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Recent papers classified by the tag implicit-solvent.

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	An image-based reaction field method for electrostatic interactions in molecular dynamics simulations of aqueous solutions [My Copy] The Journal of Chemical Physics, Vol. 131, No. 15. (2009), 154103. by Yuchun Lin, Andrij Baumketner, Shaozhong Deng, Zhenli Xu, Donald Jacobs, Wei Cai posted to implicit-solvent electrostatics by agrossfield on 2009-11-20 17:47:03 as along with 2 people dlimmer RamuAnandakrishnan
	Trypsin-ligand binding free energies from explicit and implicit solvent simulations with polarizable potential [My Copy] Journal of Computational Chemistry, Vol. 9999, No. 9999. (2009), NA. by Dian Jiao, Jiajing Zhang, Robert E. Duke, Guohui Li, Michael J. Schnieders, Pengyu Ren posted to forcefield free-energy implicit-solvent ligand-binding by agrossfield on 2009-06-16 13:07:49 as along with 2 people and 1 group flbarroso sobolevnrm baker-group
	ABSINTH: a new continuum solvation model for simulations of polypeptides in aqueous solutions. [My Copy] Journal of computational chemistry, Vol. 30, No. 5. (15 April 2009), pp. 673-699. by A. Vitalis, R. V. Pappu posted to implicit-solvent modeling-software by agrossfield on 2009-02-23 14:45:33 as along with 2 people and 1 group melo_mcr sobolevnrm baker-group
	Evaluating the transferability of coarse-grained, density-dependent implicit solvent models to mixtures and chains [My Copy] The Journal of Chemical Physics, Vol. 130, No. 3. (2009) by Erik C. Allen, Gregory C. Rutledge posted to implicit-solvent by agrossfield on 2009-01-22 14:34:58 as along with 1 person and 1 group sobolevnrm baker-group
	Improving implicit solvent simulations: a Poisson-centric view [My Copy] Current Opinion in Structural Biology, Vol. 15, No. 2. (April 2005), pp. 137-143. by N. Baker posted to implicit-solvent poisson-boltzmann water by softsimu on 2008-11-12 20:19:53 as along with 5 people oteri flbarroso ttjoseph qwermish RamuAnandakrishnan
	Interpreting the Coulomb-field approximation for generalized-Born electrostatics using boundary-integral equation theory [My Copy] The Journal of Chemical Physics, Vol. 129, No. 14. (2008) by Jaydeep P. Bardhan posted to generalized-born implicit-solvent by agrossfield on 2008-10-17 01:03:51 as along with 2 people and 1 group sobolevnrm onufriev baker-group
	An analytical approach to computing biomolecular electrostatic potential. II. Validation and applications [My Copy] The Journal of Chemical Physics, Vol. 129, No. 7. (2008), 075102. by John C. Gordon, Andrew T. Fenley, Alexey Onufriev posted to implicit-solvent by agrossfield on 2008-08-22 13:25:06 as along with 3 people flbarroso Scis0000002 RamuAnandakrishnan
	An analytical approach to computing biomolecular electrostatic potential. I. Derivation and analysis [My Copy] The Journal of Chemical Physics, Vol. 129, No. 7. (2008), 075101. by Andrew T. Fenley, John C. Gordon, Alexey Onufriev posted to implicit-solvent by agrossfield on 2008-08-22 13:24:49 as along with 3 people flbarroso afenley RamuAnandakrishnan
	Modeling Self-Assembly Processes Driven by Nonbonded Interactions in Soft Materials† [My Copy] The Journal of Physical Chemistry B, Vol. 112, No. 34. (28 August 2008), pp. 10388-10398. by Martin McCullagh, Tatiana Prytkova, Stefano Tonzani, Nicolas D. Winter, George C. Schatz posted to coarse-grain implicit-membrane implicit-solvent by agrossfield on 2008-08-21 20:11:48 as along with 1 person qshao
	Solvent-free model for self-assembling fluid bilayer membranes: Stabilization of the fluid phase based on broad attractive tail potentials [My Copy] The Journal of Chemical Physics, Vol. 123, No. 22. (2005), 224710. by Ira R. Cooke, Markus Deserno posted to implicit-solvent membranes by softsimu on 2008-06-06 17:47:12 as along with 2 people cjryan edws
	A novel algorithm for creating coarse-grained, density dependent implicit solvent models [My Copy] The Journal of Chemical Physics, Vol. 128, No. 15. (2008) by Erik C. Allen, Gregory C. Rutledge posted to coarse-grain implicit-solvent by agrossfield on 2008-05-27 13:10:48 as along with 1 person and 1 group sobolevnrm baker-group
	Recent advances in implicit solvent-based methods for biomolecular simulations. [My Copy] Current opinion in structural biology, Vol. 18, No. 2. (04 April 2008), pp. 140-148. by Jianhan Chen, Charles L. Brooks, Jana Khandogin posted to implicit-solvent review by choonpeng on 2008-04-02 01:30:29 as along with 8 people and 2 groups krapnik RamuAnandakrishnan mikaellund oteri nickolay flbarroso sobolevnrm onufriev Structural Biology Group TorVergata baker-group
	Implicit solvent simulation models for biomembranes [My Copy] European Biophysics Journal, Vol. 35, No. 2. (11 January 2006), pp. 104-124. by Grace Brannigan, Lawrence Lin, Frank Brown posted to coarse-graining implicit-solvent by softsimu on 2008-03-18 17:50:16 as
	Implicit modeling of nonpolar solvation for simulating protein folding and conformational transitions. [My Copy] Physical chemistry chemical physics : PCCP, Vol. 10, No. 4. (28 January 2008), pp. 471-481. by J. Chen, C. L. Brooks posted to implicit-solvent solvent-effects by choonpeng on 2008-02-26 02:07:23 as along with 2 people yxue flbarroso
	Conformational Sampling with Implicit Solvent Models: Application to the PHF6 Peptide in Tau Protein [My Copy] Biophysical Journal, Vol. 92, No. 1. (01 January 2007), pp. 34-45. by A. Huang, C. Stultz posted to implicit-solvent by choonpeng on 2008-02-26 01:32:51 as along with 1 person flbarroso
	What role do surfaces play in GB models? A new-generation of surface-generalized born model based on a novel gaussian surface for biomolecules. [My Copy] J Comput Chem, Vol. 27, No. 1. (January 2006), pp. 72-89. by Z. Yu, M. P. Jacobson, R. A. Friesner posted to implicit-solvent by choonpeng on 2008-02-24 05:40:17 as along with 3 people and 1 group BragilMassoud qzhang onufriev TSRI_MGL
	Secondary Structure Bias in Generalized Born Solvent Models: Comparison of Conformational Ensembles and Free Energy of Solvent Polarization from Explicit and Implicit Solvation [My Copy] J. Phys. Chem. B, Vol. 111, No. 7. (22 February 2007), pp. 1846-1857. by D. R. Roe, A. Okur, L. Wickstrom, V. Hornak, C. Simmerling posted to implicit-solvent by choonpeng on 2008-02-24 05:06:00 as along with 5 people and 1 group RamuAnandakrishnan flbarroso baaden sobolevnrm onufriev baker-group
	Simulations of multi-directional forced unfolding of titin I27. [My Copy] J Mol Graph Model, Vol. 24, No. 5. (March 2006), pp. 396-403. by R. D. Toofanny, P. M. Williams posted to force-probe-md implicit-solvent by choonpeng on 2007-08-26 14:37:08 as
	Effective energy function for proteins in solution. [My Copy] Proteins, Vol. 35, No. 2. (1 May 1999), pp. 133-152. by T. Lazaridis, M. Karplus posted to implicit-solvent methodology solvent-effects by choonpeng on 2007-08-26 12:27:05 as along with 6 people and 2 groups melo_mcr oceanwind marcius bluvsh1 hmk kgutwin BioinfoCIPF SGU-CIPF
	Origin of mechanical strength of bovine carbonic anhydrase studied by molecular dynamics simulation. [My Copy] Biophys J, Vol. 87, No. 6. (December 2004), pp. 4007-4020. by S. Ohta, M. T. Alam, H. Arakawa, A. Ikai posted to force-probe-md implicit-solvent by choonpeng on 2007-08-26 06:16:03 as
	Pulling geometry defines the mechanical resistance of a beta-sheet protein. [My Copy] Nat Struct Biol, Vol. 10, No. 9. (September 2003), pp. 731-737. by D. J. Brockwell, E. Paci, R. C. Zinober, et al.G. S. Beddard, P. D. Olmsted, D. A. Smith, R. N. Perham, S. E. Radford posted to force-probe-md implicit-solvent single-molecule-methods by choonpeng on 2007-06-19 10:47:51 as along with 1 person ruudvanleeuwen
	Mechanical Unfolding of TNfn3: The Unfolding Pathway of a fnIII Domain Probed by Protein Engineering, AFM and MD Simulation [My Copy] Journal of Molecular Biology, Vol. 350, No. 4. (22 July 2005), pp. 776-789. by Sean P. Ng, Ross W. Rounsevell, Annette Steward, et al.Christian D. Geierhaas, Philip M. Williams, Emanuele Paci, Jane Clarke posted to force-probe-md implicit-solvent mechanical-unfolding single-molecule-methods by choonpeng on 2007-02-03 03:06:19 as
	Implicit solvent models for flexible protein-protein docking by molecular dynamics simulation [My Copy] Proteins: Structure, Function, and Genetics, Vol. 50, No. 1. (2003), pp. 158-169. by Ting Wang, Rebecca C. Wade posted to implicit-solvent solvent-effects by choonpeng on 2006-11-24 00:56:46 as along with 2 people mikaellund flbarroso
	The use of a generalized born model for the analysis of protein conformational transitions: a comparative study with explicit solvent simulations for chemotaxis Y protein (CheY). [My Copy] J Comput Chem, Vol. 27, No. 16. (December 2006), pp. 1923-1943. by M. S. Formaneck, Q. Cui posted to implicit-solvent solvent-effects by choonpeng on 2006-11-16 02:39:10 as

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Tag implicit-solvent [24 articles] Export Sort

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