A_Coletta_Thesis's parametrization [50 articles] Export

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	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 parametrization force_field by A_Coletta_Thesis on 2009-10-01 16:12:43 as along with 2 people and 1 group allmensch GermanErlenkamp Structural Biology Group TorVergata
	Molecular mechanics models for tetracycline analogs [My Copy] Journal of Computational Chemistry, Vol. 30, No. 2. (2009), pp. 243-255. by Alexey Aleksandrov, Thomas Simonson posted to molecular_dynamics parametrization by A_Coletta_Thesis on 2009-07-03 18:29:16 as along with 1 group Structural Biology Group TorVergata
	Transferable Coarse-Grained Models for Ionic Liquids [My Copy] Journal of Chemical Theory and Computation, Vol. 5, No. 4. (14 April 2009), pp. 1091-1098. by Yanting Wang, Shulu Feng, Gregory A. Voth posted to coarse_grained force_field parametrization solvent by A_Coletta_Thesis on 2009-04-22 11:43:54 as along with 1 group Structural Biology Group TorVergata
	Evaluation of Density Functionals and Basis Sets for Carbohydrates [My Copy] Journal of Chemical Theory and Computation, Vol. 5, No. 4. (14 April 2009), pp. 679-692. by Gábor I. Csonka, Alfred D. French, Glenn P. Johnson, Carlos A. Stortz posted to dft force_field parametrization resp by A_Coletta_Thesis on 2009-04-22 10:58:13 as along with 2 people and 1 group Fortran carlosjavierna Structural Biology Group TorVergata
	A multipole-based water potential with implicit polarization for biomolecular simulations [My Copy] Journal of Computational Chemistry, Vol. 9999, No. 9999. (2008), NA. by T. R. Walsh, T. Liang posted to force_field parametrization protein water by A_Coletta_Thesis on 2009-03-16 10:48:38 as along with 1 person and 1 group middledomain Structural Biology Group TorVergata
	GolP: An atomistic force-field to describe the interaction of proteins with Au(111) surfaces in water [My Copy] Journal of Computational Chemistry, Vol. 9999, No. 9999. (2008), NA. by F. Iori, R. Di Felice, E. Molinari, S. Corni posted to ab-initio force_field parametrization protein surface by A_Coletta_Thesis on 2009-02-06 13:45:21 as along with 1 group Structural Biology Group TorVergata
	MM3(96) parameterization for camptothecin analogs: An ab initio and molecular mechanics study [My Copy] Journal of Computer-Aided Molecular Design, Vol. 11, No. 1. (1 January 1997), pp. 61-70. by Sean W. Carrigan, Jenn-Huei Lii, Phillip J. Bowen posted to camptothecin force_field parametrization by A_Coletta_Thesis on 2009-01-15 16:22:58 as along with 1 group Structural Biology Group TorVergata
	Application of the RESP Methodology in the Parametrization of Organic Solvents [My Copy] The Journal of Physical Chemistry B, Vol. 102, No. 41. (1 October 1998), pp. 8070-8079. by Thomas Fox, Peter A. Kollman posted to force_field parametrization resp by A_Coletta_Thesis on 2009-01-15 15:09:56 as along with 1 person and 1 group mikaellund Structural Biology Group TorVergata
	Quantum effects in liquid water from an ab initio-based polarizable force field [My Copy] The Journal of Chemical Physics, Vol. 127, No. 7. (2007) by Francesco Paesani, Satoru Iuchi, Gregory A. Voth posted to dielectric parametrization water by A_Coletta_Thesis on 2009-01-15 11:45:27 as along with 1 person and 1 group ruvido Structural Biology Group TorVergata
	An <I>ab initio</I> force field for the cofactors of bacterial photosynthesis [My Copy] Journal of Computational Chemistry, Vol. 24, No. 2. (2003), pp. 129-142. by Matteo Ceccarelli, Piero Procacci, Massimo Marchi posted to ab-initio dft force_field parametrization by A_Coletta_Thesis on 2009-01-15 10:32:15 as along with 1 group Structural Biology Group TorVergata
	Force-field parametrization of retro-inverso modified residues: Development of torsional and electrostatic parameters [My Copy] Journal of Computer-Aided Molecular Design, Vol. 20, No. 1. (January 2006), pp. 13-25. by Curco, David, Rodriguez-Ropero, Francisco, Aleman, Carlos posted to ab-initio dft force_field molecular_dynamics parametrization by A_Coletta_Thesis on 2009-01-15 10:28:20 as along with 1 person and 1 group AndreaColetta Structural Biology Group TorVergata
	Development of a multipoint model for sulfur in proteins: a new parametrization scheme to reproduce high-level ab initio interaction energies. [My Copy] J Comput Chem, Vol. 26, No. 3. (February 2005), pp. 283-293. by F. Wennmohs, M. Schindler posted to molecular_dynamics parametrization resp by A_Coletta_Thesis on 2009-01-14 18:19:24 as along with 1 person and 1 group AndreaColetta Structural Biology Group TorVergata
	Development and initial testing of an empirical forcefield for simulation of poly(alkylthiophenes) [My Copy] Journal of Molecular Graphics and Modelling, Vol. 27, No. 1. (August 2008), pp. 34-44. by A. Widge, Y. Matsuoka, M. Kurnikova posted to force_field molecular_dynamics parametrization by A_Coletta_Thesis on 2009-01-14 18:07:59 as along with 1 group Structural Biology Group TorVergata
	Howto prepare residues with RESP charges fitting for polarizable force fields in Amber 8 [My Copy] (5 April 2006) by Lukasz Cwiklik posted to ab-initio parametrization resp by A_Coletta_Thesis on 2009-01-14 18:03:21 as along with 1 group Structural Biology Group TorVergata
	Derivation of Force Fields for Molecular Mechanics and Dynamics from ab initio Energy Surfaces [My Copy] Proceedings of the National Academy of Sciences, Vol. 85, No. 15. (1 August 1988), pp. 5350-5354. by Jon R. Maple, Uri Dinur, Arnold T. Hagler posted to ab-initio force_field parametrization by A_Coletta_Thesis on 2009-01-14 17:10:46 as along with 1 group Structural Biology Group TorVergata
	Automatic parameterization of force field by systematic search and genetic algorithms [My Copy] Journal of Computational Chemistry, Vol. 22, No. 12. (2001), pp. 1219-1228. by Junmei Wang, Peter A. Kollman posted to ab-initio force_field molecular_dynamics parametrization by A_Coletta_Thesis on 2009-01-14 17:06:24 as along with 1 person and 1 group RamuAnandakrishnan Structural Biology Group TorVergata
	The MARTINI Force Field: Coarse Grained Model for Biomolecular Simulations [My Copy] The Journal of Physical Chemistry B, Vol. 111, No. 27. (1 July 2007), pp. 7812-7824. by Siewert J. Marrink, H. Jelger Risselada, Serge Yefimov, D. Peter Tieleman, Alex H. de Vries posted to coarse_grained force_field molecular_dynamics parametrization by A_Coletta_Thesis on 2009-01-14 16:37:44 as along with 7 people and 2 groups anuragsethi sunrise Marine choonpeng softsimu dimka sunnytov Structural Biology Group TorVergata Molecular dynamics in MSU
	First-Principle Molecular Dynamics Study of Selected Schiff and Mannich Bases: Application of Two-Dimensional Potential of Mean Force to Systems with Strong Intramolecular Hydrogen Bonds [My Copy] Journal of Chemical Theory and Computation, Vol. 4, No. 3. (1 March 2008), pp. 375-384. by Aneta Jezierska, Jaroslaw J. Panek posted to ab-initio free-energy parametrization topotecan by A_Coletta_Thesis on 2009-01-14 16:35:05 as along with 1 group Structural Biology Group TorVergata
	GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation [My Copy] Journal of Chemical Theory and Computation, Vol. 4, No. 3. (1 March 2008), pp. 435-447. by Berk Hess, Carsten Kutzner, David van der Spoel, Erik Lindahl posted to force_field molecular_dynamics parametrization by A_Coletta_Thesis on 2009-01-14 16:32:25 as along with 23 people and 2 groups sunnytov softsimu parnell rabio oteri krapnik robertvacha rodrigofaccioli pavanghatty janneb ZhangYinhe okapi flbarroso marceavi choonpeng Lombardo_7 jwm daevans mmuecke sobolevnrm r2s2 middledomain loison Structural Biology Group TorVergata baker-group
	The MARTINI Coarse-Grained Force Field: Extension to Proteins [My Copy] Journal of Chemical Theory and Computation, Vol. 4, No. 5. (1 May 2008), pp. 819-834. by Luca Monticelli, Senthil K. Kandasamy, Xavier Periole, Ronald G. Larson, D. Peter Tieleman, Siewert-Jan Marrink posted to coarse_grained force_field molecular_dynamics parametrization by A_Coletta_Thesis on 2009-01-14 16:31:31 as along with 13 people and 3 groups arnaucordomi dimka oteri sunrise flbarroso krapnik Marine middledomain sobolevnrm Ema aqeel DanielParton softsimu Structural Biology Group TorVergata Molecular dynamics in MSU baker-group
	Theoretical Determination of the Standard Reduction Potentials of Pheophytin-a in N,N-Dimethyl Formamide and Membrane [My Copy] The Journal of Physical Chemistry B, Vol. 111, No. 25. (1 June 2007), pp. 7210-7217. by Nital Mehta, Sambhu N. Datta posted to ab-initio molecular_dynamics oniom parametrization by A_Coletta_Thesis on 2009-01-14 16:06:42 as along with 1 group Structural Biology Group TorVergata
	Application of RESP charges to calculate conformational energies, hydrogen bond energies, and free energies of solvation [My Copy] Journal of the American Chemical Society, Vol. 115, No. 21. (1 October 1993), pp. 9620-9631. by Wendy D. Cornell, Piotr Cieplak, Christopher I. Bayly, Peter A. Kollman posted to molecular_dynamics parametrization resp by A_Coletta_Thesis on 2009-01-14 15:28:42 as along with 1 person and 1 group dfgreen Structural Biology Group TorVergata
	Development of the force field parameters for phosphoimidazole and phosphohistidine. [My Copy] J Comput Chem, Vol. 25, No. 11. (August 2004), pp. 1313-1321. by Y. A. Kosinsky, P. E. Volynsky, P. Lagant, et al.G. Vergoten, E. Suzuki, A. S. Arseniev, R. G. Efremov posted to ab-initio molecular_dynamics parametrization resp by A_Coletta_Thesis on 2009-01-14 15:22:16 as along with 1 person and 1 group dimka Structural Biology Group TorVergata
	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 ab-initio parametrization resp by A_Coletta_Thesis on 2009-01-14 15:20:15 as along with 5 people and 1 group fralium dsmueller pavanghatty allmensch rabio Structural Biology Group TorVergata
	Comparison of methods for deriving atomic charges from the electrostatic potential and moments [My Copy] Journal of Computational Chemistry, Vol. 19, No. 4. (1998), pp. 377-395. by Emma Sigfridsson, Ulf Ryde posted to ab-initio parametrization resp by A_Coletta_Thesis on 2009-01-14 15:18:06 as along with 1 group Structural Biology Group TorVergata
	Structure and Properties of Neat Liquids Using Nonadditive Molecular Dynamics: Water, Methanol, and N-Methylacetamide [My Copy] The Journal of Physical Chemistry, Vol. 99, No. 16. (1 April 1995), pp. 6208-6219. by James W. Caldwell, Peter A. Kollman posted to molecular_dynamics parametrization tip3p by A_Coletta_Thesis on 2009-01-14 15:11:02 as along with 1 group Structural Biology Group TorVergata
	Ab initio calculations of intramolecular parameters for a class of arylamide polymers. [My Copy] J Comput Chem, Vol. 27, No. 6. (30 April 2006), pp. 693-700. by S. Vemparala, I. Ivanov, V. Pophristic, K. Spiegel, M. L. Klein posted to ab-initio molecular_dynamics parametrization by A_Coletta_Thesis on 2009-01-14 15:06:08 as along with 1 person and 1 group AndreaColetta Structural Biology Group TorVergata
	Conformational dependence of electrostatic potential-derived charges: Studies of the fitting procedure [My Copy] Journal of Computational Chemistry, Vol. 14, No. 7. (1993), pp. 858-866. by Terry R. Stouch, Donald E. Williams posted to modeling parametrization resp by A_Coletta_Thesis on 2008-12-14 12:18:24 as along with 1 group Structural Biology Group TorVergata
	An automatic method to generate force-field parameters for hetero-compounds. [My Copy] Acta crystallographica. Section D, Biological crystallography, Vol. 59, No. Pt 2. (February 2003), pp. 274-289. by K. Nilsson, D. Lecerof, E. Sigfridsson, U. Ryde posted to ab-initio modeling molecular_dynamics parametrization by A_Coletta_Thesis on 2008-12-09 14:11:17 as along with 1 group Structural Biology Group TorVergata
	Fast centroid molecular dynamics: a force-matching approach for the predetermination of the effective centroid forces. [My Copy] The Journal of chemical physics, Vol. 122, No. 5. (1 February 2005) by T. D. Hone, S. Izvekov, G. A. Voth posted to coarse_grained molecular_dynamics parametrization by A_Coletta_Thesis on 2008-10-08 20:24:54 as
	Effective force field for liquid hydrogen fluoride from ab initio molecular dynamics simulation using the force-matching method. [My Copy] The journal of physical chemistry. B, Vol. 109, No. 14. (14 April 2005), pp. 6573-6586. by S. Izvekov, G. A. Voth posted to ab-initio coarse_grained molecular_dynamics parametrization by A_Coletta_Thesis on 2008-10-08 20:24:18 as
	Systematic Coarse-Graining of Nanoparticle Interactions in Molecular Dynamics Simulation [My Copy] The Journal of Physical Chemistry B, Vol. 109, No. 36. (1 September 2005), pp. 17019-17024. by Sergei Izvekov, Angela Violi, Gregory A. Voth posted to ab-initio coarse_grained molecular_dynamics parametrization by A_Coletta_Thesis on 2008-10-08 20:23:43 as along with 2 people and 1 group dcheong Marine Molecular dynamics in MSU
	Assessing Atomistic and Coarse-Grained Force Fields for Protein−Lipid Interactions: the Formidable Challenge of an Ionizable Side Chain in a Membrane [My Copy] J. Phys. Chem. B (18 July 2008) by Igor Vorobyov, Libo Li, Toby W. Allen posted to coarse_grained molecular_dynamics parametrization by A_Coletta_Thesis on 2008-10-07 16:36:21 as along with 3 people softsimu middledomain agrossfield
	REACH Coarse-Grained Biomolecular Simulation: Transferability between Different Protein Structural Classes [My Copy] Biophys. J. (9 May 2008), biophysj.108.131714. by Kei Moritsugu, Jeremy C. Smith posted to coarse_grained molecular_dynamics parametrization by A_Coletta_Thesis on 2008-10-07 16:35:19 as along with 7 people and 2 groups barry sobolevnrm paulschlesinger choonpeng aqeel jmccammon rok baker-group McCammon
	The multiscale coarse-graining method. I. A rigorous bridge between atomistic and coarse-grained models [My Copy] The Journal of Chemical Physics, Vol. 128, No. 24. (2008), 244114. by W. G. Noid, Jhih W. Chu, Gary S. Ayton, et al.Vinod Krishna, Sergei Izvekov, Gregory A. Voth, Avisek Das, Hans C. Andersen posted to coarse_grained molecular_dynamics parametrization by A_Coletta_Thesis on 2008-10-07 16:33:00 as along with 3 people edws sunrise softsimu
	The multiscale coarse-graining method. II. Numerical implementation for coarse-grained molecular models [My Copy] The Journal of Chemical Physics, Vol. 128, No. 24. (2008), 244115. by W. G. Noid, Pu Liu, Yanting Wang, et al.Jhih W. Chu, Gary S. Ayton, Sergei Izvekov, Hans C. Andersen, Gregory A. Voth posted to coarse_grained molecular_dynamics parametrization by A_Coletta_Thesis on 2008-10-07 16:32:02 as along with 4 people edws sunrise softsimu agrossfield
	Multiple binding modes of the camptothecin family to DNA oligomers. [My Copy] Chemistry (Weinheim an der Bergstrasse, Germany), Vol. 10, No. 22. (5 November 2004), pp. 5776-5787. by W. Bocian, R. Kawecki, E. Bednarek, et al.J. Sitkowski, A. Pietrzyk, M. P. Williamson, P. E. Hansen, L. Kozerski posted to ab-initio dft dna docking parametrization resp topotecan by A_Coletta_Thesis on 2008-10-01 10:54:50 as
	Automatic atom type and bond type perception in molecular mechanical calculations. [My Copy] J Mol Graph Model (1 February 2006) by Junmei Wang, Wei Wang, Peter A A. Kollman, David A A. Case posted to ab-initio antechamber dft molecular_dynamics parametrization resp software by A_Coletta_Thesis on 2008-09-12 11:10:27 as along with 5 people and 1 group dgruiz nigham xdeupi marcvanhouteghem AndreaColetta LabCompMed
	Spectroscopic Properties in the Liquid Phase: Combining High-Level Ab Initio Calculations and Classical Molecular Dynamics [My Copy] ChemPhysChem, Vol. 7, No. 1. (2006), pp. 148-156. by Michele Pavone, Giuseppe Brancato, Giovanni Morelli, Vincenzo Barone posted to ab-initio molecular_dynamics parametrization resp by A_Coletta_Thesis on 2008-09-10 17:02:59 as along with 1 person loison
	Force field parameters for rotation around chi torsion axis in nucleic acids. [My Copy] Journal of computational chemistry (12 May 2008) by Hirotaka Ode, Yuri Matsuo, Saburo Neya, Tyuji Hoshino posted to ab-initio dna molecular_dynamics parametrization by A_Coletta_Thesis on 2008-07-24 15:34:56 as
	Force field development for poly(dimethylsilylenemethylene) with the aid of ab initio calculations. [My Copy] J Phys Chem B, Vol. 110, No. 30. (August 2006), pp. 14929-14938. by V. E. Raptis, V. S. Melissas posted to ab-initio parametrization by A_Coletta_Thesis on 2008-07-22 17:42:18 as
	Molecular dynamics simulation of structure, thermodynamic, and dynamic properties of poly(dimethylsilamethylene), poly(dimethylsilatrimethylene) and their alternating copolymer. [My Copy] J Phys Chem B, Vol. 110, No. 32. (August 2006), pp. 16047-16058. by Z. A. Makrodimitri, V. E. Raptis, I. G. Economou posted to molecular_dynamics parametrization by A_Coletta_Thesis on 2008-07-22 17:42:18 as
	Development and validation of empirical force field parameters for netropsin. [My Copy] J Chem Inf Model, Vol. 45, No. 6. (2005), pp. 1546-1552. by U. Bren, M. Hodoscek, J. Koller posted to ab-initio dna parametrization by A_Coletta_Thesis on 2008-07-22 17:42:17 as
	Force field parametrization through fitting on inflection points in isotherms. [My Copy] Phys Rev Lett, Vol. 93, No. 8. (August 2004) by D. Dubbeldam, S. Calero, T. J. Vlugt, et al.R. Krishna, T. L. Maesen, E. Beerdsen, B. Smit posted to molecular_dynamics parametrization by A_Coletta_Thesis on 2008-07-22 17:42:17 as
	A new force field (ECEPP-05) for peptides, proteins, and organic molecules. [My Copy] J Phys Chem B, Vol. 110, No. 10. (March 2006), pp. 5025-5044. by Y. A. Arnautova, A. Jagielska, H. A. Scheraga posted to ab-initio molecular_dynamics parametrization by A_Coletta_Thesis on 2008-07-22 17:42:17 as
	Empirical force fields for biological macromolecules: Overview and issues [My Copy] Journal of Computational Chemistry, Vol. 25, No. 13. (July 2004), pp. 1584-1604. by Alexander D. Mackerell posted to ab-initio molecular_dynamics parametrization by A_Coletta_Thesis on 2008-07-22 17:42:17 as
	Molecular Dynamics Simulations of Water with Novel Shell-Model Potentials [My Copy] Journal of Physical Chemistry B, Vol. 105, No. 13. (2001), pp. 2618-2626. by P. J. van Maaren, D. van der Spoel posted to molecular_dynamics parametrization by A_Coletta_Thesis on 2008-07-22 17:42:17 as
	Towards phase transferable potential functions: Methodology and application to nitrogen [My Copy] The Journal of Chemical Physics, Vol. 103, No. 6. (1995), pp. 2272-2285. by Peter C. Jordan, Paul J. van Maaren, Janez Mavri, David van der Spoel, Herman J. C. Berendsen posted to ab-initio molecular_dynamics parametrization by A_Coletta_Thesis on 2008-07-22 17:42:17 as
	Application of the multimolecule and multiconformational RESP methodology to biopolymers: Charge derivation for DNA, RNA, and proteins [My Copy] Journal of Computational Chemistry, Vol. 16, No. 11. (1995), pp. 1357-1377. by Piotr Cieplak, Wendy D. Cornell, Christopher Bayly, Peter A. Kollman posted to parametrization resp by A_Coletta_Thesis on 2008-07-22 17:42:16 as
	Development and testing of a general amber force field. [My Copy] J Comput Chem, Vol. 25, No. 9. (July 2004), pp. 1157-1174. by J. Wang, R. M. Wolf, J. W. Caldwell, P. A. Kollman, D. A. Case posted to force_field molecular_dynamics parametrization resp by A_Coletta_Thesis on 2008-07-22 17:42:16 as

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topoisomerase	106
molecular_dynamics	104
ab-initio	89
camptothecin	52
parametrization	50
dft	33
dna	26
topotecan	24
inhibitors	23
abc	22
atp_binding_cassette	22
metadynamics	22
resp	20
force_field	18
modeling	18
spectra	16
td-dft	16
coarse_grained	15
docking	15
nmr	15
structure	14
protein	13
dim	11
indole	11
software	11
free-energy	10
tdp1	10
chemical_shifts	8
chemistry	8
folding	8
pmf	8
review	8
dielectric	7
spectroscopy	7
qsar	6
solvent	6
umbrella-sampling	6
apoptosis	5
frequency	5
giao	5
water	5
cancer	4
computation	4
fluorescence	4
irinotecan	4
isoquinoline	4
monte_carlo	4
neural_networks	4
pcm	4
domain	3
infra_red	3
leishmania	3
single_molecule	3
basis_set	2
binding	2
cd	2
clinical	2
drug_design	2
electrostatic	2
epr	2
gene	2
irreversible	2
modification	2
perturbation_theory	2
pme	2
poisson_boltzman	2
ribosome	2
rna	2
supercoiled_dna	2
supercoiling	2
thermodynamics	2
tumor	2
uv_spectra	2
vaccinia	2
activity	1
algorithm	1
aminoacid	1
anisotropy	1
antechamber	1
antibiotics	1
calorimetric	1
cluster_analysis	1
csgt	1
diffusion	1
dna_binding	1
dna_oligomer	1
dna_supercoiled	1
entropy	1
free_energy	1
genetic_algorithm	1
isocarbostyril	1
langevin	1
lanthanide	1
liouville	1
mitochondria	1
mutants	1
myoglobin	1
narciclasine	1
nucleoside	1
oniom	1
order_parameter	1
peptide	1
pk	1
population_analysis	1
psoralens	1
raman	1
reaction	1
replica_exchange	1
scaling	1
scattering	1
sequence_analysis	1
simulated_annealing	1
surface	1
synthesis	1
tip3p	1
transcription	1
wavelet	1

A_Coletta_Thesis's parametrization [50 articles] Export

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