Registro:

Referencias:

• Blumberger, J., Lamoureux, G., Klein, M.L., Peptide hydrolysis in thermolysin: Ab initio QM/MM investigation of the Glu143-assisted water addition mechanism (2007) Journal of Chemical Theory and Computation, 3 (5), pp. 1837-1850
• Case, D.A., Darden, T.A., Cheatham, T.E.I.I.I., Simmerling, C.L., Wang, J., Duke, R.E., Kollman, P.A., AMBER 12 (2012), University of California San Francisco; Collin, D., Ritort, F., Jarzynski, C., Smith, S.B., Tinoco, I., Bustamante, C., Verification of the Crooks fluctuation theorem and recovery of RNA folding free energies (2005) Nature, 437 (7056), pp. 231-234
• Crespo, A., Marti, M.A., Estrin, D.A., Roitberg, A.E., Multiple-steering QM-MM calculation of the free energy profile in chorismate mutase (2005) Journal of the American Chemical Society, 127 (19), pp. 6940-6941
• Crespo, A., Scherlis, D.A., Martí, M.A., Ordejón, P., Roitberg, A.E., Estrin, D.A., A DFT-based QM-MM approach designed for the treatment of large molecular systems: Application to chorismate mutase (2003) Journal of Physical Chemistry. B, 107 (49), pp. 13728-13736
• Crooks, G.E., Nonequilibrium measurements of free energy differences for microscopically reversible markovian systems (1998) Journal of Statistical Physics, 90 (5-6), pp. 1481-1487
• Crooks, G.E., Path-ensemble averages in systems driven far from equilibrium (2000) Physical Review E, 61 (3), pp. 2361-2366
• Cui, Q., Elstner, M., Kaxiras, E., Frauenheim, T., Karplus, M., A QM/MM implementation of the self-consistent charge density functional tight binding (SCC-DFTB) method (2001) The Journal of Physical Chemistry. B, 105 (2), pp. 569-585
• de M Seabra, G., Walker, R.C., Elstner, M., Case, D.A., Roitberg, A.E., Implementation of the SCC-DFTB method for hybrid QM/MM simulations within the amber molecular dynamics package (2007) The Journal of Physical Chemistry. A, 111 (26), pp. 5655-5664
• Hénin, J., Chipot, C., Overcoming free energy barriers using unconstrained molecular dynamics simulations (2004) The Journal of Chemical Physics, 121 (7), pp. 2904-2914
• Hornak, V., Abel, R., Okur, A., Strockbine, B., Roitberg, A., Simmerling, C., Comparison of multiple Amber force fields and development of improved protein backbone parameters (2006) Proteins, 65 (3), pp. 712-725
• Jarzynski, C., Nonequilibrium equality for free energy differences (1997) Physical Review Letters, 78 (14), pp. 2690-2693
• Jorgensen, W.L., Chandrasekhar, J., Madura, J.D., Impey, R.W., Klein, M.L., Comparison of simple potential functions for simulating liquid water (1983) The Journal of Chemical Physics, 79 (2), pp. 926-935. , http://www.scopus.com/inward/record.url?eid=2-s2.0-0004016501&partnerID=40&md5=7af48df275648024bbd5981b9583c129, Retrieved from
• Kast, P., Tewari, Y.B., Wiest, O., Hilvert, D., Houk, K.N., Goldberg, R.N., Thermodynamics of the conversion of chorismate to prephenate: Experimental results and theoretical predictions (1997) The Journal of Physical Chemistry. B, 101 (50), pp. 10976-10982
• Kumar, S., Rosenberg, J.M., Bouzida, D., Swendsen, R.H., Kollman, P.A., The weighted histogram analysis method for free-energy calculations on biomolecules. I. The method (1992) Journal of Computational Chemistry, 13 (8), pp. 1011-1021
• Laio, A., Parrinello, M., Escaping free-energy minima (2002) Proceedings of the National Academy of Sciences of the United States of America, 99 (20), pp. 12562-12566
• Lee Woodcock, H., Hodošček, M., Sherwood, P., Lee, Y.S., Schaefer, H.F., III, Brooks, B.R., Exploring the quantum mechanical/molecular mechanical replica path method: A pathway optimization of the chorismate to prephenate Claisen rearrangement catalyzed by chorismate mutase (2003) Theoretical Chemistry Accounts, 109 (3), pp. 140-148
• Liphardt, J., Dumont, S., Smith, S.B., Tinoco, I., Bustamante, C., Equilibrium information from nonequilibrium measurements in an experimental test of Jarzynski's equality (2002) Science (New York, N.Y.), 296 (5574), pp. 1832-1835
• Nitsche, M.A., Ferreria, M., Mocskos, E.E., González Lebrero, M.C., GPU accelerated implementation of density functional theory for hybrid QM/MM simulations (2014) Journal of Chemical Theory and Computation, 10, pp. 959-967
• Ozer, G., Valeev, E.F., Quirk, S., Hernandez, R., Adaptive steered molecular dynamics of the long-distance unfolding of neuropeptide Y (2010) Journal of Chemical Theory and Computation, 6 (10), pp. 3026-3038
• Park, S., Khalili-Araghi, F., Tajkhorshid, E., Schulten, K., Free energy calculation from steered molecular dynamics simulations using Jarzynski's equality (2003) The Journal of Chemical Physics, 119 (6), p. 3559
• Perdew, J., Burke, K., Ernzerhof, M., Generalized gradient approximation made simple (1996) Physical Review Letters, 77 (18), p. 3865
• Pohorille, A., Jarzynski, C., Chipot, C., Good practices in free-energy calculations (2010) The Journal of Physical Chemistry. B, 114 (32), pp. 10235-10253
• Ranaghan, K.E., Ridder, L., Szefczyk, B., Sokalski, W.A., Hermann, J.C., Mulholland, A.J., Transition state stabilization and substrate strain in enzyme catalysis: Ab initio QM/MM modelling of the chorismate mutase reaction (2004) Organic & Biomolecular Chemistry, 2 (7), pp. 968-980
• Romero, J.M., Martin, M., Ramirez, C.L., Dumas, V.G., Marti, M.A., Efficient calculation of enzyme reaction free energy profiles using a hybrid differential relaxation algorithm: Application to mycobacterial zinc hydrolases (2015) Advances in Protein Chemistry and Structural Biology, 100, pp. 33-65
• Saira, O.-P., Yoon, Y., Tanttu, T., Möttönen, M., Averin, D.V., Pekola, J.P., Test of the Jarzynski and Crooks fluctuation relations in an electronic system (2012) Physical Review Letters, 109 (18), p. 180601
• Smith, C.R., Smith, G.K., Yang, Z., Xu, D., Guo, H., Quantum mechanical/molecular mechanical study of anthrax lethal factor catalysis (2010) Theoretical Chemistry Accounts, 128 (1), pp. 83-90
• Tuckerman, M., Berne, B.J., Martyna, G.J., Reversible multiple time scale molecular dynamics (1992) The Journal of Chemical Physics, 97 (3), p. 1990
• Tuckerman, M.E., Parrinello, M., Integrating the Car–Parrinello equations. II. Multiple time scale techniques (1994) The Journal of Chemical Physics, 101 (2), p. 1316
• Warshel, A., Karplus, M., Calculation of ground and excited state potential surfaces of conjugated molecules. I. Formulation and parametrization (1972) Journal of the American Chemical Society, 94 (16), pp. 5612-5625
• Warshel, A., Levitt, M., Theoretical studies of enzymic reactions: Dielectric, electrostatic and steric stabilization of the carbonium ion in the reaction of lysozyme (1976) Journal of Molecular Biology, 103, pp. 227-249
• Woodcock, H.L., Hodoscek, M., Brooks, B.R., Exploring SCC-DFTB paths for mapping QM/MM reaction mechanisms (2007) The Journal of Physical Chemistry. A, 111 (26), pp. 5720-5728
• Xiong, H., Crespo, A., Marti, M., Estrin, D., Roitberg, A.E., Free energy calculations with non-equilibrium methods: Applications of the Jarzynski relationship (2006) Theoretical Chemistry Accounts, 116 (1-3), pp. 338-346
• Xu, D., Guo, H., Quantum mechanical/molecular mechanical and density functional theory studies of a prototypical zinc peptidase (carboxypeptidase A) suggest a general acid-general base mechanism (2009) Journal of the American Chemical Society, 131 (28), pp. 9780-9788
• Zhang, C., Wu, S., Xu, D., Catalytic mechanism of angiotensin-converting enzyme and effects of the chloride ion (2013) The Journal of Physical Chemistry. B, 117 (22), pp. 6635-6645
• Zheng, L., Chen, M., Yang, W., Random walk in orthogonal space to achieve efficient free-energy simulation of complex systems (2008) Proceedings of the National Academy of Sciences of the United States of America, 105 (51), pp. 20227-20232
• Zwanzig, R.W., High-temperature equation of state by a perturbation method. I. Nonpolar gases (1954) The Journal of Chemical Physics, 22 (8), p. 1420

Citas:

---------- APA ----------

---------- CHICAGO ----------

---------- MLA ----------

---------- VANCOUVER ----------