DOCK, protein structure-based

In order to monitor the importance of isomeric hydrogen placements for docking and structure-based design, a large dataset of protein-ligand complexes was automatically... 

Connolly developed a computational technique for docking two protein structures based on matching complementary patterns of knobs and holes (106). The algorithm was used to predict the association of the a and fi subunits of hemoglobin to form the corrext a-/ dimer. 

Barril, X. and Fradera, X. (2006) Incorporating protein flexibility into docking and structure-based drug design. Expert Opinion on Drug Discovery, 1 (4), 335-349. 

Inorganic Three-dimensional Structure Databases Molecular Docking and Structure-based Design Protein Data Bank (PDB) A Database of 3D Structural Information of Biological Macromolecules Structural Similarity Measures for Database Searching Structure and Substructure Searching Structure Databases Structure Representation Three-dimensional Structure Searching,... 

Computer Graphics and Molecular Modeling Conformational Analysis 1 Electrostatic Catalysis Molecular Docking and Structure-based Design Protein Structure Prediction in ID, 2D, and 3D Structural Chemistry Application of Mathematics Symmetry and Chirality Continuous Measures Symmetry in Chemistry. 

Although somewhat out of date, the program is still available from QCPE and has an after-life in at least two recent programs MIMUMBA for conformational analysis and FlexX for the automatic and flexible docking of ligands into receptor sites of proteins (see Molecular Docking and Structure-based Design). 

Protein structure know 11 dt novo design, receptor-based 3D searching stnjcture-based design, docking... 

Zhang and co-workers worked on the structure-based, computer-assisted search for low molecular weight, non-peptidic protein tyrosine phosphate IB (PTPIB) inhibitors, also using the DOCK methodology [89], They identified several potent and selective PTPIB inhibitors by saeening the ACD. 

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