Tag amber [67 articles] Export

Recent papers classified by the tag amber.

	Development and testing of a general amber force field. [My Copy] J Comput Chem, Vol. 25, No. 9. (15 July 2004), pp. 1157-1174. by J. Wang, R. M. Wolf, J. W. Caldwell, P. A. Kollman, D. A. Case posted to potential amber by rdf on 2009-10-28 15:08:55 as along with 10 people and 1 group paddydu nigham lillekatt xdeupi gane5h kazemi megs easybakemuffin AndreaColetta pavanghatty LabCompMed
	Influence of the g- conformation of Ser and Thr on the structure of transmembrane helices. [My Copy] Journal of structural biology (17 September 2009) by Xavier Deupi, Mireia Olivella, Arantxa Sanz, Nicole Dölker, Mercedes Campillo, Leonardo Pardo posted to tm5 theory structure ser plasticity helix hbond flexibility dynamics amber activation by xdeupi on 2009-09-25 14:15:01 as
	Comparison of simple potential functions for simulating liquid water [My Copy] The Journal of Chemical Physics, Vol. 79, No. 2. (1983), pp. 926-935. by William L. Jorgensen, Jayaraman Chandrasekhar, Jeffry D. Madura, Roger W. Impey, Michael L. Klein posted to principle amber by fralium on 2009-09-24 15:37:18 as along with 17 people and 1 group jmparks bmduggan kulinskii ibuch Lombardo_7 paddydu dfgreen softsimu mleis ttjoseph ffranca easybakemuffin ashaytan RamuAnandakrishnan r2s2 pavanghatty Diego_Prada CMB
	Parameterization of aromatic azido groups: application as photoaffinity probes in molecular dynamics studies [My Copy] Journal of Molecular Modeling by Gilles Pieffet, Pavel Petukhov posted to theory spectroscopy modeling md fluorescence amber by xdeupi on 2009-09-15 14:25:43 as
	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 p2 molecular_dynamics amber by nickolay on 2009-09-09 22:01:34 as along with 18 people and 3 groups krapnik csrocha mmuecke flbarroso charris5 pavanghatty tahereh62 lna jwm ttjoseph xdeupi tovrstra bilab RamuAnandakrishnan IrinaMoreira adilson_mohr mikaellund gisle Radiation_Damage Stressosome LabCompMed
	A new proposal concerning the botanical origin of Baltic amber [My Copy] Proceedings of the Royal Society B: Biological Sciences, Vol. 276, No. 1672. (7 October 2009), pp. 3403-3412. by Alexander P. Wolfe, Ralf Tappert, Karlis Muehlenbachs, et al.Marc Boudreau, Ryan C. McKellar, James F. Basinger, Amber Garrett posted to fossil baltic amber by keithramsey on 2009-09-05 22:49:35 as
	AMBER force-field parameters for phosphorylated amino acids in different protonation states: phosphoserine, phosphothreonine, phosphotyrosine, and phosphohistidine [My Copy] Journal of Molecular Modeling, Vol. 12, No. 3. (1 February 2006), pp. 281-289. by Nadine Homeyer, Anselm Horn, Harald Lanig, Heinrich Sticht posted to amber by pavanghatty on 2009-08-27 21:31:16 as along with 2 people pmung GermanErlenkamp
	CHAMBER: Comprehensive support for CHARMM force fields within the AMBER software [My Copy] International Journal of Quantum Chemistry, Vol. 9999, No. 9999. (2009), NA. by Michael F. Crowley, Mark J. Williamson, Ross C. Walker posted to amber charmm force-fields by carlosjavierna on 2009-08-05 17:05:49 as
	Using FPGA Devices to Accelerate Biomolecular Simulations [My Copy] Computer In Computer, Vol. 40, No. 3. (2007), pp. 66-73. by S. R. Alam, P. K. Agarwal, M. C. Smith, J. S. Vetter, D. Caliga posted to amber src6 by anallam on 2009-07-27 19:26:46 as along with 7 people and 1 group gferencz aso6678 hamish peskin smithmc mmuecke adilson_mohr rit_ee732
	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
	Conformational preferences of substituted prolines in the collagen triple helix [My Copy] Biopolymers, Vol. 64, No. 2. (2002), pp. 63-71. by Sean D. Mooney, Peter A. Kollman, Teri E. Klein posted to amber forcefield by paddydu on 2009-06-26 13:30:48 as
	A new set of molecular mechanics parameters for hydroxyproline and its use in molecular dynamics simulations of collagen-like peptides [My Copy] Journal of Computational Chemistry, Vol. 26, No. 15. (2005), pp. 1612-1616. by Sanghyun Park, Randall J. Radmer, Teri E. Klein, Vijay S. Pande posted to amber forcefield by paddydu on 2009-06-26 10:37:44 as
	AMBER, a package of computer programs for applying molecular mechanics, normal mode analysis, molecular dynamics and free energy calculations to simulate the structural and energetic properties of molecules [My Copy] Computer Physics Communications, Vol. 91, No. 1-3. (2 September 1995), pp. 1-41. by David A. Pearlman, David A. Case, James W. Caldwell, et al.Wilson S. Ross, Iii Cheatham, Steve Debolt, David Ferguson, George Seibel, Peter Kollman posted to amber force-field nma protein-dynamics by abovell on 2009-06-15 18:35:41 as along with 2 people papatonyhill gruppo
	A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules [My Copy] Journal of the American Chemical Society, Vol. 117, No. 19. (1 May 1995), pp. 5179-5197. by Wendy D. Cornell, Piotr Cieplak, Christopher I. Bayly, et al.Ian R. Gould, Kenneth M. Merz, David M. Ferguson, David C. Spellmeyer, Thomas Fox, James W. Caldwell, Peter A. Kollman posted to amber post-defense potential by kgutwin on 2009-05-20 08:03:04 as along with 6 people Lombardo_7 softsimu coomteng flbarroso pavanghatty dfgreen
	Molecular dynamics simulation of nucleic acids: Successes, limitations, and promise [My Copy] Biopolymers, Vol. 56, No. 4. (4 December 2001), pp. 232-256. by Thomas E. Cheatham, Matthew A. Young posted to acid amber field force md nucleic by dsmueller on 2009-05-11 22:30:17 as along with 1 person simone
	How well does a restrained electrostatic potential (RESP) model perform in calculating conformational energies of organic and biological molecules? [My Copy] Journal of Computational Chemistry, Vol. 21, No. 12. (2000), pp. 1049-1074. by Junmei Wang, Piotr Cieplak, Peter A. Kollman posted to amber md by dsmueller on 2009-05-11 22:16:01 as along with 5 people and 1 group fralium pavanghatty A_Coletta_Thesis allmensch rabio Structural Biology Group TorVergata
	Exploring the Helix-Coil Transition via All-Atom Equilibrium Ensemble Simulations [My Copy] Biophysical Journal, Vol. 88, No. 4. (1 April 2005), pp. 2472-2493. by Eric J. Sorin, Vijay S. Pande posted to acid amber gromacs md nucleic by dsmueller on 2009-05-11 22:08:47 as
	VMD: Visual molecular dynamics [My Copy] Journal of Molecular Graphics, Vol. 14, No. 1. (February 1996), pp. 33-38. by W. Humphrey posted to ache amber amyloid beta-propeller binary binarytrehalose desmond ethanol gaff glycerol hsa hydrationwater hydrogenbond icenano iqt letter lysozyme massspec mdintro ornl pdb reading research_intro residence_times rotationaldiff slaving structure_function swell td ten_rules tip3p tobias trehalose water by pavanghatty on 2009-04-26 01:52:09 as along with 6 people and 1 group whitead csrocha r2s2 choonpeng RamuAnandakrishnan tji Jiang Research Group
	A reappraisal of what we have learnt during three decades of computer simulations on water [My Copy] Journal of Molecular Liquids In Molecular Liquids. Water at the New Millenium, Vol. 101, No. 1-3. (November 2002), pp. 219-260. by Bertrand Guillot posted to amber glycerol trehalose by pavanghatty on 2009-04-21 21:51:57 as along with 5 people flbarroso loison ruvido softsimu onufriev
	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 sccdftb qmmm amber by charris5 on 2009-04-17 14:55:50 as along with 3 people and 1 group krapnik vahmurk xdeupi LabCompMed
	An approach to computing electrostatic charges for molecules [My Copy] Journal of Computational Chemistry, Vol. 5, No. 2. (1984), pp. 129-145. by U. Chandra Singh, Peter A. Kollman posted to amber glycerol trehalose by pavanghatty on 2009-04-16 21:37:29 as along with 4 people and 1 group whitead tovrstra dfgreen kimikazu Jiang Research Group
	A new force field for molecular mechanical simulation of nucleic acids and proteins [My Copy] Journal of the American Chemical Society, Vol. 106, No. 3. (1 February 1984), pp. 765-784. by Scott J. Weiner, Peter A. Kollman, David A. Case, et al.Chandra U. Singh, Caterina Ghio, Guliano Alagona, Salvatore Profeta, Paul Weiner posted to amber glycerol trehalose by pavanghatty on 2009-04-16 21:17:19 as along with 1 person dfgreen
	Force fields for protein simulations. [My Copy] Adv Protein Chem, Vol. 66 (2003), pp. 27-85. by J. W. Ponder, D. A. Case posted to amber glycerol trehalose by pavanghatty on 2009-04-16 20:52:39 as along with 4 people and 2 groups karbak marcius papatonyhill hmk BioinfoCIPF SGU-CIPF
	A Molecular Basis for the Selectivity of Thiadiazole Urea Inhibitors with Stromelysin-1 and Gelatinase-A from Generalized Born Molecular Dynamics Simulations [My Copy] Journal of Medicinal Chemistry, Vol. 47, No. 12. (1 June 2004), pp. 3065-3074. by Robert C. Rizzo, Samuel Toba, Irwin D. Kuntz posted to amber mmgbsa by GermanErlenkamp on 2009-03-25 10:36:10 as
	A three-point method for evaluations of AMBER force field parameters: an application to copper-based artificial nucleases [My Copy] Theoretical Chemistry Accounts: Theory, Computation, and Modeling (Theoretica Chimica Acta) by Yanyan Zhu, Yan Wang, Guangju Chen, Chang-Guo Zhan posted to amber forcefields by loison on 2009-03-19 08:48:45 as
	An AMBER/DYANA/MOLMOL Phosphorylated Amino Acid Library Set and Incorporation into NMR Structure Calculations [My Copy] Journal of Biomolecular NMR, Vol. 33, No. 1. (September 2005), pp. 15-24. by John Craft, Glen Legge posted to amber phosphorylation phosphoserine phosphothreonine phosphotyrosine by GermanErlenkamp on 2009-03-17 07:49:36 as along with 1 person Lombardo_7
	A well-behaved electrostatic potential based method using charge restraints for deriving atomic charges: the RESP model [My Copy] The Journal of Physical Chemistry, Vol. 97, No. 40. (1 October 1993), pp. 10269-10280. by Christopher I. Bayly, Piotr Cieplak, Wendy Cornell, Peter A. Kollman posted to amber charges gaff partial resp by paddydu on 2009-03-12 15:38:55 as along with 2 people Scis0000002 dfgreen
	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
	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
	Coarse-graining the Self-assembly of β-helical Protein Building Blocks [My Copy] The Journal of Physical Chemistry B, Vol. 111, No. 50. (1 December 2007), pp. 14006-14011. by David Curco, Ruth Nussinov, Carlos Aleman posted to amber coarse-graining force-field potential by krapnik on 2009-02-20 12:57:39 as
	Computational Structure Activity Relationship Studies on the CD1d/Glycolipid/TCR Complex Using AMBER and AUTODOCK [My Copy] Journal of Chemical Information and Modeling, Vol. 0, No. 0. (0000) by Janos Nadas, Chenglong Li, Peng G. Wang posted to amber autodock sar structure-activity-relationship by carlosjavierna on 2009-02-19 14:37:32 as
	Performance of the general amber force field in modeling aqueous POPC membrane bilayers [My Copy] Journal of Computational Chemistry, Vol. 28, No. 12. (12 April 2007), pp. 2051-2058. by Balázs Jójárt, Tamás A. Martinek posted to amber lipid md membrane simulation by dimka on 2008-11-11 21:48:17 as along with 4 people and 1 group sunnytov xdeupi easybakemuffin viktor21614 LabCompMed
	Molecular Modeling of Geometries, Charge Distributions, and Binding Energies of Small, Druglike Molecules Containing Nitrogen Heterocycles and Exocyclic Amino Groups in the Gas Phase and in Aqueous Solution [My Copy] J. Chem. Theory Comput. (18 September 2008) by Brian R. White, Carston R. Wagner, Donald G. Truhlar, Elizabeth A. Amin posted to amber charge comparison force_field mmff by middledomain on 2008-09-24 19:38:44 as
	Empirical force-field assessment: The interplay between backbone torsions and noncovalent term scaling [My Copy] Journal of Computational Chemistry, Vol. 26, No. 7. (May 2005), pp. 682-690. by Eric J. Sorin, Vijay S. Pande posted to amber computing distributed dynamics folding fs molecular peptide protein by GermanErlenkamp on 2008-08-28 15:54:38 as along with 2 people and 1 group A_Coletta_Thesis allmensch Structural Biology Group TorVergata
	Systematic Comparison of Empirical Forcefields for Molecular Dynamic Simulation of Insulin [My Copy] J. Phys. Chem. B (12 August 2008) by Nevena Todorova, Sue F. Legge, Herbert Treutlein, Irene Yarovsky posted to amber charmm comparison force_field gromos by middledomain on 2008-08-12 15:09:51 as along with 1 person agrossfield
	Protein model refinement using an optimized physics-based all-atom force field [My Copy] Proceedings of the National Academy of Sciences, Vol. 105, No. 24. (17 June 2008), pp. 8268-8273. by Anna Jagielska, Liliana Wroblewska, Jeffrey Skolnick posted to amber electrostatics folding by RamuAnandakrishnan on 2008-06-19 12:23:29 as along with 4 people and 2 groups krapnik jmccammon barry zwang structural_bioinformatics McCammon
	Geometrical and Electronic Structure Variability of the Sugar−phosphate Backbone in Nucleic Acids [My Copy] The Journal of Physical Chemistry B, Vol. 112, No. 27. (1 July 2008), pp. 8188-8197. by Daniel Svozil, Judit E. Šponer, Ivan Marchan, et al.Alberto Pérez, Thomas E. Cheatham, F. Forti, F. Javier Luque, Modesto Orozco, Jiří Šponer posted to amber ccsd force_field nucleic_acids by middledomain on 2008-06-19 10:24:36 as along with 1 person and 1 group oteri Structural Biology Group TorVergata
	Extension of the GLYCAM06 biomolecular force field to lipids, lipid bilayers and glycolipids [My Copy] Molecular Simulation, Vol. 34, No. 4. (2008), pp. 349-364. by M. B. Tessier, M. L. Demarco, A. B. Yongye, R. J. Woods posted to amber force_field ligand by RamuAnandakrishnan on 2008-06-17 18:14:43 as
	Energetics of Infinite Homopolypeptide Chains: A New Look at Commonly Used Force Fields [My Copy] J. Phys. Chem. B (14 May 2008) by Evgeni Penev, Joel Ireta, Joan-Emma Shea posted to amber ameoba charmm comparison dft force_field opls by middledomain on 2008-05-14 09:46:35 as along with 1 person Vadikus
	A Test on Peptide Stability of AMBER Force Fields with Implicit Solvation [My Copy] The Journal of Physical Chemistry B, Vol. 112, No. 22. (1 June 2008), pp. 6878-6886. by M. Scott Shell, Ryan Ritterson, Ken A. Dill posted to amber force_field peptide solvation by middledomain on 2008-05-12 13:23:49 as along with 2 people allmensch onufriev
	Development of polyphosphate parameters for use with the AMBER force field [My Copy] Journal of Computational Chemistry, Vol. 24, No. 9. (2003), pp. 1016-1025. by Kristin L. Meagher, Luke T. Redman, Heather A. Carlson posted to amber md_simulation by barry on 2008-04-25 20:57:25 as along with 1 person blackbart
	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 amber ff99sb md_simulation by barry on 2008-04-25 20:56:25 as along with 10 people arnaucordomi Vadikus bmduggan baaden lna allmensch choonpeng kazemi GermanErlenkamp RamuAnandakrishnan
	Calculated conformer energies for organic molecules with multiple polar functionalities are method dependent: Taxol (case study) [My Copy] BMC Chemical Biology, Vol. 1, No. 1. (2001) by Ami Lakdawala, Minmin Wang, Neysa Nevins, et al.Dennis Liotta, Danuta R. Roszak, Marek Lozynski, James Snyder posted to amber conformation force_field mm2 mm3 mmff by middledomain on 2008-04-15 20:12:18 as
	Peptide free-energy profile is strongly dependent on the force field: Comparison of C96 and AMBER95 [My Copy] Journal of Computational Chemistry, Vol. 21, No. 9. (2000), pp. 748-762. by Satoshi Ono, Nobuyuki Nakajima, Junichi Higo, Haruki Nakamura posted to amber force-field peptides by softsimu on 2008-04-03 22:17:27 as
	Evaluation of AMBER force field parameters for copper(II) with pyridylmethyl-amine and benzimidazolylmethyl-amine ligands: a quantum chemical study [My Copy] Chemical Physics Letters, Vol. In Press, Accepted Manuscript by Yanyan Zhu, Yanwei Su, Xichen Li, Yan Wang, Guangju Chen posted to amber by middledomain on 2008-03-11 12:04:04 as
	A versatile AMBER-Gaussian QM/MM interface through PUPIL [My Copy] Journal of Computational Chemistry, Vol. 9999, No. 9999. (2008), NA. by Juan Torras, Gustavo, Erik Deumens, S. B. Trickey, Adrian E. Roitberg posted to amber md qm_mm by RamuAnandakrishnan on 2008-02-13 14:41:45 as
	Parameters of monovalent ions in the AMBER-99 forcefield: assessment of inaccuracies and proposed improvements. [My Copy] The journal of physical chemistry. B, Vol. 111, No. 41. (18 October 2007), pp. 11884-11887. by Alan A. Chen, Rohit V. Pappu posted to force_field amber by middledomain on 2008-01-22 17:13:25 as along with 2 people and 1 group robertvacha sobolevnrm baker-group
	HIV-1 protease flaps spontaneously open and reclose in molecular dynamics simulations. [My Copy] Proc Natl Acad Sci U S A, Vol. 103, No. 4. (24 January 2006), pp. 915-920. by V. Hornak, A. Okur, R. C. Rizzo, C. Simmerling posted to amber implicit_solvent md by RamuAnandakrishnan on 2007-12-14 16:16:11 as along with 3 people dfgreen aqeel allmensch
	The implementation of a fast and accurate QM/MM potential method in Amber [My Copy] Journal of Computational Chemistry, Vol. 29, No. 7. (2008), pp. 1019-1031. by Ross C. Walker, Michael F. Crowley, David A. Case posted to amber qm-mm by softsimu on 2007-12-12 00:26:40 as along with 2 people onufriev RamuAnandakrishnan
	A modified version of the Cornell et al. force field with improved sugar pucker phases and helical repeat. [My Copy] J Biomol Struct Dyn, Vol. 16, No. 4. (February 1999), pp. 845-862. by T. E. Cheatham, P. Cieplak, P. A. Kollman posted to amber force_field by lillekatt on 2007-11-25 09:36:36 as along with 2 people ffranca gruppo

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md	22
dynamics	12
force_field	12
trehalose	11
modeling	9
glycerol	8
theory	8
gaff	5
mymd	5
potential	5
charmm	4
comparison	4
force-field	4
forcefield	4
molecular_dynamics	4
orthogonal	4
qm_mm	4
thesis	4
activation	3
field	3
membrane	3
protein	3
acid	2
agonist	2
alanine	2
binding	2
folding	2
force	2
forcefields	2
gromacs	2
gromos	2
helix	2
implicit_solvent	2
ligand	2
ligands	2
md_simulation	2
mmff	2
molecular-dynamics	2
nucleic	2
ornl	2
peptide	2
pyrrolysine	2
rhodopsin	2
water	2
acids	1
ala	1
ameoba	1
amyloid	1
autodock	1
beta-propeller	1
binarytrehalose	1
charges	1
computing	1
desmond	1
distributed	1
electrostatic	1
energy	1
ethanol	1
explicit_solvent	1
ff99	1
ff99sb	1
fluorescence	1
fossil	1
gibbs	1
hbond	1
hydrationwater	1
icenano	1
iqt	1
letter	1
lysozyme	1
mdintro	1
mmgbsa	1
native_structure	1
partial	1
peptides	1
phosphorylated	1
phosphorylation	1
phosphothreonine	1
phosphotyrosine	1
plot	1
principle	1
qm-mm	1
qmmm	1
reading	1
research_intro	1
restrained	1
rorce	1
selenocysteine	1
side-chain	1
software	1
structure-activity-relationship	1
structures_of_proteins	1
suppressor	1
tar-argininamide	1
tar-ligands	1
tar-tat	1
ten_rules	1
tip3p	1
tm5	1
tobias	1

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