carlosjavierna's molecular-dynamics [56 articles] Export Sort

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	Apo and Nickel-Bound Forms of the Pyrococcus horikoshii Species of the Metalloregulatory Protein: NikR Characterized by Molecular Dynamics Simulations [My Copy] Biochemistry, Vol. 48, No. 50. (22 December 2009), pp. 12024-12033. by Daniel J. Sindhikara, Adrian E. Roitberg, Kenneth M. Merz posted to molecular-dynamics-simulations molecular-dynamics kenethmerz by carlosjavierna on 2009-12-17 06:06:12 as
	Common Folding Mechanism of a β-Hairpin Peptide via Non-native Turn Formation Revealed by Unbiased Molecular Dynamics Simulations [My Copy] Journal of the American Chemical Society, Vol. 131, No. 50. (23 December 2009), pp. 18147-18152. by Lipi Thukral, Jeremy C. Smith, Isabella Daidone posted to por-conseguir molecular-dynamics-simulations molecular-dynamics folding beta-hairpin by carlosjavierna on 2009-12-17 04:24:41 as
	The L49F mutation in alpha erythroid spectrin induces local disorder in the tetramer association region: Fluorescence and molecular dynamics studies of free and bound alpha spectrin [My Copy] Protein Science, Vol. 9999, No. 9999. (2009), NA. by Yuanli Song, Nina H. Pipalia, -M posted to leu leucine molecular-dynamics phe phenylalanine by carlosjavierna on 2009-08-05 06:44:18 as
	Deconstructing the Native State: Energy Landscapes, Function, and Dynamics of Globular Proteins [My Copy] The Journal of Physical Chemistry B, Vol. 113, No. 26. (2 July 2009), pp. 8800-8812. by Pavel I. Zhuravlev, Christopher K. Materese, Garegin A. Papoian posted to featured-article molecular-dynamics molecular-dynamics-simulations by carlosjavierna on 2009-07-13 06:13:40 as along with 1 person and 1 group jmccammon McCammon
	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
	Optimized Molecular Dynamics Force Fields Applied to the Helix−Coil Transition of Polypeptides [My Copy] The Journal of Physical Chemistry B, Vol. 113, No. 26. (2 July 2009), pp. 9004-9015. by Robert B. Best, Gerhard Hummer posted to coil force-field force-fields helix hummer molecular-dynamics polypeptides by carlosjavierna on 2009-07-13 06:02:42 as
	Molecular Dynamics Study of a Polymeric Reverse Osmosis Membrane [My Copy] The Journal of Physical Chemistry B, Vol. 0, No. 0. (0000) by Edward Harder, D. Eric Walters, Yaroslav D. Bodnar, Ron S. Faibish, Benoît Roux posted to molecular-dynamics molecular-dynamics-simulations roux-benoit by carlosjavierna on 2009-07-12 15:28:44 as
	Polarization Effects Stabilize Bacteriorhodopsin’s Chromophore Binding Pocket: A Molecular Dynamics Study [My Copy] The Journal of Physical Chemistry B, Vol. 0, No. 0. (0000) by G. Babitzki, R. Denschlag, P. Tavan posted to molecular-dynamics molecular-dynamics-simulations by carlosjavierna on 2009-07-12 15:15:39 as
	Absolute Hydration Entropies of Alkali Metal Ions from Molecular Dynamics Simulations [My Copy] The Journal of Physical Chemistry B, Vol. 113, No. 30. (30 July 2009), pp. 10255-10260. by Jens Carlsson, Johan Åqvist posted to aqvist carlssonj molecular-dynamics molecular-dynamics-simulations by carlosjavierna on 2009-07-12 15:12:55 as along with 2 people francescamocci sobolevnrm
	Temperature-Dependent Mechanisms for the Dynamics of Protein-Hydration Waters: A Molecular Dynamics Simulation Study [My Copy] The Journal of Physical Chemistry B, Vol. 113, No. 28. (16 July 2009), pp. 9386-9392. by M. Vogel posted to molecular-dynamics molecular-dynamics-simulations proteins water by carlosjavierna on 2009-07-11 15:04:23 as along with 2 people and 1 group willard whitead Jiang Research Group
	Mechanical Properties of Glassy Polyethylene Nanofibers via Molecular Dynamics Simulations [My Copy] Macromolecules, Vol. 42, No. 13. (14 July 2009), pp. 4887-4895. by Sezen Buell, Krystyn J. Van Vliet, Gregory C. Rutledge posted to molecular-dynamics molecular-dynamics-simulations by carlosjavierna on 2009-07-08 16:14:00 as
	Molecular dynamics simulation study on conformational behavior of Aβ(1–40) and Aβ(1–42) in water and methanol [My Copy] Journal of Molecular Structure: THEOCHEM, Vol. 907, No. 1-3. (15 August 2009), pp. 51-56. by Cao Yang, Xiaolei Zhu, Jinyu Li, Kai Chen posted to conformational conformational-behavior molecular-dynamics molecular-dynamics-simulations by carlosjavierna on 2009-07-07 03:43:12 as
	Molecular Dynamics Simulation of Nanoconfinement Induced Organization of n-Decane [My Copy] Langmuir, Vol. 25, No. 13. (7 July 2009), pp. 7553-7560. by Valliappa Kalyanasundaram, Douglas E. Spearot, Ajay P. Malshe posted to molecular-dynamics molecular-dynamics-simulations by carlosjavierna on 2009-07-06 03:13:23 as
	Molecular Dynamics Simulations of Water Transport through Butanol Films [My Copy] The Journal of Physical Chemistry A, Vol. 113, No. 30. (30 July 2009), pp. 8586-8590. by A. Gilde, N. Siladke, C. P. Lawrence posted to molecular-dynamics molecular-dynamics-simulations by carlosjavierna on 2009-07-05 19:41:17 as
	Structure and Stability of (α-CD)3 Aggregate and OEG@(α-CD)3 Pseudorotaxane in Aqueous Solution: A Molecular Dynamics Study [My Copy] The Journal of Physical Chemistry B, Vol. 0, No. 0. (0000) by Cleber P. Anconi, Clebio S. Nascimento, Wagner B. De Almeida, Hélio F. Dos Santos posted to cyclodextrin molecular-dynamics molecular-dynamics-simulations by carlosjavierna on 2009-07-05 18:45:22 as
	Flaviviral Protease Inhibitors Identified by Fragment-Based Library Docking into a Structure Generated by Molecular Dynamics [My Copy] Journal of Medicinal Chemistry, Vol. 52, No. 15. (13 August 2009), pp. 4860-4868. by Dariusz Ekonomiuk, Xun-Cheng Su, Kiyoshi Ozawa, et al.Christophe Bodenreider, Siew P. Lim, Gottfried Otting, Danzhi Huang, Amedeo Caflisch posted to docking molecular-dynamics molecular-dynamics-simulations by carlosjavierna on 2009-07-05 17:42:28 as along with 3 people and 1 group ubcg08l pmung jmccammon McCammon
	Molecular Dynamics Simulation of the Diffusion of Au and Pt Nanoclusters on Carbon Nanotubes [My Copy] The Journal of Physical Chemistry C, Vol. 113, No. 24. (18 June 2009), pp. 10416-10421. by Dong H. Seo, Hyun Y. Kim, Ji H. Ryu, Hyuck M. Lee posted to molecular-dynamics molecular-dynamics-simulations by carlosjavierna on 2009-06-12 23:15:35 as
	Cation Behavior in Faujasite Zeolites upon Water Adsorption: A Combination of Monte Carlo and Molecular Dynamics Simulations [My Copy] The Journal of Physical Chemistry C, Vol. 113, No. 24. (18 June 2009), pp. 10696-10705. by Cyril Abrioux, Benoit Coasne, Guillaume Maurin, François Henn, Marie Jeffroy, Anne Boutin posted to molecular-dynamics molecular-dynamics-simulations monte-carlo by carlosjavierna on 2009-06-12 23:14:59 as
	Molecular Dynamics Simulations on the Interface between Titanium Dioxide and Water Droplets: A New Model for the Contact Angle [My Copy] The Journal of Physical Chemistry C, Vol. 113, No. 23. (11 June 2009), pp. 10189-10197. by B. Ohler, W. Langel posted to molecular-dynamics molecular-dynamics-simulations by carlosjavierna on 2009-06-05 16:52:11 as along with 1 person willard
	Molecular dynamics studies on the interactions of PTP1B with inhibitors: from the first phosphate-binding site to the second one [My Copy] Protein Engineering, Design and Selection, Vol. 22, No. 6. (1 June 2009), pp. 349-355. by Jing-Fang Wang, Ke Gong, Dong-Qing Wei, Yi-Xue Li, Kuo-Chen Chou posted to molecular-dynamics molecular-dynamics-simulations by carlosjavierna on 2009-06-03 14:44:52 as
	Protein Conformational Transitions: The Closure Mechanism of a Kinase Explored by Atomistic Simulations [My Copy] Journal of the American Chemical Society, Vol. 131, No. 1. (14 January 2009), pp. 244-250. by Anna Berteotti, Andrea Cavalli, Davide Branduardi, Francesco L. Gervasio, Maurizio Recanatini, Michele Parrinello posted to modeling molecular-dynamics molecular-dynamics-simulations molecular-modeling open-to-closed by carlosjavierna on 2009-03-15 18:25:26 as along with 1 person and 1 group iivanov McCammon
	Side-Chain to Backbone Interactions Dictate the Conformational Preferences of a Cyclopentane Arginine Analogue [My Copy] The Journal of Organic Chemistry, Vol. 74, No. 6. (20 March 2009), pp. 2403-2412. by Guillem Revilla-López, Juan Torras, Ana I. Jiménez, Carlos Cativiela, Ruth Nussinov, Carlos Alemán posted to arg argi arginine modeling molecular-dynamics molecular-dynamics-simulations molecular-modeling by carlosjavierna on 2009-03-15 17:38:42 as
	Role of Cardiolipins in the Inner Mitochondrial Membrane: Insight Gained through Atom-Scale Simulations [My Copy] The Journal of Physical Chemistry B, Vol. 113, No. 11. (19 March 2009), pp. 3413-3422. by Tomasz Róg, Hector Martinez-Seara, Nana Munck, Matej Orešič, Mikko Karttunen, Ilpo Vattulainen posted to modeling molecular-dynamics molecular-dynamics-simulations molecular-modeling by carlosjavierna on 2009-03-15 17:06:28 as along with 2 people and 1 group sobolevnrm paulschlesinger baker-group
	Molecular Dynamics Study of the Cu2+ Binding-Induced “Structuring” of the N-Terminal Domain of Human Prion Protein [My Copy] The Journal of Physical Chemistry B, Vol. 113, No. 11. (19 March 2009), pp. 3277-3279. by Gianni Valensin, Elena Molteni, Daniela Valensin, Magdalena Taraszkiewicz, Henryk Kozlowski posted to modeling molecular-dynamics molecular-dynamics-simulations molecular-modeling by carlosjavierna on 2009-03-15 16:39:00 as along with 1 person scampos
	1,2-Dichloroethane in Haloalkane Dehalogenase Protein and in Water Solvent: A Case Study of the Confinement Effect on Structural and Dynamical Properties [My Copy] The Journal of Physical Chemistry B, Vol. 113, No. 11. (19 March 2009), pp. 3257-3263. by Arul N. Murugan, Hans Ågren posted to modeling molecular-dynamics molecular-dynamics-simulations molecular-modeling by carlosjavierna on 2009-03-15 16:35:54 as
	Computational Validation of Protein Nanotubes [My Copy] Nano Letters, Vol. 9, No. 3. (11 March 2009), pp. 1096-1102. by Idit Buch, Bernard R. Brooks, Haim J. Wolfson, Ruth Nussinov posted to bernardrbrooks modeling molecular-dynamics molecular-dynamics-simulations molecular-modeling by carlosjavierna on 2009-03-15 16:03:37 as
	Ion-Specific Interactions between Halides and Basic Amino Acids in Water† [My Copy] The Journal of Physical Chemistry A, Vol. 113, No. 10. (12 March 2009), pp. 1969-1975. by Jan Heyda, Tomáš Hrobárik, Pavel Jungwirth posted to amino-acids molecular-dynamics molecular-dynamics-simulations molecular-modeling by carlosjavierna on 2009-03-11 03:09:59 as
	Experimental and Theoretical Characterization of Adsorbed Water on Self-Assembled Monolayers: Understanding the Interaction of Water with Atmospherically Relevant Surfaces† [My Copy] The Journal of Physical Chemistry A, Vol. 113, No. 10. (12 March 2009), pp. 2060-2069. by Samar G. Moussa, Theresa M. Mcintire, Milán Szőri, et al.Martina Roeselová, Douglas J. Tobias, Ronald L. Grimm, John C. Hemminger, Barbara J. Finlayson-Pitts posted to douglasjtobias molecular-dynamics molecular-dynamics-simulations molecular-modeling by carlosjavierna on 2009-03-11 01:50:56 as
	Molecular Dynamics Simulations of Methane Hydrate Decomposition† [My Copy] The Journal of Physical Chemistry A, Vol. 113, No. 10. (12 March 2009), pp. 1913-1921. by Evgeniy M. Myshakin, Hao Jiang, Robert P. Warzinski, Kenneth D. Jordan posted to md molecular-dynamics molecular-dynamics-simulations molecular-modeling by carlosjavierna on 2009-03-10 00:07:08 as
	Identification and Characterization of an Intermediate Taxol Binding Site Within Microtubule Nanopores and a Mechanism for Tubulin Isotype Binding Selectivity [My Copy] Journal of Chemical Information and Modeling, Vol. 49, No. 2. (23 February 2009), pp. 424-436. by Holly Freedman, Torin J. Huzil, Tyler Luchko, Richard F. Ludueña, Jack A. Tuszynski posted to ala docking host-guest host-guest-chemistry molecular-dynamics molecular-dynamics-simulations targeted-molecular-dynamics by carlosjavierna on 2009-02-27 03:40:08 as
	Dynamic control of protein conformation transition in chromatographic separation based on hydrophobic interactionsMolecular dynamics simulation [My Copy] Journal of Chromatography A (17 January 2009) by L. Zhang, D. Lu, Z. Liu posted to molecular-dynamics molecular-dynamics-simulations by carlosjavierna on 2009-02-26 19:26:31 as
	Many-Body Polarization Effects and the Membrane Dipole Potential [My Copy] Journal of the American Chemical Society, Vol. 0, No. 0. (0000) by Edward Harder, Alexander D. Mackerell, Benoît Roux posted to mackerell molecular-dynamics molecular-dynamics-simulations molecular-modeling roux by carlosjavierna on 2009-02-24 16:42:25 as along with 2 people and 1 group sobolevnrm kafuitay baker-group
	Molecular Dynamics Simulation of Fullerene C60 in Ethanol Solution [My Copy] The Journal of Physical Chemistry C, Vol. 0, No. 0. (0000) by Zhen Cao, Yuxing Peng, Shu Li, Lei Liu, Tianying Yan posted to ethanol ethanol-solution molecular-dynamics molecular-dynamics-simulations by carlosjavierna on 2009-02-22 05:06:14 as along with 1 person and 1 group Marine Molecular dynamics in MSU
	Liposome−Prilocaine Interaction Mapping Evaluated through STD NMR and Molecular Dynamics Simulations [My Copy] The Journal of Physical Chemistry B, Vol. 113, No. 8. (26 February 2009), pp. 2365-2370. by Luís F. Cabeça, Mónica Pickholz, Eneida de Paula, Anita J. Marsaioli posted to md molecular-dynamics molecular-dynamics-simulations by carlosjavierna on 2009-02-21 17:31:32 as along with 1 person and 1 group sobolevnrm baker-group
	Computational Modeling Study on Formation of Acyclic Clavulanate Intermediates in Inhibition of Class A β-Lactamase: Water-Assisted Proton Transfer [My Copy] The Journal of Physical Chemistry A, Vol. 113, No. 8. (26 February 2009), pp. 1608-1613. by Rui Li, Dacheng Feng, Shengyu Feng posted to beta-lactamase molecular-dynamics molecular-dynamics-simulations by carlosjavierna on 2009-02-21 17:24:07 as
	Water Isotope Effect on the Phosphatidylcholine Bilayer Properties: A Molecular Dynamics Simulation Study [My Copy] The Journal of Physical Chemistry B, Vol. 113, No. 8. (26 February 2009), pp. 2378-2387. by Tomasz Róg, Krzysztof Murzyn, Jeannine Milhaud, Mikko Karttunen, Marta Pasenkiewicz-Gierula posted to bilayer md molecular-dynamics molecular-dynamics-simulations water by carlosjavierna on 2009-02-21 14:58:51 as along with 2 people and 1 group sobolevnrm priyaps baker-group
	Why Water Reorientation Slows without Iceberg Formation around Hydrophobic Solutes [My Copy] The Journal of Physical Chemistry B, Vol. 113, No. 8. (26 February 2009), pp. 2428-2435. by Damien Laage, Guillaume Stirnemann, James T. Hynes posted to hydrophobicity md molecular-dynamics molecular-dynamics-simulations water by carlosjavierna on 2009-02-21 14:56:02 as along with 2 people Diego_Prada willard
	Computations of Standard Binding Free Energies with Molecular Dynamics Simulations [My Copy] The Journal of Physical Chemistry B, Vol. 113, No. 8. (26 February 2009), pp. 2234-2246. by Yuqing Deng, Benoît Roux posted to fe featured-article free-energy molecular-dynamics molecular-dynamics-simulations roux roux-benoit by carlosjavierna on 2009-02-21 14:19:49 as along with 10 people and 2 groups loison anuragsethi flbarroso mikaellund sobolevnrm barry jmccammon willard agrossfield ibuch baker-group McCammon
	Factors That Affect the Degree of Twist in β-Sheet Structures: A Molecular Dynamics Simulation Study of a Cross-β Filament of the GNNQQNY Peptide [My Copy] The Journal of Physical Chemistry B, Vol. 113, No. 6. (12 February 2009), pp. 1728-1737. by Xavier Periole, Aldo Rampioni, Michele Vendruscolo, Alan E. Mark posted to alanemark beta-sheet molecular-dynamics molecular-dynamics-simulations xavierperiole by carlosjavierna on 2009-02-20 17:10:21 as
	The Interaction of Monotopic Membrane Enzymes with a Lipid Bilayer: A Coarse-Grained MD Simulation Study [My Copy] Biochemistry, Vol. 0, No. ja. (0000) by Kia Balali-Mood, Peter Bond, Mark Sansom posted to coarse-grained-md coarse-grained-molecular-dynamics molecular-dynamics molecular-dynamics-simulations by carlosjavierna on 2009-02-20 04:57:22 as along with 2 people and 1 group sobolevnrm paulschlesinger baker-group
	Molecular Dynamics Simulations on Binding Models of Dervan-Type Polyamide + Cu(II) Nuclease Ligands to DNA [My Copy] The Journal of Physical Chemistry B, Vol. 113, No. 3. (22 January 2009), pp. 839-848. by Yanyan Zhu, Yan Wang, Guangju Chen posted to dna md molecular-dynamics molecular-dynamics-simulations by carlosjavierna on 2009-02-20 03:26:32 as
	Thermodynamics and Folding Pathways of Trpzip2: An Accelerated Molecular Dynamics Simulation Study [My Copy] The Journal of Physical Chemistry B, Vol. 113, No. 3. (22 January 2009), pp. 803-808. by Lijiang Yang, Qiang Shao, Yi Q. Gao posted to md molecular-dynamics molecular-dynamics-simulations by carlosjavierna on 2009-02-20 03:25:39 as
	Hydrogen-Bonding Structure and Dynamics of Aqueous Carbonate Species from Car−Parrinello Molecular Dynamics Simulations [My Copy] The Journal of Physical Chemistry B, Vol. 113, No. 3. (22 January 2009), pp. 794-802. by Padma P. Kumar, Andrey G. Kalinichev, James R. Kirkpatrick posted to md molecular-dynamics molecular-dynamics-simulations by carlosjavierna on 2009-02-20 03:24:45 as
	Electrostatic Polarization Effects and Hydrophobic Hydration in Ethanol−Water Solutions from Molecular Dynamics Simulations [My Copy] The Journal of Physical Chemistry B, Vol. 113, No. 3. (22 January 2009), pp. 767-778. by Yang Zhong, Sandeep Patel posted to md molecular-dynamics molecular-dynamics-simulations by carlosjavierna on 2009-02-20 03:23:37 as along with 2 people sunrise willard
	Force Field for Molecular Dynamics Studies of Glycine/Water Mixtures in Crystal/Solution Environments [My Copy] The Journal of Physical Chemistry B, Vol. 113, No. 3. (22 January 2009), pp. 752-758. by Sivashangari Gnanasambandam, Zhongqiao Hu, Jianwen Jiang, Raj Rajagopalan posted to ff force-field gly glycine md molecular-dynamics molecular-dynamics-simulations by carlosjavierna on 2009-02-20 03:20:35 as
	Native-like RNA Tertiary Structures Using a Sequence-Encoded Cleavage Agent and Refinement by Discrete Molecular Dynamics [My Copy] Journal of the American Chemical Society, Vol. 0, No. 0. (0000) by Costin M. Gherghe, Christopher W. Leonard, Feng Ding, Nikolay V. Dokholyan, Kevin M. Weeks posted to discrete-molecular-dynamics md molecular-dynamics molecular-dynamics-simulations by carlosjavierna on 2009-02-20 02:40:30 as along with 1 person yvo1
	Multifrequency Electron Spin Resonance Spectra of a Spin-Labeled Protein Calculated from Molecular Dynamics Simulations [My Copy] Journal of the American Chemical Society, Vol. 131, No. 7. (25 February 2009), pp. 2597-2605. by Deniz Sezer, Jack H. Freed, Benoît Roux posted to molecular-dynamics molecular-dynamics-simulations roux by carlosjavierna on 2009-02-20 02:39:29 as
	Molecular Dynamics Simulation of DNA-Functionalized Gold Nanoparticles [My Copy] The Journal of Physical Chemistry C, Vol. 113, No. 6. (12 February 2009), pp. 2316-2321. by One-Sun Lee, George C. Schatz posted to dna molecular-dynamics by carlosjavierna on 2009-02-19 18:19:24 as along with 3 people and 1 group charlesvardeman georgwachter sobolevnrm baker-group
	Molecular Dynamics Study of Pore Inner Wall Modification Effect in Structure of Water Molecules Confined in Single-Walled Carbon Nanotubes [My Copy] The Journal of Physical Chemistry C, Vol. 113, No. 3. (22 January 2009), pp. 882-889. by Yudan Zhu, Mingjie Wei, Qing Shao, Linghong Lu, Xiaohua Lu, Wenfeng Shen posted to carbon-nanotubes molecular-dynamics nanotubes by carlosjavierna on 2009-02-19 05:00:33 as
	Influence of preformed Asp23-Lys28 salt bridge on the conformational fluctuations of monomers and dimers of Abeta peptides with implications for rates of fibril formation. [My Copy] The journal of physical chemistry. B, Vol. 113, No. 4. (29 January 2009), pp. 1162-1172. by Govardhan Reddy, John E. Straub, D. Thirumalai posted to molecular-dynamics salt-bridge by carlosjavierna on 2009-02-19 04:47:12 as along with 1 person zfekete

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review	103
arg	70
arginine	61
folding	61
molecular-dynamics-simulations	59
molecular-dynamics	56
proteins	55
molecular-recognition	46
general	44
por-conseguir	43
phosphorilation	36
crystal-structure	34
molecular-modeling	34
tyr	32
cys	31
lys	29
cysteine	28
beta-lactamase	28
ser	28
tyrosine	26
mutagenesis	26
pro	26
his	25
proline	23
conformational-change	22
serine	22
lysine	22
thr	22
amino-acids	22
host-guest-chemistry	21
gly	21
phosphorylation	21
alpha-helix	20
disorder	20
peptides	20
histidine	19
threonine	19
ala	18
docking	18
phe	18
trp	17
protein	16
qmmm	16
x-ray	16
glycine	16
alanine	15
enantiomers	15
hydrogen-bonds	15
leu	14
mini-review	14
beta-sheet	13
conformational	13
qm-mm	12
cyclodextrin	12
modeling	12
md	12
tryptophan	12
qsar	11
proteinas	11
gln	10
unfolding	10
beta-cyclodextrin	10
leucine	10
glu	10
host-guest	10
free-energy	9
family	9
side-chain	9
enantioselectivity	8
peptide	8
conformational-states	8
conformer	8
glutamic-acid	8
phenylalanine	8
genetic_code	8
polyproline-ii	8
glycosylation	8
dft	8
val	7
glutamate	7
minireview	7
glutamine	7
binding-sites	7
helix	7
asp	7
mutation	7
conformations	6
dna	6
beta-hairpin	6
codon	6
binding-site	6
ile	6
methylation	6
amino-acid	6
met	6
aspartate	6
homology-modeling	5
binding-mode	5
chiral	5
monte-carlo	5
residue-analysis	5
sar	5
valine	5
potential-energy-surface	4
methionine	4
chaperone	4
replica-exchange-molecular-dynamics	4
force-fields	4
inclusion-complex	4
databases	4
ubiquitination	4
acetylation	4
force-field	4
aspartic-acid	4
honig-barry-h	4
tripeptide	4
residue	4
disulfide_bonds	4
hiv	4
water	4
coiled-coil	3
sequences	3
replica-exchange-md	3
unfolded	3
two-binding-sites	3
stereoselectivity	3
protein-folding	3
atoms-in-molecules	3
amber	3
isoleucine	3
peps	3
roux-benoit	3
cancer	3
protein-ligand-binding	3
rotamer	3
conformation	3
software	3
free-energy-landscape	3
perspective	3
roux	3
beta-turn	3
dipeptide	3
coil	3
active-site	3
karplus-m	3
open-to-closed	3
folding-rates	3
disordered-proteins	3
molecular_basis	3
chaperones	2
cconformational-analysis	2
rotamer-libraries	2
fe	2
alzheimer	2
stereochemistry	2
protein-protein-interactions	2
replica-exchange	2
thornton	2
electrostatic-interactions	2
b-sheet	2
flexibility	2
structural-basis	2
kenethmerz	2
asn	2
hobza	2
dynamics	2
carbon-nanotubes	2
metallo-beta-lactamase	2
hydrophobic	2
basico	2
chiral-recognition	2
protein-engineering	2
ff	2
disulfide	2
parkinson	2
asparagine	2
thorntonjm	2
featured-article	2
prion	2
misfolding	2
web-tools	2
aromatic-residues	2
hobzapavel	2
beta-hairpins	2
beta-bulge	2
desorden	2
structure-activity-relationship	2
potential-of-mean-force	2
principal-component-analysis	2
pca	2
beta-lactam-antibiotic-resistance	2
carbapenemases	2
nanotubes	2
ubiquitylation	2
hydrophobic-interactions	2
comformational-population	2
levitt	2
hydrophobicity	2
enzimas	2
enzyme-substrate-complex	1
binding_energy	1
density-functionals	1
amino_acid_sequence	1
pro-chirality	1
bernardrbrooks	1
markae	1
targeted-molecular-dynamics	1
first-principles-molecular-dynamics	1
amyloid-b-protein	1
abinitio-md	1
hiv-1-integrase	1
dimethylation	1
diastereoselectivity	1
conformation-transitions	1
cephalosporinase	1
gamma-turns	1
two-active-sites	1
protein-folding-rates	1
docking-methods	1
shv-1	1
argi	1
coarse-grained-md	1
recognition	1
solvation	1
iron-containing-proteins	1
similarity-methods	1
change	1
hydrogen_bond	1
synthesis	1
jirisponer	1
dihedral	1
enantiomeric-separation	1
fingerprint-methods	1
regioselectivity	1
pmf	1
clinical-diagnosis	1
carbohydrates	1
induced-fit	1
beta_lactamase	1
daggett	1
gilsonmk	1
thanslocation	1
conformational_changes	1
rna	1
post-translational-modification	1
conformational-free-energy-surface	1
trp-cage	1
mass-spectrometry	1
protein-architecture	1
c-terminal-domain	1
alfa-cyclodextrin	1
clbrooksiii	1
libraries	1
michaellklein	1
chemistry	1
salt-bridge	1
main-chain-flexibility	1
binding	1
bayly-christopher-i	1
serina	1
simulations	1
dimers	1
therapeutics	1
case	1
diabetes	1
molecular_dynamics_simulations	1
heme	1
conserved-residues	1
protein-drug-interactions	1
thermodynamics	1
angel-e-garcia	1
signal_peptides	1
inouey	1
autodock	1
ciq	1
merzkm	1
pharmacology	1
umbrella-sampling	1
douglasjtobias	1
dipeptides	1
first-principles-md	1
car-parrinello-md	1
deacetylation	1
lxxll-motif	1
pbp1b	1
ethanol-solution	1
alanemark	1
friesnerr	1
his-heme	1
groesl	1
xavierperiole	1
catalytic_residues	1
protein-translocation	1
beta-lactam-antibiotics	1
austin	1
drug-design	1
cooperativity	1
computational-study	1
car-parrinello-molecular-dynamics	1
discrete-molecular-dynamics	1
perpective	1
deimination	1
jialigao	1
sulfated-b-cyclodextrin	1
bilayer	1
helix-bundles	1
hsa	1
aqueous-solubility	1
antibiotic	1
3d-qsar	1
mackerell	1
conformational-behavior	1
hummer	1
molecular	1
signal_peptide	1
conformational-energy-landscape	1
gly-gly-gly	1
goddardwaiii	1
ionic-peptides	1
drug-protein-interactions	1
fe-landscape	1
protein-dynamics	1
dna-carbon-nanotube	1
hiv-1	1
hydrogen-bondsdensity-functional-theory	1
crystal_structure	1
charmm	1
mutant	1
basis-sets	1
phosphoserine	1
nucleator	1
homology	1
free-energy-differences	1
refolding	1
porins	1
aqvist	1
dynamic	1
dillka	1
allosteric	1
gly-gly	1
pande-vijay-s	1
abinitio-molecular-dynamics	1
enantiomeric-excess	1
thermodynamic-studies	1
george-georgiou	1
side-chain-amino-acids	1
extended-spectrum-beta-lactamase	1
tuckermanme	1
coarse-grained-molecular-dynamics	1
mining-minima-method	1
polypeptides	1
chiral-separation	1
antibiotic_resistance	1
kinetics	1
phenilalanine	1
dipeptido	1
swope-william	1
drug-receptor-interactions	1
decarboxilation	1
carlssonj	1
pitera-jed-w	1
substrate-recognition	1
normal-mode-analysis	1
conformational_change	1
analysis	1
succination	1
superfamilies	1
mm-gbsa	1
ethanol	1
trp-zipper	1
donaldgtruhlar	1
inhibitors	1
metalloenzymes	1
computer-imulations	1
remd	1

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