	1
cancer	1
relationship	1
macromolecules	1

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