Software

The group contributes to a diverse range of both commercial and open source software for the simulation of molecules, materials and biological systems. Some of these key packages are highlighted below.


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Q-Chem

Q-Chem is a powerful commercial quantum chemistry program. It is designed to perform accurate computations at the Hartree--Fock, Correlated Post-SCF and Density-Functional levels on large molecular systems. Members of the group in Nottingham not only use this software for research but also contribute to its development, making new methodological advances available to a wide user base. For further information see http://www.q-chem.com/



DALTON / LS-DALTON

Named after John Dalton, the father of atomic theory, DALTON is an extensive suite of programs for performing electronic structure calculations. In particular, it is highly flexible for the calculation of a wide range of molecular properties using a range of wave function and density-functional based approaches. LS-DALTON is geared towards linear scaling quantum-chemical calculation on modern highly parallel architectures. These programs are available free of charge to both academic and commercial users. For further information see http://daltonprogram.org



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LONDON

Named after Fritz London, the LONDON program is designed for studying the properties of molecules in the presence of strong magnetic fields. The programme allows for a seamless treatment of molecules in fields from 0 to 235000 Tesla! Such fields span a wide range of applications from spectroscopic properties like NMR shielding constants, central to characterisation of compounds in chemistry, through to field strengths experienced by atoms and molecules in the atmospheres of astronomical objects like White Dwarf stars. For further information see http://www.londonprogram.org



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Zippity

Zippity is a simple and effective method for similarity searching in virtual high-throughput screening, requiring only a string-based representation of the molecules (e.g., SMILES) and standard compression software, available on all modern desktop computers. Software to carry out compression-based similarity is available at http://comp.chem.nottingham.ac.uk/download/zippity

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DichroCalc

DichroCalc is a web-interface for computing the circular and linear dichroism of proteins. It is based on exciton theory and uses parameterisations, based on ab initio quantum chemical calculations, of chromophoric groups in proteins. It is possible to choose from a number of different parameters and calculate CD and LD spectra using a simple web-interface. To date, DichroCalc is the only interface available offering circular and linear dichroism calculations.

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TMACC

TMACC are highly predictive topological maximum cross correlation descriptors for the derivation of quantitative structure−activity relationships (QSARs), based on the widely used autocorrelation method. They require neither the calculation of three-dimensional conformations nor an alignment of structures. Open source software for generating the TMACC descriptors is freely available from http://comp.chem.nottingham.ac.uk/download/tmacc/


GlycoPred
Glycopred is an accurate predictor of glycosylation sites, which is based on random forest and has been used to extract comprehensible rules about the glycosylation process. GPP is available online at http://comp.chem.nottingham.ac.uk/glyco/ The methodology is described in the open access paper: http://dx.doi.org/10.1186/1471-2105-9-500