Biomolecular modeling

In the context of molecular simulation, particularly biomolecular modelling, a critical aspect for numerical simulation is the presence of long-range Coulombic forces which render the force computations much more costly... 

St-Amant, A. Density Functional Methods in Biomolecular Modeling, Reviews in Computational Chemistry 7, K. Lipkowitz and D. B. Boyd, eds. New York, VCH Publishers, 217-259. 

Alain St-Amant, Density Functional Methods in Biomolecular Modeling. 

Oil-water partitioning, solubilities, and vapor-pressure experiments on smaU-molecule compounds are often used as models to obtain energies for biomolecular modeling. For example, measured partition coefficients, K, are often inserted into the formula-RT In K to obtain quantities thought to represent microscopic contact interaction free energies (Chan and Dill, 1997). 

St-Amant A. Density functional methods in biomolecular modeling. In Lipkowitz KB, Boyd DB, eds. Reviews in Computational Chemistry. Vol. 7. New York VCH, 1995 217-259. 

Most comprehensive software programs suitable for protein modeling are commercial packages, some of which are listed in Table 15.2. The application of HyperChem in the biomolecular modeling has been described (Chapter 14) and can be extended to the modeling of protein structures. The aspects of protein modeling will be illustrated with two freeware programs and two online servers. 

In all these deoxycytidine runs, computation time is approximately proportional to the number of function and gradient evaluations. This is typical in molecular computations, as the evaluation and differentiation of the potential energy are expensive and the time-determining factors. The trends observed here extend to biomolecular models and suggest that, with local preconditioning, TN and LM-BFGS are the methods of choice. 

Sequence analysis and biomolecular modeling. PRO-SIMULATE for molecular simulations with GROMOS, AMBER, and OPLS force fields. PROQUANTUM for semiempirical (MOPAC) and ab initio (CADPAC) calculations via a graphical interface. 

Tel. 703-658-4854, fax 703-658-4887, e-mail syazdi presto.ig.com Desktop molecular modeling. NEMESIS SAMPLER for simple modeling. PRO-EXPLORE for sequence analysis and biomolecular modeling. PRO-SIMULATE for molecular simulations with GROMOS, AMBER, and BOSS via a graphical interface. PRO-QUANTUM for semiempirical (MOPAC, extended Hiickel) and ab initio (CADPAC) calculations via a graphical interface. FDCALC and ESCALC for electrostatics calculations. N-DEE for analysis of NMR data. PC-PROT-I- (sequence analysis), PC-TAMMO-I- (protein—lipid modeling), and MASCA (statistics). Macintosh, PCs, and UNIX workstations. 

Computational scientists have developed many tools for modelling molecules. Computer models are not perfect recreations of reality. Instead, approximations and assumptions have to made, and the model compromised for the sake of computational efficiency. As the size of the system gets larger, and so the size and number of molecules increases, so to does the computational expense of the calculation. This means that the larger the system, the more compromises and approximations must be made. This act of compromise has led computational scientists to develop four main levels of biomolecular modelling ... 

A wide variety of experimental methods have provided insight into protein, and in particular enzyme structure, and these structures are in turn the raw materials of much biomolecular modelling. The most important experimental technique for studying protein structure to date has been X-ray crystallography. A well-ordered crystal of the protein is required. Finding appropriate conditions to produce suitable crystals can be challenging, for example... 

Dr. Michael J. E. Sternberg Imperial Cancer Research Fund Biomolecular Modelling Laboratory 44 Lincoln s Inn Fields London WC2A 3PX United Kingdom m.stemberg icrf.icnet.uk... 

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