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Topic: Molecular modelling

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	Molecular Modelling: Principles and Applications
		Molecular modelling used to be restricted to a small number of scientists who had access to the necessary computer hardware and software.
		These models enable the energy of any arrangement of the atoms and molecules in the system to be calculated, and allow the modeller to determine how the energy of the system varies as the positions of the atoms and molecules change.
		Molecular modelling is a rapidly developing discipline, and has benefitted from the dramatic improvements in computer hardware and software of recent years.
	www.booksites.net /leach1/molecular (1869 words)

	Molecular modelling - Wikipedia, the free encyclopedia
		Molecular modelling is a collective term that refers to theoretical methods and computational techniques to model or mimic the behaviour of molecules.
		Molecular mechanics is synonymous with molecular modelling, as it is refers to the use of classical mechanics/Newtonian mechanics to describe the physical basis behind the models.
		Molecular modelling methods are now routinely used to investigate the structure, dynamics and thermodynamics of inorganic, biological, and polymeric systems.
	en.wikipedia.org /wiki/Molecular_modelling (766 words)

	WABRI \| Research Projects - Biomolecular modelling: from drug discovery to nanotechnology \| Western Australia ...
		The methods of computer simulation and molecular modelling, such as Monte Carlo (MC) and molecular dynamics (MD), continue to come of age making significant contributions to a wide variety of experimental fields, ranging from molecular biology and drug design to nanotechnology and biomaterials design.
		Molecular dynamics simulations help determine the role of the dynamic plasticity of amino acid sidechains and water molecules in determining the strength and specificity of interaction.
		Computer simulation methods are being used to investigate the molecular structure of encapsulated drug molecules in copolymeric biodegradable materials, the mechanism of penetration of water and its pH and ionic force dependence, and the mechanism of interaction of the drug with the various chemical polymeric components that might influence its loading and delivery.
	www.wabri.org.au /research/molec_modelling.html (1907 words)

	Molecular Modelling
		Molecular modelling is a powerful tool for describing and predicting properties of molecular entities in molecular materials.
		An electrostatic interaction model has been parameterized from large-scale quantum chemical calculations with the purpose to model conducting and optical properties of large molecules and assemblies of molecules.
		A model for calculating the effects of molecular vibrations on molecular properties have been developed, which has made it possible to calculate for example temperature and isotope effects on properties of much larger molecules than previously.
	www.risoe.dk /ita/regneserver/projects/molecular_modelling.htm (310 words)

	An Introduction to Molecular Modeling
		Computational chemistry/molecular modeling is the science (or art) of representing molecular structures numerically and simulating their behavior with the equations of quantum and classical physics.
		As the nuclei are moved to new coordinates and molecular energies are re-calculated, a quantitative description of molecular energy is derived.
		Molecular mechanics is a mathematical formalism which attempts to reproduce molecular geometries, energies and other features by adjusting bond lengths, bond angles and torsion angles to equilibrium values that are dependent on the hybridization of an atom and its bonding scheme (this atom description is referred to as the atom type).
	www.netsci.org /Science/Compchem/feature01.html (3950 words)

	Quick Tour
		Molecular Modeling, is one of the fastest growing fields in science.
		Shown are the backbone structure of the protein, a bound fatty acid molecule within the protein, and a small shell of water surrounding the protein.
		Using molecular modeling scientists will be better able to design new and more potent drugs against diseases such as Cancer, AIDS, and Arthritis.
	www.nyu.edu /pages/mathmol/quick_tour.html (612 words)

	Geometry in Action: Molecular Modeling
		Many questions in molecular modeling can be understood geometrically in terms of arrangements of spheres in three dimensions.
		Classical molecular modeling has dealt with biological molecules which generally have a tree-like structure, but applications to nanotechnology require dealing with more complicated diamond-like structures; it is unclear to what extent this affects the relevant algorithms.
		Michel Sanner of Scripps studies algorithms for molecular modeling, and published a paper on molecular surface accessability at the 11th ACM Symp.
	www.ics.uci.edu /~eppstein/gina/molmod.html (405 words)

	Computational chemistry and molecular modelling
		However, the development of computers, and sophisticated ‘ab initio’ molecular orbital methods (based on the same basic approaches such as the variational principle), mean that it is now possible to calculate molecular properties on desktop PCs.
		Modelling and experiments are best done in conjunction: modelling helps interpret experiments, and experiments test computer models.
		Many different computational chemistry and molecular modelling methods are used - you’ll learn about some of these in the future.
	www.chm.bris.ac.uk /pt/ajm/sb04/L6_p5.htm (232 words)

	Molecular Modelling - Bioorganic Chemistry
		The presence of an intramolecular hydrogen bond in such products is an indication of the possible mechanism of the reaction which has been studied in detail.
		Models for the addition of Grignard compounds to nitrones
		The calculated models fully agree with the observed experimental results.
	wzar.unizar.es /acad/fac/cie/quiorg/asimetrica/research/models.html (308 words)

	Molecular Modelling: Basic Principles and Applications British Journal of Biomedical Science - Find Articles
		Modelling is not a field to be entered lightly because it is important to understand the physics, physical chemistry and mathematics if the results of a modelling session are to have any real value.
		The authors have been very successful in writing a book which, with a minimum of chemistry and mathematics, gives an overview of what molecular modelling is, how the models obtained may be used for different purposes, and their strengths and limitations.
		This is a book to be recommended for graduate students and others about to start work in the area of molecular modelling, and for those with a good working knowledge of physical chemistry who wish to understand the potentials and the limitations of modelling.
	www.findarticles.com /p/articles/mi_qa3874/is_199901/ai_n8841659 (296 words)

	Ludwig Institute Annual Report 1999-2000 Molecular Modelling Laboratory
		This is why computational and molecular modelling techniques have been a standard part of drug design and development in pharmaceutical companies for more than 10 years.
		In particular the development of models for the EGF receptor complex formed by two EGF and two EGF receptor molecules have led to a new understanding of the binding mechanisms of EGF mutants and the activation of the EGF receptor.
		In this model, each EGF ligand molecule is in contact with the L2 domain of one of the EGF receptor molecules and with the L1 domain of the other EGF receptor molecule.
	www.ludwig.edu.au /annual9900/labs/modelling.html (2075 words)

	Molecular modelling shows nanotechnologists the way (October 2002) - Features - nanotechweb.org
		Computational modelling using first-principles quantum mechanics and/or mesoscale simulations enables scientists to visualize and predict behaviour at or near the nanoscale.
		The simulations determined which molecular and formulation conditions led to the formation of "reverse micelles" - nanoscale water droplets in a surfactant medium.
		While modelling tools are now well developed at the quantum and, to some extent, the mesoscale level, there are a number of limitations.
	nanotechweb.org /articles/feature/1/10/3 (915 words)

	Chemdraw ultra: Molecular modelling, structure drawing, Semi-empirical calculations, structure display, MOPAC, ...
		HyperChem is a sophisticated molecular modeling environment that is known for its quality, flexibility, and ease of use.
		Ionic, metallic, covalent and molecular crystals may be constructed using a database of all 230 space groups, with choice of cell type and unique axis where appropriate.
		Molecular Modeling Pro Plus includes all of the features of the Pro version and adds the ability to study QSAR and QSPR relationships.
	www.chemistry-software.com /molecmod.htm (479 words)

	Molecular Modelling Software
		General-purpose molecular modelling program which uses the graphics facilities of Silicon Graphics workstations for display of structures, and for molecular-mechanics and quantum-chemistry calculations.
		Molecular mechanics and dynamics technique to evaluate the energies and geometries of molecules in vacuo or in solution, and to display and examine graphically the results of the modeling calculations.
		Molecular modeling programme that lets a user manipulate a structure in a direct and intuitive manner.
	www.chemistry-software.com /software_guide/modelling_index.htm (806 words)

	CHEMISTRY WITH MOLECULAR MODELLING - Admissions - Trinity College Dublin
		Molecular modelling is the use of computer modelling to understand and explore chemistry.
		Advancements in molecular modelling have lead to an explosive growth in a range of applications.
		Special lectures are given to introduce the concepts of molecular modelling to high light applications.
	www.tcd.ie /Admissions/courses/course.php?ID=63 (512 words)

	Computation Synopsis
		Molecular mechanics describes molecular energetics in terms of a set of classical potentials.
		Quantum chemistry describes molecular energetics in terms of explicit interactions between electrons and nuclei.
		The extent to which the orbitals of each atom contribute to a given molecular orbital (expressed as a set of molecular orbital coefficients) is estimated using the method of "linear variation".
	cmm.info.nih.gov /modeling/guide_documents/tocs/computation_synopsis.html (578 words)

	Free Molecular Modelling Programs - MarcsHomepage
		This page is a review of some programs for molecule viewing and modelling I found to be useful.
		A modeller is used to create input for simulation-programs (to understand the function and mechanism of a given molecule) or to create pictures from these datasets for publications.
		You may find a more or less complete list of molecule-viewers and modelling-programs on the World Index of Molecular Visualization Resources, tutorials for the programs may be found on their respective homepages.
	www.marcsaric.de /index.php/Free_Molecular_Modelling_Programs (384 words)

	Contacts in the field Molecular Modelling
		Molecular dynamics modelling at the University of Stuttgart in Germany.
		Molecular dynamics simulation and modelling at the University of Tuscany in Italy.
		The molecular dynamics of proteins are extensively dealt with including modelling of the electron transport properties of proteins and protein/solvent, protein/substrate interactions.
	www.npl.co.uk /smd/smd_contacts/molecular_modelling.html (118 words)

	Research Center for Complex Molecular Systems and Biomolecules
		The subject of the Center is to further develop basic theoretical and experimental research of the energy and charge transfer in biomolecules and in complex molecular systems.
		A team from ICT will investigate the interactions between molecules, atoms, and ions by the means of methods of statistical thermodynamics, statistical physics, and molecular modelling.
		The subject of the theoretical research of the froup from Palackeho University in Olomouc is the study of the protein structure and dynamics, and of the nezyme reactions.
	www.molecular.cz /research.php (240 words)

	Modelling of Molecular Networks. Granada 2002.
		With all the new information available about genomes and proteomes, it is possible to conceive of genes and proteins more as part of a network than as isolated entities.
		Molecular function becomes then a function of cellular context and not only an individual property.
		Molecular networks in the context of the whole organism.
	www.pdg.cnb.uam.es /GRANADA2002 (508 words)

	BUBL LINK: Molecular modelling
		Resource for the study of molecular structure, in which X-ray crystallography and molecular mechanics techniques are used to calculate the structures of "interesting" molecules.
		Subject areas include computer-aided molecular design, quantum chemistry, visualisation, classification and handling of chemical data, rational drug design, protein and peptide modelling, molecular mechanics/dynamics simulation of polymers and biopolymers, prediction of biological activities (QSAR) and physico-chemical properties (QSPR), genetic algorithms and neural nets, and catalyst modelling.
		Theochem publishes research related to the theory and modelling of molecular systems, including electronic structure, graphical approaches to structure and properties, molecular modelling, reaction dynamics and scattering, spectroscopic and experimental studies, and statistical mechanics.
	bubl.ac.uk /link/m/molecularmodelling.htm (525 words)

	MGMS Welcome
		The MGMS was set up in 1981 as a society dedicated solely to the interests of molecular modelling and related aspects of computational chemistry.
		The journal is published in full colour and is devoted to high quality practical and theoretical papers on the use of computers for the investigation of molecular structure, function and interaction.
		In order to support postdoctoral and young, independent researchers, and to celebrate the 25th Anniversary of the foundation of the MGMS, the Society is establishing the MGMS Silver Jubilee Prize.
	www.mgms.org (535 words)

	Molecular Modelling: Principles and Applications, second edition
		The impetus for this second edition is a desire to include some of the new techniques that have emerged in recent years and also extend the scope of the book to cover certain areas that were under-represented (even neglected) in the first edition.
		Molecular mechanics is the subject of chapter 4 and then in Chapter 5 we consider energy minimisation and other "static" techniques.
		Crystal and molecular structure of the lithium salt of nicotinamide adenine dinucleotide dihydrate NAD, DPN, cozymase, codehydrase I. Journal of the American Chemical Society.
	www.booksites.net /leach2/molecular/molecular_modelling_2.html (3584 words)

	Resources for the MHC Molecular Lab
		Molecular modeling is used by chemists to find optimum structures and pathways for chemical reactions.
		The chemistry curricilum at Mount Holyoke College introduces molecular modeling in general chemistry and in later courses continues to show students how molecular modeling coupled with experiments can be used to understand chemical phenomena.
		This site provides guides to the hardware and software available in the molecular modeling lab as well as links to how these are used in the curriculum.
	www.mtholyoke.edu /acad/chem/mmlab (108 words)

	Pharmaceutical Molecular modeling glossary
		Consists of the exploration of energetically favorable spatial arrangements (shapes) of a molecule (conformations) using molecular mechanics, molecular dynamics, quantum chemical calculations or analysis of experimentally- determined structural data, e.g., NMR or crystal structures.
		Molecular mechanics and quantum chemical methods are employed to compute conformational energies, whereas systematic and random searches, Monte Carlo, molecular dynamics, and distance geometry are methods (often combined with energy minimization procedures) used to explore the conformational space.
		A procedure used in molecular dynamics simulations, in which the system is allowed to equilibrate at high temperatures, and then cooled down slowly to remove kinetic energy and to permit trajectories to settle into local minimum energy conformations.
	www.genomicglossaries.com /content/molecular_modeling_gloss.asp (6233 words)

	Emilio Xavier Esposito - Computer-Aided Molecular Design / Drug Discovery / Molecular Modelling (Site not responding. Last check: 2007-11-02)
		Comparative modelling is the bridging of bioinformatics to molecular biology and computational biochemistry.
		X-ray structures of solved proteins are used in conjunction with comparative modelling methods to predict the structures of unsolved proteins of interest.
		Using the solved X-ray structures of protein or protein structures based on comparative modelling, ligands are placed into the defined binding region and energy calculations are performed to determine the most-likely binding configuration.
	www.chem.ndsu.nodak.edu /staff/esposito.htm (548 words)

	Molecular Modelling
		Molecular surfaces are mathematical functions based on atomic position and atomic radii
		The CAChe Model Building and Visualizing Applications that we use has Editor desaigned for model input.
		The CAChe Model Building and Visualizing Applications uses a Tabulator that converts the solved wavefunction from quantum mechanical applications into graphical representations of electron density, electrostatic potential, and molecular orbital surfaces.
	www.cs.stedwards.edu /chem/Chemistry/CHEM47/FA98/Lesson2/Modelling.html (861 words)

	Laboratory for Molecular Simulation Home Page
		The Laboratory for Molecular Simulation brings molecular modeling and computational chemistry closer to the experimental scientist by offering advanced training and assistance to those who already use these tools in their research, and beginning training to those who have not yet used them.
		Advanced modeling software is available to use mathematical methods to calculate the properties of individual molecules, solids, and liquids.
		The LMS computer lab is available for use by professors who wish to include molecular modelling in their course material.
	www.chem.tamu.edu /LMS (930 words)

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