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T LILJEFORS Progress in forcefield calculations of molecular
WADE A R ORTIZ and E GAGO Comparative binding energy
OPREA and G R MARSHALL Receptorbased prediction
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3D QSAR active site algorithm alignment amino acid analogs analysis application approach atomic charges binding affinities binding energy binding free energy bioisosteric biological activity bonds calculations Chem chemical chemistry chemistry-space coefficient CoMFA compounds Comput Comput.-Aided Mol conformation correlation crystal structures database dataset density derived distance diversity drug design electron electrostatic potential entropy enzyme enzyme inhibitors EVA descriptor evaluation experimental field-graph flexible force-field G-WHIM Gaussian geometry grid HIV-1 protease HIV-1 protease inhibitors hydrogen hydrogen-bond hydrophobic initio interaction energies kcal/mol Kohonen network ligand ligand-receptor method metrics molecular dynamics molecular dynamics simulations molecular electrostatic potential molecular mechanics molecular similarity molecular surface molecules neurons obtained optimization parameters peptide pharmacophore Phys prediction properties protease inhibitors protein protein-ligand complexes QM/MM QSAR studies quantum receptor regression relative binding scoring function semiempirical solvation solvent steric Struct substrate target structure techniques thermolysin three-dimensional VALIDATE values variables Waals WHIM descriptors