yongzhao's watchlist [49 articles] Export

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	Pairwise solute descreening of solute charges from a dielectric medium [My Copy] Chemical Physics Letters, Vol. 246, No. 1. (17 November 1995), pp. 122-129. by G. D. Hawkins, C. J. Cramer, D. G. Truhlar posted to cgreview by baaden on 2006-02-08 08:31:37 as along with 1 person sigalov
	Order-N methodologies and their applications [My Copy] Physics Reports, Vol. 358, No. 1. (February 2002), pp. 1-74. by S. Y. Wu, C. S. Jayanthi posted to cgreview by baaden on 2006-01-18 11:54:40 as
	Genetic algorithms for protein folding simulations. [My Copy] J Mol Biol, Vol. 231, No. 1. (5 May 1993), pp. 75-81. by R. Unger, J. Moult posted to cgreview folding by baaden on 2006-01-09 14:41:51 as along with 2 people dgront ejames
	Exploring conformational space with a simple lattice model for protein structure. [My Copy] J Mol Biol, Vol. 243, No. 4. (4 November 1994), pp. 668-682. by D. A. Hinds, M. Levitt posted to cgreview coarse-graining folding by baaden on 2006-01-09 14:18:56 as along with 1 person nigham
	Folding and stability of helical proteins: carp myogen. [My Copy] J Mol Biol, Vol. 106, No. 2. (15 September 1976), pp. 421-437. by A. Warshel, M. Levitt posted to cgreview folding by baaden on 2006-01-09 14:13:16 as
	A simplified representation of protein conformations for rapid simulation of protein folding. [My Copy] J Mol Biol, Vol. 104, No. 1. (14 June 1976), pp. 59-107. by M. Levitt posted to cgreview folding by baaden on 2006-01-09 14:03:27 as along with 3 people stefanorb dgront nigham
	Computer simulation of protein folding. [My Copy] Nature, Vol. 253, No. 5494. (27 February 1975), pp. 694-698. by M. Levitt, A. Warshel posted to cgreview folding by baaden on 2006-01-09 14:02:46 as along with 3 people flbarroso nigham dgront
	Brownian dynamics simulations of protein folding: access to milliseconds time scale and beyond. [My Copy] Proc Natl Acad Sci U S A, Vol. 95, No. 8. (14 April 1998), pp. 4288-4292. by A. Rojnuckarin, S. Kim, S. Subramaniam posted to brownian_dynamics cgreview folding by baaden on 2006-01-09 13:54:09 as
	Molecular dynamics simulations of peptides and proteins with amplified collective motions. [My Copy] Biophys J, Vol. 84, No. 6. (June 2003), pp. 3583-3593. by Z. Zhang, Y. Shi, H. Liu posted to cgreview coarse-graining elastic_network methods by baaden on 2005-08-04 13:33:46 as along with 2 people and 1 group aqeel sobolevnrm baker-group
	Dynamics of large proteins through hierarchical levels of coarse-grained structures. [My Copy] J Comput Chem, Vol. 23, No. 1. (15 January 2002), pp. 119-127. by P. Doruker, R. L. Jernigan, I. Bahar posted to cgreview coarse-graining elastic_network by baaden on 2005-08-04 13:31:56 as along with 2 people and 2 groups ana aqeel structural_bioinformatics Bioinformatics
	Generalized-ensemble algorithms for molecular simulations of biopolymers. [My Copy] Biopolymers, Vol. 60, No. 2. (2001), pp. 96-123. by A. Mitsutake, Y. Sugita, Y. Okamoto posted to cgreview methods replica_exchange by baaden on 2005-08-04 13:06:13 as along with 3 people dgruiz shuns andreasauerwein
	Replica-exchange extensions of simulated tempering method. [My Copy] J Chem Phys, Vol. 121, No. 6. (8 August 2004), pp. 2491-2504. by A. Mitsutake, Y. Okamoto posted to cgreview replica_exchange by baaden on 2005-08-04 13:04:42 as along with 1 person Sylvain_Prigent
	Refinement of NMR structures using implicit solvent and advanced sampling techniques. [My Copy] J Am Chem Soc, Vol. 126, No. 49. (15 December 2004), pp. 16038-16047. by J. Chen, W. Im, C. L. Brooks posted to cgreview sampling structure_refinement by baaden on 2005-08-04 13:03:42 as along with 2 people bmduggan bilab
	Density guided importance sampling: application to a reduced model of protein folding. [My Copy] Bioinformatics, Vol. 21, No. 12. (15 June 2005), pp. 2839-2843. by G. L. Thomas, R. B. Sessions, M. J. Parker posted to cgreview sampling by baaden on 2005-08-04 13:02:09 as
	Multicopy molecular dynamics simulations suggest how to reconcile crystallographic and product formation data for camphor enantiomers bound to cytochrome P-450cam. [My Copy] J Inorg Biochem, Vol. 81, No. 3. (31 August 2000), pp. 121-131. by B. Das, V. Helms, V. Lounnas, R. C. Wade posted to cgreview methods multicopy by baaden on 2005-08-04 12:32:23 as
	Predicting slow structural transitions in macromolecular systems: Conformational flooding. [My Copy] PHYSICAL REVIEW. E. STATISTICAL PHYSICS, PLASMAS, FLUIDS, AND RELATED INTERDISCIPLINARY TOPICS, Vol. 52, No. 3. (September 1995), pp. 2893-2906. by H. Grubmüller posted to cgreview coarse-graining methods sampling by baaden on 2005-08-04 12:23:03 as
	Protein dynamics simulations from nanoseconds to microseconds. [My Copy] Curr Opin Struct Biol, Vol. 9, No. 2. (April 1999), pp. 157-163. by S. Doniach, P. Eastman posted to cgreview review by baaden on 2005-08-04 12:16:05 as
	Efficient exploration of reactive potential energy surfaces using Car-Parrinello molecular dynamics. [My Copy] Phys Rev Lett, Vol. 90, No. 23. (13 June 2003) by M. Iannuzzi, A. Laio, M. Parrinello posted to cgreview dynamics methods by baaden on 2005-08-03 12:23:50 as
	Escaping free-energy minima. [My Copy] Proc Natl Acad Sci U S A, Vol. 99, No. 20. (1 October 2002), pp. 12562-12566. by A. Laio, M. Parrinello posted to cgreview dynamics methods by baaden on 2005-08-03 12:22:43 as along with 6 people and 1 group howerja ibuch apaydin and_ped10 Diego_Prada AndreaColetta Jiang Research Group
	Reconstructing the density of states by history-dependent metadynamics. [My Copy] Phys Rev Lett, Vol. 92, No. 17. (30 April 2004) by C. Micheletti, A. Laio, M. Parrinello posted to cgreview dynamics methods by baaden on 2005-08-03 12:19:42 as along with 1 person and_ped10
	Simulation of gel phase formation and melting in lipid bilayers using a coarse grained model. [My Copy] Chem Phys Lipids, Vol. 135, No. 2. (June 2005), pp. 223-244. by S. J. Marrink, J. Risselada, A. E. Mark posted to cgreview coarse-graining lipid_bilayers simulations by baaden on 2005-07-31 17:29:07 as along with 1 person divadyrral
	The energy landscape as a unifying theme in molecular science. [My Copy] Philos Transact A Math Phys Eng Sci, Vol. 363, No. 1827. (15 February 2005) by D. J. Wales posted to cgreview coarse-graining by baaden on 2005-07-31 16:49:22 as
	Simulating the Physical World : From Quantum Mechanics to Fluid Dynamics [My Copy] In Simulating the Physical World : From Quantum Mechanics to Fluid Dynamics (30 June 2006), pp. 1-400. by Herman J. C. Berendsen posted to cgreview coarse-graining fokker_planck mesoscale methods molecular_dynamics protein_dynamics simulations soft_matter by baaden on 2005-07-31 15:17:02 as
	Statistically based reduced representation of amino acid side chains. [My Copy] J Chem Inf Comput Sci, Vol. 44, No. 3. (n 2004), pp. 817-830. by J. K. Rainey, M. C. Goh posted to cgreview coarse-graining protein_structure proteins by baaden on 2005-07-31 14:32:15 as along with 1 person blackbart
	On the model granularity to simulate protein dynamics: A biological physics view on biomolecular computing [My Copy] Natural Computing, Vol. 3, No. 4. (December 2004), pp. 377-393. by Mitsunori Takano, Junichi Higo, Hironori Nakamura, Masaki Sasai posted to cgreview coarse-graining molecular_dynamics protein_dynamics proteins by baaden on 2005-07-31 14:24:59 as
	Predictions of protein flexibility: First-order measures [My Copy] Proteins: Structure, Function, and Bioinformatics, Vol. 56, No. 4. (20 May 2004), pp. 661-668. by Julio A. Kovacs, Pablo Chacón, Ruben Abagyan posted to cgreview coarse-graining flexibility proteins by baaden on 2005-07-31 14:22:29 as along with 3 people apaydin aqeel vavi
	Statistical Mechanics of Coarse-Graining [My Copy] Lecture Notes in Physics, Vol. 640 (January 2004), pp. 69-115. by Pep Español posted to cgreview fokker_planck by baaden on 2005-07-31 14:20:31 as
	A structural perspective on protein-protein interactions. [My Copy] Curr Opin Struct Biol, Vol. 14, No. 3. (June 2004), pp. 313-324. by R. B. Russell, F. Alber, P. Aloy, et al.F. P. Davis, D. Korkin, M. Pichaud, M. Topf, A. Sali posted to cgreview coarse-graining proteins by baaden on 2005-07-31 14:17:16 as along with 13 people and 1 group bicko anita chad_davis dgront sriram_s ruvido cjeans Evangelia Pao-Yang marti higueruelo jteyra timg structure-bii
	New Advances in Normal Mode Analysis of Supermolecular Complexes and Applications to Structural Refinement [My Copy] Current Protein and Peptide Science, Vol. 5, No. 2. (April 2004), pp. 119-123. by J. Ma posted to cgreview coarse-graining nma review by baaden on 2005-07-31 14:09:19 as along with 1 person aqeel
	Multi-scale Molecular Modeling of Chemical Reactivity [My Copy] Molecular Simulation, Vol. 30, No. 11 - 12. (January 2004), pp. 699-748. by Erik E. Santiso, Keith E. Gubbins posted to cgreview coarse-graining methods physchem review by baaden on 2005-07-31 14:00:20 as
	Normal-modes-based prediction of protein conformational changes guided by distance constraints. [My Copy] Biophys J, Vol. 88, No. 5. (May 2005), pp. 3109-3117. by W. Zheng, B. R. Brooks posted to cgreview coarse-graining elastic_network methods proteins by baaden on 2005-07-31 13:12:29 as along with 1 person aqeel
	Spectrin-level modeling of the cytoskeleton and optical tweezers stretching of the erythrocyte. [My Copy] Biophys J, Vol. 88, No. 5. (May 2005), pp. 3707-3719. by J. Li, M. Dao, C. T. Lim, S. Suresh posted to cgreview coarse-graining elastic_network mesoscale by baaden on 2005-07-31 12:48:29 as
	Rigid-cluster models of conformational transitions in macromolecular machines and assemblies. [My Copy] Biophys J, Vol. 89, No. 1. (July 2005), pp. 43-55. by M. K. Kim, R. L. Jernigan, G. S. Chirikjian posted to cgreview coarse-graining elastic_network methods by baaden on 2005-07-31 12:45:59 as along with 1 person aqeel
	Long-timescale simulation methods. [My Copy] Curr Opin Struct Biol, Vol. 15, No. 2. (April 2005), pp. 151-156. by R. Elber posted to cgreview coarse-graining methods by baaden on 2005-07-31 12:36:40 as
	Simple but predictive protein models. [My Copy] Trends Biotechnol (19 July 2005) by Feng Ding, Nikolay V V. Dokholyan posted to cgreview coarse-graining proteins by baaden on 2005-07-31 12:32:27 as along with 1 person choonpeng
	Mapping potential energy surfaces. [My Copy] J Chem Phys, Vol. 121, No. 3. (15 July 2004), pp. 1193-1200. by Y. Wu, J. D. Schmitt, R. Car posted to cgreview coarse-graining methods parameterization by baaden on 2005-07-31 12:30:32 as
	Coarse-grained simulations of lipid bilayers. [My Copy] J Chem Phys, Vol. 121, No. 23. (15 December 2004), pp. 11942-11948. by M. J. Stevens posted to cgreview coarse-graining lipid_bilayers soft_matter by baaden on 2005-07-31 12:22:41 as along with 1 person dimka
	Coarse-grained computations for a micellar system. [My Copy] J Chem Phys, Vol. 122, No. 4. (22 January 2005) by D. I. Kopelevich, A. Z. Panagiotopoulos, I. G. Kevrekidis posted to cgreview coarse-graining physchem soft_matter by baaden on 2005-07-31 12:19:33 as along with 1 person softsimu
	Coarse-grained kinetic computations for rare events: application to micelle formation. [My Copy] J Chem Phys, Vol. 122, No. 4. (22 January 2005) by D. I. Kopelevich, A. Z. Panagiotopoulos, I. G. Kevrekidis posted to cgreview coarse-graining physchem soft_matter by baaden on 2005-07-31 12:18:39 as
	Study of the Villin headpiece folding dynamics by combining coarse-grained Monte Carlo evolution and all-atom molecular dynamics. [My Copy] Proteins, Vol. 58, No. 2. (1 February 2005), pp. 459-471. by G. M. De Mori, G. Colombo, C. Micheletti posted to cgreview coarse-graining folding by baaden on 2005-07-31 12:17:47 as
	Mesoscale model of polymer melt structure: self-consistent mapping of molecular correlations to coarse-grained potentials. [My Copy] J Chem Phys, Vol. 122, No. 10. (8 March 2005) by H. S. Ashbaugh, H. A. Patel, S. K. Kumar, S. Garde posted to cgreview coarse-graining parameterization by baaden on 2005-07-31 12:16:40 as
	A coarse-grained model for double-helix molecules in solution: spontaneous helix formation and equilibrium properties. [My Copy] J Chem Phys, Vol. 122, No. 12. (22 March 2005) by H. L. Tepper, G. A. Voth posted to cgreview coarse-graining by baaden on 2005-07-31 12:15:37 as
	A random walk through the dynamics of homogeneous vapor-liquid nucleation. [My Copy] J Chem Phys, Vol. 122, No. 17. (1 May 2005) by D. M. Huang, P. Attard posted to cgreview coarse-graining physchem by baaden on 2005-07-31 12:14:42 as
	Artifacts in dynamical simulations of coarse-grained model lipid bilayers. [My Copy] J Chem Phys, Vol. 122, No. 20. (22 May 2005) by A. F. Jakobsen, O. G. Mouritsen, G. Besold posted to cgreview coarse-graining lipid_bilayers soft_matter by baaden on 2005-07-31 12:13:44 as
	Atomistic molecular-dynamics simulations of the size and shape of polyethylene in hexane at infinite dilution. [My Copy] J Chem Phys, Vol. 122, No. 20. (22 May 2005) by G. Zifferer, A. Kornherr posted to cgreview coarse-graining polymers soft_matter by baaden on 2005-07-31 12:13:09 as
	Long dynamics simulations of proteins using atomistic force fields and a continuum representation of solvent effects: calculation of structural and dynamic properties. [My Copy] Proteins, Vol. 60, No. 3. (15 August 2005), pp. 464-484. by Xianfeng Li, Sergio A. Hassan, Ernest L. Mehler posted to cgreview implicit_solvent by baaden on 2005-07-31 12:08:58 as along with 3 people jjurban bmduggan flbarroso
	Coarse graining using pretabulated potentials: Liquid benzene. [My Copy] J Chem Phys, Vol. 122, No. 24. (22 June 2005) by N. Zacharopoulos, N. Vergadou, D. N. Theodorou posted to cgreview coarse-graining by baaden on 2005-07-31 12:07:30 as
	Coarse-grained models for proteins [My Copy] Current Opinion in Structural Biology, Vol. 15, No. 2. (April 2005), pp. 144-150. by V. Tozzini posted to cgreview coarse-grained by baaden on 2005-07-30 06:16:16 as along with 9 people flbarroso krapnik RamuAnandakrishnan aqeel ltrabuco simone cottrell choonpeng iantunbridge
	Multiscale coupling of mesoscopic- and atomistic-level lipid bilayer simulations. [My Copy] J Chem Phys, Vol. 122, No. 24. (22 June 2005) by R. Chang, G. S. Ayton, G. A. Voth posted to cgreview coarse-graining lipid_bilayers by baaden on 2005-07-30 06:13:09 as

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docking	37
docking_design	21
flex	19
screening	16
induced_fit	11
loop	10
potential_app	10
cross_docking	8
cryoem	8
hiv	8
review	8
side_chain	8
normal_mode_analysis	7
ga	5
library	5
mine	5
multiple	5
score	5
hivin	4
conformation_sampling	3
domain_analysis	3
p450	3
search	3
essential_dynamics	2
rotamer_lib	2
shape	2
autodock	1
bace	1
colony_energy	1
database	1
essential-dynamics	1
gaussian_network_model	1
ligand	1
ligand_based	1
metadynamics	1
molecular_dynamics	1
motion_database	1
protein_protein_docking	1
qsar	1
reranking	1
rmsd	1
rt	1
sampling	1
structures	1
t_cell	1
visualization	1

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