Monte Carlo simulation proteins

Biirgi R, Kollman PA, van Gunsteren WF (2002) Simulating proteins at constant pH An approach combining molecular dynamics and Monte Carlo simulation. Proteins 47 469-480. 

Marrone TJ, Resat H, Hodge CN, Chang CH, McCammon JA. Solvation studies of DMP323 and A76928 bound to HIV protease—analysis of water sites using grand canonical Monte Carlo simulations. Protein Sci 1998 7 573-579. 

AR Ortiz, A Kolinski, J Skolnick. Fold assembly of small proteins using Monte Carlo simulations driven by restraints derived from multiple sequence alignments. J Mol Biol 277 419-448, 1998. 

A Kolinski, J Skolmck. Monte Carlo simulations of protein folding. I. Lattice model and interaction scheme. Pi-otem 18 338-352, 1994. 

Shimada J, Shakhnovich El. The ensemble folding kinetics of protein G from an all-atom Monte Carlo simulation. Proc Natl Acad Sci USA 2002 99 11175-80. 

Woo, H. J. Dinner, A. R. Roux, B., Grand canonical Monte Carlo simulations of water in protein environments, J. Chem. Phys. 2004,121, 6392-6400. 

The original proposal of the approach, supported by a Monte Carlo simulation study [36], has been further validated with both pre-clinical [38, 39] and clinical studies [40]. It has been shown to be robust and accurate, and is not highly dependent on the models used to fit the data. The method can give poor estimates of absorption or bioavailability in two sets of circumstances (i) when the compound shows nonlinear pharmacokinetics, which may happen when the plasma protein binding is nonlinear, or when the compound has cardiovascular activity that changes blood flow in a concentration-dependent manner or (ii) when the rate of absorption is slow, and hence flip-flop kinetics are observed, i.e., when the apparent terminal half-life is governed by the rate of drug input. 

Monte Carlo/simulated annealing (MC/SA) algorithm for sequential assignment in uniformly 13C, 15N-labeled proteins [137]. The two-dimensional (2D) NCACX and NCOCX spectra measured for the fibril samples of full-length Syrian hamster prion protein (residues 23-231) have been analyzed by the MC/SA protocol, from which it has been concluded that the fibril core is formed primarily in the region of residues 173-224 [54]. 

The OPLS parameters (charges and Lennard-Jones terms) were obtained primarily via Monte Carlo simulations with particular emphasis on reproducing the experimental densities and heats of vaporization of liquids. Those simulations were performed iteratively as part of the parametrization, so better agreement with experiment is obtained than in previous studies where the simulations were usually carried out after the parametrization. Once the OPLS parametrization was completed, further simulations were also performed in order to test the new set of parameters in the calculation of other thermodynamic and structural properties of the system, besides its density and its heat of vaporization. Parameters have now been generated, among others, for water, alkanes, alkenes, alcohols, amides, alkyl chlorides, amines, carboxylic esters and acids, various sulfur and nitrogen compounds, and nitriles. A protein force field has been established as well. 

Polymers to Proteins, NIC Symposium Series, Jiilich, Germany, 2004, pp. 83—140. Monte Carlo Simulation of Polymers Coarse-Grained Models. 

Irback, A., Mohanty, S. PROFASI a Monte Carlo simulation package for protein folding and aggregation. J. Comput. Chem. 2006, 27,1548-55. 

O Toole, E.M., Panagiotopoulos, A.Z. Monte Carlo simulation of folding transitions of simple model proteins using a chain growth algorithm. J. Chem. Phys. 1992, 97, 8644-52. 

Monte Carlo Simulations of the Hydration of a Protein Receptor for an Oligosaccharide, H. Beierbeck and R. U. Lemieux, Abstr, 75th Canadian Chem. Conf, Edmonton, Alberta, Canada, June 1-4 (1992). 

It is my pleasure to introduce Volume 73 of Annual Reports on NMR. In common with previous volumes, it contains reports from a few of the many areas of NMR active research. The first contribution is by T. W. T. Tsai and J. C. C. Chan on Recent Progress in the Solid-State NMR Studies of Biomineralization the topic Recent Advances in the NMR Spectroscopy of Chlorine, Bromine and Iodine is covered by B. J. Butler, J. M. Hook and J. B. Harper M. D. Lingwood and S. Han report on Solution-State Dynamic Nuclear Polarization the topic of Solid-State NMR of Membrane Proteins Moving Towards Greater Complexity is covered by L. K. Thompson Chromatographic NMR is the topic chosen by S. Caldarelli the final contribution on Kinetic Monte Carlo Simulation of DNMR Spectra is by Z. Szalay and J. Rohonczy. My grateful thanks are due to all of these reporters for their interesting and timely contributions. 

The RSA model received renewed attention after Feder [12] observed that the adsorption on the surface of apo-ferritin molecules (large iron-storage proteins with a diameter of about 10 nm), which adsorb irreversibly, reached saturation at a coverage (k = 0.518. Monte Carlo simulations of Random Sequential Adsorption of disks on a surface last prohibitively long in the vicinity of the jamming point however Feder [12] noted that in the vicinity of the jamming coverage, 9 has a power-law dependence on time ... 

Verkhivker GM, Bouzida D, Gehlhaar DK, Rejto PA, Freer ST, Rose PM (2002) Monte Carlo simulation of the peptide recognition at the consensus binding site of the constant fragment of the human immunoglobulin G the energy landscape analysis of a hot spot at the intermolecular interface, Proteins, 48 539-557... 

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