middledomain's library 232 articles Export

	An optimum strategy for solution chemistry using semiempirical molecular orbital method: Importance of description of charge distribution [My Copy] Journal of Computational Chemistry, Vol. 9999, No. 9999. (2009), NA. by Norio Takenaka, Yoshiyuki Koyano, Yukinori Nakagawa, Masataka Nagaoka posted to no-tag by middledomain on 2009-10-25 15:10:47 as
	How the choice of a computational model could rule the chemical interpretation: The Ni(II) catalyzed ethylene dimerization as a case study [My Copy] Journal of Computational Chemistry, Vol. 9999, No. 9999. (2009), NA. by Vincent Tognetti, Pascal Le Floch, Carlo Adamo posted to no-tag by middledomain on 2009-10-18 22:16:01 as
	A new force field for simulating phosphatidylcholine bilayers [My Copy] Journal of Computational Chemistry, Vol. 9999, No. 9999. (2009), NA. by David Poger, Wilfred F. Van Gunsteren, Alan E. Mark posted to no-tag by middledomain on 2009-10-18 22:15:40 as
	Polarizable Force Field for Protein with Charge Response Kernel [My Copy] Journal of Chemical Theory and Computation, Vol. 5, No. 10. (13 October 2009), pp. 2809-2821. by Miho Isegawa, Shigeki Kato posted to no-tag by middledomain on 2009-10-18 22:14:54 as
	Polarizable Simulations with Second-Order Interaction Model—Force Field and Software for Fast Polarizable Calculations: Parameters for Small Model Systems and Free Energy Calculations [My Copy] Journal of Chemical Theory and Computation, Vol. 0, No. 0. (0000) by George A. Kaminski, Sergei Y. Ponomarev, Aibing B. Liu posted to no-tag by middledomain on 2009-10-18 22:14:38 as
	Polarizable Intermolecular Potentials for Water and Benzene Interacting with Halide and Metal Ions [My Copy] Journal of Chemical Theory and Computation, Vol. 0, No. 0. (0000) by Fabien Archambault, Christophe Chipot, Ignacio Soteras, F. Javier Luque, Klaus Schulten, François Dehez posted to no-tag by middledomain on 2009-10-18 22:14:22 as
	Fluorine Bonding — How Does It Work In Protein−Ligand Interactions? [My Copy] Journal of Chemical Information and Modeling, Vol. 0, No. 0. (0000) by Peng Zhou, Jianwei Zou, Feifei Tian, Zhicai Shang posted to no-tag by middledomain on 2009-10-18 22:13:30 as
	Conformational Analysis of Macrocycles: Finding What Common Search Methods Miss [My Copy] Journal of Chemical Information and Modeling, Vol. 0, No. 0. (0000) by Pascal Bonnet, Dimitris K. Agrafiotis, Fangqiang Zhu, Eric Martin posted to no-tag by middledomain on 2009-10-18 22:13:00 as
	Flexible Alignment of Small Molecules Using the Penalty Method [My Copy] Journal of Chemical Information and Modeling, Vol. 0, No. 0. (0000) by Whanchul Shin, Seung A. Hyun, Chong H. Chae, Jae K. Chon posted to no-tag by middledomain on 2009-08-15 14:47:52 as
	pKa Prediction from “Quantum Chemical Topology” Descriptors [My Copy] Journal of Chemical Information and Modeling, Vol. 0, No. 0. (0000) by A. P. Harding, D. C. Wedge, P. L. A. Popelier posted to no-tag by middledomain on 2009-07-30 19:18:06 as
	Force-field parameters of the Psi and Phi around glycosidic bonds to oxygen and sulfur atoms [My Copy] Journal of Computational Chemistry, Vol. 9999, No. 9999. (2009), NA. by Minoru Saito, Isao Okazaki posted to force_field parameterization by middledomain on 2009-05-06 19:25:31 as
	CHARMM Additive All-Atom Force Field for Acyclic Polyalcohols, Acyclic Carbohydrates, and Inositol [My Copy] Journal of Chemical Theory and Computation, Vol. 0, No. 0. (0000) by Elizabeth R. Hatcher, Olgun Guvench, Alexander D. Mackerell posted to charmm parameterization by middledomain on 2009-05-06 18:36:49 as
	Balance of Attraction and Repulsion in Nucleic-Acid Base Stacking: CCSD(T)/Complete-Basis-Set-Limit Calculations on Uracil Dimer and a Comparison with the Force-Field Description [My Copy] Journal of Chemical Theory and Computation, Vol. 0, No. 0. (0000) by Claudio A. Morgado, Petr Jurečka, Daniel Svozil, Pavel Hobza, Jiří Šponer posted to comparison force_field stacking by middledomain on 2009-05-06 18:35:26 as along with 1 person Romaniz
	Electrostatically Embedded Many-Body Approximation for Systems of Water, Ammonia, and Sulfuric Acid and the Dependence of Its Performance on Embedding Charges [My Copy] Journal of Chemical Theory and Computation, Vol. 0, No. 0. (0000) by Hannah R. Leverentz, Donald G. Truhlar posted to ammonia charge water by middledomain on 2009-05-06 18:27:00 as along with 1 person flbarroso
	Prediction of octanol-water partition coefficients of organic compounds by multiple linear regression, partial least squares, and artificial neural network [My Copy] Journal of Computational Chemistry, Vol. 9999, No. 9999. (2009), NA. by Hassan Golmohammadi posted to neural_networks by middledomain on 2009-04-12 14:52:28 as
	Van der Waals Interactions in Density-Functional Theory: Rare-Gas Diatomics [My Copy] Journal of Chemical Theory and Computation, Vol. 5, No. 4. (14 April 2009), pp. 719-727. by Felix O. Kannemann, Axel D. Becke posted to comparison dft by middledomain on 2009-04-12 14:44:25 as along with 2 people Fortran Gershom
	High-Level ab Initio Calculations To Improve Protein Backbone Dihedral Parameters [My Copy] Journal of Chemical Theory and Computation, Vol. 0, No. 0. (0000) by Hideaki Fujitani, Azuma Matsuura, Sino Sakai, Hiroyuki Sato, Yoshiaki Tanida posted to force_field by middledomain on 2009-04-12 14:42:29 as along with 2 people carlosjavierna Fortran
	Hydrogen Bonding and π-Stacking: How Reliable are Force Fields? A Critical Evaluation of Force Field Descriptions of Nonbonded Interactions [My Copy] Journal of Chemical Information and Modeling, Vol. 49, No. 4. (27 April 2009), pp. 944-955. by Robert S. Paton, Jonathan M. Goodman posted to comparison force_field hydrogen_bonding by middledomain on 2009-04-12 14:38:02 as along with 2 people massivemayhem carlosjavierna
	A Novel In Silico Approach to Drug Discovery via Computational Intelligence [My Copy] Journal of Chemical Information and Modeling, Vol. 0, No. 0. (0000) by David Hecht, Gary B. Fogel posted to neural_networks by middledomain on 2009-04-12 14:30:19 as along with 3 people Scis0000002 zimbo1 sschurer
	Feature Selection and Linear/Nonlinear Regression Methods for the Accurate Prediction of Glycogen Synthase Kinase-3β Inhibitory Activities [My Copy] Journal of Chemical Information and Modeling, Vol. 0, No. 0. (0000) by Mohammad Goodarzi, Matheus P. Freitas, Richard Jensen posted to ant_colony feature_selection machine_learning mlr neural_networks svm by middledomain on 2009-04-05 13:39:43 as
	Multiple classifier integration for the prediction of protein structural classes [My Copy] Journal of Computational Chemistry, Vol. 9999, No. 9999. (2009), NA. by Lei Chen, Lin Lu, Kairui Feng, et al.Wenjin Li, Jie Song, Lulu Zheng, Youlang Yuan, Zhenbin Zeng, Kaiyan Feng, Wencong Lu, Yudong Cai posted to machine_learning weka by middledomain on 2009-04-05 13:35:02 as
	QM/MM Calculations in Drug Discovery: A Useful Method for Studying Binding Phenomena? [My Copy] Journal of Chemical Information and Modeling, Vol. 0, No. 0. (0000) by Paul M. Gleeson, Duangkamol Gleeson posted to no-tag by middledomain on 2009-02-23 12:24:51 as along with 1 person carlosjavierna
	Molecular Modeling of Complex Chemical Systems [My Copy] Journal of the American Chemical Society, Vol. 130, No. 50. (17 December 2008), pp. 16824-16827. by Donald G. Truhlar posted to docking force_field by middledomain on 2009-02-23 11:56:02 as along with 1 person flbarroso
	Protein Influence on Electronic Spectra Modeled by Multipoles and Polarizabilities [My Copy] Journal of Chemical Theory and Computation, Vol. 0, No. 0. (0000) by Pär Söderhjelm, Charlotte Husberg, Angela Strambi, Massimo Olivucci, Ulf Ryde posted to multpoles polarizability qmmm by middledomain on 2009-02-23 11:52:57 as
	Molecular Mechanics Force Field for Octahedral Organometallic Compounds with Inclusion of the Trans Influence [My Copy] Journal of Chemical Theory and Computation, Vol. 0, No. 0. (0000) by Ivan Tubert-Brohman, Maurus Schmid, Markus Meuwly posted to force_field valbond by middledomain on 2009-02-23 11:46:08 as
	Application of Multiplexed Replica Exchange Molecular Dynamics to the UNRES Force Field: Tests with α and α+β Proteins [My Copy] Journal of Chemical Theory and Computation, Vol. 0, No. 0. (0000) by Cezary Czaplewski, Sebastian Kalinowski, Adam Liwo, Harold A. Scheraga posted to force_field protein unres by middledomain on 2009-02-23 11:43:36 as
	X-Pol Potential: An Electronic Structure-Based Force Field for Molecular Dynamics Simulation of a Solvated Protein in Water [My Copy] Journal of Chemical Theory and Computation, Vol. 5, No. 3. (10 March 2009), pp. 459-467. by Wangshen Xie, Modesto Orozco, Donald G. Truhlar, Jiali Gao posted to electrosatics force_field md xpol by middledomain on 2009-02-23 11:16:05 as
	Lipid Models for United-Atom Molecular Dynamics Simulations of Proteins [My Copy] Journal of Chemical Theory and Computation, Vol. 5, No. 3. (10 March 2009), pp. 615-626. by Andreas Kukol posted to all_atom force_field gromos lipid membrane by middledomain on 2009-02-23 11:12:30 as along with 3 people and 1 group arnaucordomi dimka Marine Molecular dynamics in MSU
	P<FONT SIZE='-2'>ACKMOL</FONT>: A package for building initial configurations for molecular dynamics simulations [My Copy] Journal of Computational Chemistry, Vol. 30, No. 13. (2009), pp. 2157-2164. by L. Martínez, R. Andrade, E. G. Birgin, J. M. Martínez posted to configurations md packing by middledomain on 2009-02-23 10:59:43 as along with 2 people and 1 group whitead klexa Jiang Research Group
	The SAAP force field: Development of the single amino acid potentials for 20 proteinogenic amino acids and Monte Carlo molecular simulation for short peptides [My Copy] Journal of Computational Chemistry, Vol. 9999, No. 9999. (2009), NA. by Michio Iwaoka, Naoki Kimura, Daisuke Yosida, Toshiya Minezaki posted to force_field protein saap by middledomain on 2009-02-01 13:11:51 as
	Effect of Data Standardization on Chemical Clustering and Similarity Searching [My Copy] Journal of Chemical Information and Modeling, Vol. 0, No. 0. (0000) by Chia-Wei Chu, John D. Holliday, Peter Willett posted to machine_learning by middledomain on 2009-01-11 14:06:49 as along with 2 people sschurer reyez
	Inductive Transfer of Knowledge: Application of Multi-Task Learning and Feature Net Approaches to Model Tissue-Air Partition Coefficients [My Copy] Journal of Chemical Information and Modeling, Vol. 0, No. 0. (0000) by Alexandre Varnek, Cédric Gaudin, Gilles Marcou, Igor Baskin, Anil K. Pandey, Igor V. Tetko posted to machine_learning by middledomain on 2009-01-11 13:55:49 as along with 1 person and 1 group igbaskin Cheminformatics
	Incorporating Phase-Dependent Polarizability in Nonadditive Electrostatic Models for Molecular Dynamics Simulations of the Aqueous Liquid−Vapor Interface [My Copy] Journal of Chemical Theory and Computation, Vol. 5, No. 2. (10 February 2009), pp. 359-373. by Brad A. Bauer, G. Lee Warren, Sandeep Patel posted to polarizable water by middledomain on 2009-01-11 13:35:44 as along with 2 people kulinskii tovrstra
	Crystal structure prediction of flexible molecules using parallel genetic algorithms with a standard force field [My Copy] Journal of Computational Chemistry, Vol. 30, No. 13. (2009), pp. 1973-1985. by Seonah Kim, Anita M. Orendt, Marta B. Ferraro, Julio C. Facelli posted to no-tag by middledomain on 2009-01-11 13:33:10 as along with 1 person dimka
	<I>In silico</I> prediction of drug solubility: 4. Will simple potentials suffice? [My Copy] Journal of Computational Chemistry, Vol. 9999, No. 9999. (2008), NA. by Kai Lüder, Lennart Lindfors, Jan Westergren, Sture Nordholm, Rasmus Persson, Mikaela Pedersen posted to no-tag by middledomain on 2009-01-04 14:13:12 as
	Efficient table lookup without inverse square roots for calculation of pair wise atomic interactions in classical simulations [My Copy] Journal of Computational Chemistry, Vol. 9999, No. 9999. (2008), NA. by Lennart Nilsson posted to charmm force_field by middledomain on 2008-12-20 16:02:58 as along with 1 person RamuAnandakrishnan
	Polarizable empirical force field for nitrogen-containing heteroaromatic compounds based on the classical Drude oscillator. [My Copy] Journal of computational chemistry, Vol. 30, No. 12. (September 2009), pp. 1821-1838. by P. E. Lopes, G. Lamoureux, A. D. Mackerell posted to charmm drude force_field polarizable by middledomain on 2008-12-20 15:22:45 as along with 1 person flbarroso
	Influence of ionization on the conformational preferences of peptide models. Ramachandran surfaces of <I>N</I>-formyl-glycine amide and <I>N</I>-formyl-alanine amide radical cations [My Copy] Journal of Computational Chemistry, Vol. 9999, No. 9999. (2008), NA. by Adrià Gil, Mariona Sodupe, Juan Bertran posted to conformation peptide by middledomain on 2008-12-20 15:15:25 as
	Modeling the H bond donor strength of &bond;OH, &bond;NH, and &bond;CH sites by local molecular parameters [My Copy] Journal of Computational Chemistry, Vol. 9999, No. 9999. (2008), NA. by Johannes Schwöbel, Ralf-Uwe Ebert, Ralph Kühne, Gerrit Schüürmann posted to electrostatic by middledomain on 2008-11-30 16:07:56 as
	Toward an <I>ab initio</I> fragment database for bioisosterism: Dependence of QCT properties on level of theory, conformation, and chemical environment [My Copy] Journal of Computational Chemistry, Vol. 9999, No. 9999. (2008), NA. by Michael Devereux, Paul L. A. Popelier, Iain M. Mclay posted to qct by middledomain on 2008-11-16 11:02:22 as
	Counteracting stagnation in genetic algorithm calculations by implementation of a micro genetic algorithm strategy [My Copy] Phys. Chem. Chem. Phys. (2008) by Zhongfu Zhou, Kenneth D. Harris posted to genetic_algorithm by middledomain on 2008-11-02 11:36:30 as
	The Important Role of Lone-Pairs in Force Field (MM4) Calculations on Hydrogen Bonding in Alcohols [My Copy] The Journal of Physical Chemistry A, Vol. 112, No. 46. (20 November 2008), pp. 11903-11913. by Jenn-Huei Lii, Norman L. Allinger posted to force_field hydrogen_bonding mm4 by middledomain on 2008-11-02 11:35:33 as
	Water as a Biomolecule [My Copy] ChemPhysChem, Vol. 9, No. 18. (2008), pp. 2677-2685. by Philip Ball posted to water by middledomain on 2008-10-19 17:08:48 as along with 1 person softsimu
	Toward a Coarse-Grained Protein Model Coupled with a Coarse-Grained Solvent Model: Solvation Free Energies of Amino Acid Side Chains [My Copy] Journal of Chemical Theory and Computation, Vol. 4, No. 11. (11 November 2008), pp. 1891-1901. by Wei Han, Cheuk-Kin Wan, Yun-Dong Wu posted to force_field torsion by middledomain on 2008-10-19 17:07:49 as along with 3 people sunrise rbaron agrossfield
	The accuracy of local MP2 methods for conformational energies [My Copy] Molecular Physics: An International Journal at the Interface Between Chemistry and Physics, Vol. 106, No. 15. (2008), pp. 1899-1906. by Jakub Kaminsky, Ricardo A. Mata, Hans-Joachim Werner, Frank Jensen posted to conformation dft mp2 by middledomain on 2008-10-12 19:34:13 as along with 1 person kubikuk
	Protein Folding: Complexity to Make More Complexity?. In the Pipeline: [My Copy] posted to folding protein by middledomain on 2008-10-05 12:52:32 as
	Evaluation of an inverse molecular design algorithm in a model binding site [My Copy] Proteins: Structure, Function, and Bioinformatics, Vol. 9999, No. 9999. (2008), NA. by David J. Huggins, Michael D. Altman, Bruce Tidor posted to electrostatic by middledomain on 2008-10-05 12:50:27 as along with 3 people and 2 groups dfgreen mijam barry structural_bioinformatics McCammon
	Can Descriptors of the Electron Density Distribution Help To Distinguish Functional Groups? [My Copy] J. Chem. Inf. Model. (3 October 2008) by Julien Burton, Nathalie Meurice, Laurence Leherte, Daniel P. Vercauteren posted to atom_type by middledomain on 2008-10-05 12:42:13 as
	An Interface between the Universal Force Field and the Effective Fragment Potential Method [My Copy] J. Phys. Chem. B (17 September 2008) by Deborah Zorn, Victor S. Lin, Marek Pruski, Mark S. Gordon posted to eff force_field uff by middledomain on 2008-09-24 19:46:43 as
	Peptide Folding Using Multiscale Coarse-Grained Models [My Copy] J. Phys. Chem. B (20 September 2008) by Ian F. Thorpe, Jian Zhou, Gregory A. Voth posted to coarse_grained force_field peptide by middledomain on 2008-09-24 19:44:45 as along with 3 people agrossfield A_Coletta_Thesis paulschlesinger

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force_field	62
water	22
docking	21
charmm	19
polarization	16
protein	15
dft	13
torsion	13
conformation	11
amber	10
comparison	10
peptide	10
md	8
solvation	8
mp2	7
neural_networks	7
charge	6
scoring_functions	6
ccsd	5
electrostatic	5
hydrogen_bonding	5
machine_learning	5
qct	5
virtual_screening	5
b3lyp	4
gromos	4
parameterization	4
polarizable	4
qmmm	4
qsar	4
rotation	4
alanine	3
dipeptides	3
electrosatics	3
flexx	3
glide	3
hts	3
litpres	3
mmff	3
pi-pi_interactions	3
prediction	3
proteins	3
review	3
ab_initio	2
amino_acid	2
coarse_grained	2
comformation	2
dipeptide	2
dipole	2
drude	2
feature_selection	2
folding	2
genetic_algorithm	2
glycine	2
h-bonding	2
ion	2
ligand	2
methanol	2
nmr	2
nucleic_acids	2
petide	2
pla	2
polarizability	2
scoring	2
torsion_paper	2
trappe	2
web_interface	2
xpol	2
alcohol	1
all_atom	1
ameoba	1
ammonia	1
ant_colony	1
anticancer	1
apt	1
arginine	1
aromatic	1
asedock	1
astex	1
atom_type	1
autodock	1
autoshim	1
base-pairs	1
basis_set_limit	1
benzene	1
binding	1
c60	1
charge_on_spring_model	1
chemical_space	1
configurations	1
consensus_scoring	1
crystal	1
crystal_prediction	1
dehydration	1
denovo	1
de_novo_design	1
development	1
dipole_moment	1
dock	1
drug_interactions	1
eff	1
efp	1
electronegativity	1
electrophilicity	1
enthalpy	1
epr	1
flexible	1
gandi	1
gas_phase	1
glenn	1
gold	1
graph_theory	1
gromacs	1
gui	1
hardness	1
hiv	1
hyde	1
hydrophobicity	1
industry	1
interactions	1
internal	1
internal_energy	1
iqa	1
ir	1
joyce	1
kriging	1
lennard-jones	1
lipid	1
liquids	1
london_dispersion	1
martini	1
mddr	1
membrane	1
merck	1
methyl_rotation	1
mine	1
mlr	1
mm	1
mm2	1
mm3	1
mm4	1
moe	1
molecular_complexity	1
multipole_expansion	1
multpoles	1
opls	1
optimization	1
packing	1
pharma	1
polar_interactions	1
prodrugs	1
protein-ligand	1
psa	1
pubchem	1
q2mm	1
q-dock	1
qm	1
quantum_mechanics	1
reflex	1
rotamers	1
saap	1
sam	1
sar	1
semi_empirical	1
skelgen	1
solvant_accessible_surface	1
spc	1
stacking	1
svm	1
tip3p	1
tip4p	1
torson	1
transition_metal_complexes	1
uff	1
unres	1
valbond	1
vdw	1
weka	1

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