flbarroso's free_energy [54 articles] Export

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	Computational analysis of the cathepsin B inhibitors activities through LR-MMPBSA binding affinity calculation based on docked complex [My Copy] Journal of Computational Chemistry, Vol. 30, No. 14. (2009), pp. 2165-2175. by Zhigang Zhou, Yanli Wang, Stephen H. Bryant posted to solvent_accessible_surface pb free_energy docking cathepsin by flbarroso on 2009-09-12 23:24:25 as
	Structure-Based Identification of Small Molecule Binding Sites Using a Free Energy Model [My Copy] Journal of Chemical Information and Modeling, Vol. 46, No. 6. (1 November 2006), pp. 2631-2637. by Ryan G. Coleman, Anna C. Salzberg, Alan C. Cheng posted to free_energy drug-design by flbarroso on 2009-08-16 20:33:27 as along with 3 people and 1 group caporaso cjeans tjimenez biomedical-nlp
	Free energies of chemical reactions in solution and in enzymes with ab initio quantum mechanics/molecular mechanics methods. [My Copy] Annual review of physical chemistry, Vol. 59, No. 1. (2008), pp. 573-601. by H. Hu, W. Yang posted to enzyme free_energy qmmm by flbarroso on 2009-07-25 22:27:34 as along with 1 person skoddet
	Hydration Free Energies of Amino Acids: Why Side Chain Analog Data Are Not Enough [My Copy] The Journal of Physical Chemistry B, Vol. 113, No. 26. (2 July 2009), pp. 8967-8974. by Gerhard König, Stefan Boresch posted to born free_energy md solvation by flbarroso on 2009-07-21 19:19:22 as along with 2 people carlosjavierna sobolevnrm
	Dissecting the free energy of drug binding to DNA. [My Copy] Anti-cancer drug design, Vol. 11, No. 8. (December 1996), pp. 569-580. by J. B. Chaires posted to free_energy polyelectrolytes by flbarroso on 2009-07-21 19:05:06 as
	Electrostatic and non-electrostatic contributions to the binding free energies of anthracycline antibiotics to DNA. [My Copy] Journal of molecular biology, Vol. 274, No. 2. (28 November 1997), pp. 253-267. by M. Baginski, F. Fogolari, J. M. Briggs posted to antibiotics binding dna electrostatics free_energy by flbarroso on 2009-07-21 19:04:37 as
	Heat does not come in different colours: entropy–enthalpy compensation, free energy windows, quantum confinement, pressure perturbation calorimetry, solvation and the multiple causes of heat capacity effects in biomolecular interactions [My Copy] Biophysical Chemistry, Vol. 93, No. 2-3. (28 November 2001), pp. 215-230. by A. Cooper posted to calorimetry entropy free_energy protein by flbarroso on 2009-07-21 18:26:49 as
	A method to calculate the probability distribution for systems with large energy barriers [My Copy] Chemical Physics, Vol. 213, No. 1-3. (15 December 1996), pp. 63-76. by O. Engkvist posted to free_energy simulation by flbarroso on 2009-07-21 15:30:45 as
	Examining methods for calculations of binding free energies: LRA, LIE, PDLD-LRA, and PDLD/S-LRA calculations of ligands binding to an HIV protease. [My Copy] Proteins, Vol. 39, No. 4. (1 June 2000), pp. 393-407. by Y. Y. Sham, Z. T. Chu, H. Tao, A. Warshel posted to free_energy hiv lie simulation by flbarroso on 2009-07-19 19:03:32 as
	On the electrostatic component of protein-protein binding free energy. [My Copy] PMC biophysics, Vol. 1, No. 1. (2008) by K. Talley, C. Ng, M. Shoppell, P. Kundrotas, E. Alexov posted to electrostatics free_energy protein-protein by flbarroso on 2009-07-19 19:01:55 as
	Converging free energy estimates: MM-PB(GB)SA studies on the protein-protein complex Ras-Raf. [My Copy] Journal of computational chemistry, Vol. 25, No. 2. (30 January 2004), pp. 238-250. by H. Gohlke, D. A. Case posted to born free_energy pb protein-protein ras-raf solvent_accessible_surface by flbarroso on 2009-07-19 02:14:56 as along with 3 people bmduggan onufriev lillekatt
	Comparison of the potentials of mean force for alanine tetrapeptide between integral equation theory and simulation [My Copy] Biophysical Chemistry, Vol. 78, No. 1-2. (5 April 1999), pp. 113-126. by N. Prabhu posted to continnum dielectric discontinuities free_energy peptide simulation by flbarroso on 2009-07-19 02:00:57 as
	Comparison of charge models for fixed-charge force fields: small-molecule hydration free energies in explicit solvent. [My Copy] The journal of physical chemistry. B, Vol. 111, No. 9. (8 March 2007), pp. 2242-2254. by D. L. Mobley, E. Dumont, J. D. Chodera, K. A. Dill posted to force-fields free_energy solvation by flbarroso on 2009-07-17 19:56:59 as along with 3 people tovrstra ashaytan bentenin
	Solvation free energies of amino acid side chain analogs for common molecular mechanics water models. [My Copy] The Journal of chemical physics, Vol. 122, No. 13. (1 April 2005) by M. R. Shirts, V. S. Pande posted to free_energy md solvation water by flbarroso on 2009-07-17 19:52:50 as along with 1 person blackbart
	Some Topics in the Theory of Fluids [My Copy] The Journal of Chemical Physics, Vol. 39, No. 11. (1963), pp. 2808-2812. by B. Widom posted to free_energy widom by flbarroso on 2009-07-17 02:01:48 as along with 2 people zhaidong mikaellund
	Recent developments in methodologies for calculating the entropy and free energy of biological systems by computer simulation. [My Copy] Current opinion in structural biology In Theory and simulation / Macromolecular assemblages, Vol. 17, No. 2. (April 2007), pp. 181-186. by Hagai Meirovitch posted to entropy folding free_energy protein simulation by flbarroso on 2009-07-17 00:08:38 as along with 5 people and 1 group xdeupi sunhwan aqeel dmobley cchang Chang group
	Solvation free energy of protein reproduced by the combination of the extended scaled particle theory and the Poisson-Boltzmann equation [My Copy] Journal of Molecular Liquids, Vol. 65-66 (November 1995), pp. 381-384. by M. Irisa posted to electrostatics free_energy pb solvation by flbarroso on 2009-07-16 17:33:24 as
	Free energies of solvation in aqueous and organic solutions for solutes with amide, keto and ester functional groups [My Copy] Chemical Physics, Vol. 222, No. 1. (September 1997), pp. 9-15. by C. Aleman posted to free_energy solvation by flbarroso on 2009-07-16 17:31:10 as
	Calculation of the dispersion energy contribution to the solvation free energy [My Copy] Chemical Physics Letters, Vol. 229, No. 3. (28 October 1994), pp. 244-249. by C. Amovilli posted to free_energy solvation by flbarroso on 2009-07-16 17:30:21 as
	Free energy calculations on dimer stability of the HIV protease using molecular dynamics and a continuum solvent model1 [My Copy] Journal of Molecular Biology, Vol. 303, No. 4. (03 November 2000), pp. 567-582. by Wei Wang, Peter A. Kollman posted to continnum free_energy hiv md protein-protein by flbarroso on 2009-07-16 17:18:08 as along with 1 person bmduggan
	Calculating Structures and Free Energies of Complex Molecules: Combining Molecular Mechanics and Continuum Models [My Copy] Accounts of Chemical Research, Vol. 33, No. 12. (1 December 2000), pp. 889-897. by Peter A. Kollman, Irina Massova, Carolina Reyes, et al.Bernd Kuhn, Shuanghong Huo, Lillian Chong, Matthew Lee, Taisung Lee, Yong Duan, Wei Wang, Oreola Donini, Piotr Cieplak, Jaysharee Srinivasan, David A. Case, Thomas E. Cheatham posted to continnum electrostatics folding free_energy md protein-protein by flbarroso on 2009-07-15 04:19:56 as along with 2 people edws Lombardo_7
	Free Energy Simulations Come of Age: Protein−Ligand Recognition [My Copy] Accounts of Chemical Research, Vol. 35, No. 6. (1 June 2002), pp. 430-437. by Thomas Simonson, Georgios Archontis, Martin Karplus posted to binding free_energy by flbarroso on 2009-07-15 04:18:31 as along with 2 people dfgreen dmobley
	Free energy calculations: Applications to chemical and biochemical phenomena [My Copy] Chemical Reviews, Vol. 93, No. 7. (1 November 1993), pp. 2395-2417. by Peter Kollman posted to free_energy by flbarroso on 2009-07-15 04:01:06 as along with 2 people dcheong stephenbond
	Empirical free energy calculations: a blind test and further improvements to the method [My Copy] Journal of Molecular Biology, Vol. 268, No. 2. (02 May 1997), pp. 401-411. by J. Novotny posted to antibody-antigen electrostatics free_energy hydrophobicity lysozyme pb by flbarroso on 2009-07-15 03:58:26 as
	Free Energy Determinants of Secondary Structure Formation: II. Antiparallel β-Sheets [My Copy] Journal of Molecular Biology, Vol. 252, No. 3. (22 September 1995), pp. 366-376. by A. Yang posted to electrostatics folding free_energy pb prediction by flbarroso on 2009-07-15 03:48:00 as along with 1 person chiufanlee
	Free Energy Balance in Protein Folding [My Copy] In Advances in Protein Chemistry Volume 46, Vol. 46 (1995), pp. 27-58. by B. Honig, A. Yang posted to folding free_energy by flbarroso on 2009-07-15 03:46:56 as
	pH-Induced denaturation of proteins: a single salt bridge contributes 3-5 kcal/mol to the free energy of folding of T4 lysozyme [My Copy] Biochemistry, Vol. 29, No. 9. (1 March 1990), pp. 2403-2408. by D. Eric Anderson, Wayne J. Becktel, Frederick W. Dahlquist posted to electrostatics folding free_energy lysozyme ph by flbarroso on 2009-07-15 03:45:23 as
	Structural determinants of trypsin affinity and specificity for cationic inhibitors [My Copy] PRS, Vol. 8, No. 12. (1999), pp. 2621-2629. by I. Fabio Polticell, I. Paolo Ascenz, I. Martino Bolognes, G. Barry Honi posted to binding free_energy trypsin by flbarroso on 2009-07-15 03:36:10 as
	Free Energy Determinants of Secondary Structure Formation: I. α-Helices [My Copy] Journal of Molecular Biology, Vol. 252, No. 3. (22 September 1995), pp. 351-365. by A. Yang posted to electrostatics free_energy pb protein by flbarroso on 2009-07-15 03:35:06 as along with 1 person chiufanlee
	[20] Use of molecular dynamics and free energy perturbation calculations in anti-human immunodeficiency virus drug design [My Copy] In Retroviral proteases, Vol. 241 (1994), pp. 370-384. by M. Mccarrick, P. Kollman posted to drug-design free_energy md by flbarroso on 2009-07-15 01:11:32 as
	MM/PBSA analysis of molecular dynamics simulations of bovine beta-lactoglobulin: free energy gradients in conformational transitions? [My Copy] Proteins, Vol. 59, No. 1. (1 April 2005), pp. 91-103. by F. Fogolari, E. Moroni, M. Wojciechowski, M. Baginski, L. Ragona, H. Molinari posted to beta-lactoglobulin free_energy md pb by flbarroso on 2009-07-14 03:39:04 as
	Structures and relative free energies of partially folded states of proteins [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 100, No. 25. (9 December 2003), pp. 14817-14821. by Michele Vendruscolo, Emanuele Paci, Martin Karplus, Christopher M. Dobson posted to folding free_energy by flbarroso on 2009-07-14 02:53:15 as along with 1 person allmensch
	The consequences of scoring docked ligand conformations using free energy correlations. [My Copy] European journal of medicinal chemistry, Vol. 42, No. 7. (July 2007), pp. 921-933. by F. Spyrakis, A. Amadasi, M. Fornabaio, et al.D. J. Abraham, A. Mozzarelli, G. E. Kellogg, P. Cozzini posted to docking free_energy by flbarroso on 2009-06-28 00:11:38 as
	Insights into affinity and specificity in the complexes of [small alpha]-lytic protease and its inhibitor proteins: binding free energy from molecular dynamics simulation [My Copy] Phys. Chem. Chem. Phys., Vol. 11, No. 25. (2009), pp. 4968-4981. by Nan-Jie Deng, Piotr Cieplak posted to binding free_energy md protease by flbarroso on 2009-06-23 13:57:38 as along with 1 person ucbcjbm
	Helmholtz Free Energy of Peptide Hydrogen Bonds in Proteins [My Copy] Journal of Molecular Biology, Vol. 260, No. 5. (2 August 1996), pp. 644-648. by M. Sippl posted to free_energy by flbarroso on 2009-06-19 16:42:48 as
	A statistical-mechanical study of the pair correlations for a liquid with non-central forces [My Copy] Chemical Physics Letters, Vol. 162, No. 1-2. (06 October 1989), pp. 39-42. by A. Zakharov, E. Aero posted to free_energy by flbarroso on 2009-06-19 16:37:56 as
	Potential Energy and Free Energy Landscapes [My Copy] The Journal of Physical Chemistry B, Vol. 110, No. 42. (1 October 2006), pp. 20765-20776. by David J. Wales, Tetyana V. Bogdan posted to free_energy by flbarroso on 2009-06-19 03:00:06 as along with 2 people jlh64 Diego_Prada
	The free energy of a macroscopic system [My Copy] Archive for Rational Mechanics and Analysis, Vol. 17, No. 5. (1 January 1964), pp. 377-410. by Michael E. Fisher posted to free_energy by flbarroso on 2009-06-19 02:59:36 as
	Potential of mean force for protein-protein interaction studies [My Copy] Proteins: Structure, Function, and Genetics, Vol. 46, No. 2. (2002), pp. 190-196. by Lin Jiang, Ying Gao, Fenglou Mao, Zhijie Liu, Luhua Lai posted to bioinformatics free_energy protein-protein by flbarroso on 2009-06-19 02:47:10 as
	Molecular recognition and binding free energy calculations in drug development. [My Copy] Current pharmaceutical biotechnology, Vol. 9, No. 2. (April 2008), pp. 87-95. by B. N. Dominy posted to binding free_energy by flbarroso on 2009-06-15 16:26:29 as
	Calculation of protein-ligand binding free energy by using a polarizable potential [My Copy] Proceedings of the National Academy of Sciences, Vol. 105, No. 17. (29 April 2008), pp. 6290-6295. by Dian Jiao, Pavel A. Golubkov, Thomas A. Darden, Pengyu Ren posted to binding free_energy polarizable by flbarroso on 2009-06-15 16:20:01 as along with 6 people and 3 groups krapnik onufriev jmccammon biehl sobolevnrm barry baker-group structural_bioinformatics McCammon
	Charge optimization leads to favorable electrostatic binding free energy. [My Copy] Physical review. E, Statistical physics, plasmas, fluids, and related interdisciplinary topics, Vol. 59, No. 5 Pt B. (May 1999), pp. 5958-5961. by E. Kangas, B. Tidor posted to electrostatics free_energy by flbarroso on 2009-06-15 16:17:19 as along with 1 person dfgreen
	Free energy surfaces of beta-hairpin and alpha-helical peptides generated by replica exchange molecular dynamics with the AGBNP implicit solvent model. [My Copy] Proteins, Vol. 56, No. 2. (1 August 2004), pp. 310-321. by A. K. Felts, Y. Harano, E. Gallicchio, R. M. Levy posted to continnum free_energy md solvation by flbarroso on 2009-06-15 16:14:41 as
	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 binding continnum free_energy polarizable trypsin by flbarroso on 2009-06-15 16:12:14 as along with 2 people and 1 group agrossfield sobolevnrm baker-group
	The chemical potential of water: molecular dynamics computer simulation of the CF and SPC models [My Copy] Chemical Physics Letters, Vol. 189, No. 3. (7 February 1992), pp. 273-277. by J. Quintana posted to free_energy by flbarroso on 2009-06-04 20:40:58 as
	Small Molecule Hydration Free Energies in Explicit Solvent: An Extensive Test of Fixed-Charge Atomistic Simulations [My Copy] Journal of Chemical Theory and Computation, Vol. 5, No. 2. (10 February 2009), pp. 350-358. by David L. Mobley, Christopher I. Bayly, Matthew D. Cooper, Michael R. Shirts, Ken A. Dill posted to free_energy solvation by flbarroso on 2009-04-28 18:33:18 as along with 3 people and 1 group carlosjavierna pmk sobolevnrm baker-group
	Binding free energies and free energy components from molecular dynamics and Poisson-Boltzmann calculations. Application to amino acid recognition by aspartyl-tRNA synthetase, [My Copy] Journal of Molecular Biology, Vol. 306, No. 2. (16 February 2001), pp. 307-327. by Georgios Archontis, Thomas Simonson, Martin Karplus posted to binding electrostatics free_energy md by flbarroso on 2009-03-28 22:07:03 as along with 2 people dfgreen dmobley
	The linear interaction energy method for predicting ligand binding free energies. [My Copy] Comb Chem High Throughput Screen, Vol. 4, No. 8. (December 2001), pp. 613-626. by J. Aqvist, J. Marelius posted to binding free_energy lie by flbarroso on 2009-03-28 22:03:56 as along with 2 people baaden dimka
	Free energy simulations come of age: protein-ligand recognition. [My Copy] Accounts of chemical research, Vol. 35, No. 6. (June 2002), pp. 430-437. by T. Simonson, G. Archontis, M. Karplus posted to complexation free_energy protein by flbarroso on 2009-03-28 21:56:21 as
	A molecular dynamics study and free energy analysis of complexes between the Mlc1p protein and two IQ motif peptides. [My Copy] Biophysical journal, Vol. 91, No. 7. (1 October 2006), pp. 2436-2450. by A. Ganoth, R. Friedman, E. Nachliel, M. Gutman posted to electrostatics free_energy md myosin protein-peptide by flbarroso on 2009-03-28 21:39:28 as

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electrostatics	444
protein-protein	235
protein	179
folding	172
bioinformatics	117
md	116
binding	114
beta-lactoglobulin	87
protein-polyelectrolyte	80
pb	70
drug-design	68
continnum	67
force-fields	65
applications	62
lysozyme	56
solvation	56
docking	55
free_energy	54
calcium-binding	52
pka	50
water	49
prediction	48
modeling	44
hydrophobicity	43
whey	39
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ph	36
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calmodulin	31
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mc	31
albumin	31
alfa-lactalbumin	30
protein-surface	29
aggregation	28
virial	28
liquids	28
chitosan	28
drug-delivery	26
dielectric	26
crystallization	25
coacervate	25
membrane	25
reviews	25
simulation	24
complexation	23
charge-regulation	23
electrophoresis	21
polarizable	21
born	21
colloids	20
amyloid	20
enzyme	19
milk	17
ion-binding	17
alzheimer	17
polymer	17
barnase	16
light-scattering	16
peptide	16
rmc	16
dna	15
pectin	15
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microcapsules	14
nanoparticles	14
van-der-waals	14
ionic-strength	13
lactoferrin	13
barstar	12
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pi	6
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pk	6
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trypsin	6
ph-effect	6
hofmeister	5
activity_coefficients	5
ion-pairs	5
separation	5
myosin	5
patch	5
hiv	5
protein-dna	5
fluid	5
ribonuclease	5
osmotic	5
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emulsions	5
prion	5
molecular_dynamics_package	5
thermodynamics	5
immunoglobulin	5
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intermolecular-forces	5
chymotrypsin	4
ca_chain_models	4
spectroscopy	4
hamaker	4
validation_protein	4
ovalbumin	4
design	4
cytochrome	4
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on-the-wrong-side	4
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nacl	4
widom	3
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afm	3
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debye-huckel	3
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ca	3
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lie	3
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igg	2
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alignment	2
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fructose	1
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acetylcholinesterase	1
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tanford-kirkwood	1
rnasea	1
prion_proteins	1
drude	1
toxin	1
multi-objective	1
crambin	1
pvs	1
lidocaine	1
gel-filtration	1
cyclodextrin	1
protease	1
bapta	1
ovomucoid	1
epr	1
hydration	1
pectase	1
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ab_initio	1
zeolites	1
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science	1
cements	1
melatonin	1
fulleran	1
kallikrein	1
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microtubules	1
ionic_liquids	1
qsar	1
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contact_map	1
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quantum_chemistry	1
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virus_structure_and_assembly	1
nmr_experiments	1
trifluoperazine	1
lennard_jones	1
vaccines	1
random_numbers	1
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genomes	1
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scattering	1
surfaces	1
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peg	1
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electron-transfer	1
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peptides	1
tubulin	1
quantum_chemical	1
gama-globulin	1
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parallelization	1
histidines	1
calcyclin	1
polysaccharide	1
counterion-condensation	1
pss	1
tannins	1
ras-raf	1
trichosurin	1

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