Comparison of Automatic Three-Dimensional Model Builders Using 639 X-ray Structures

By J. Sadowski, J. Gasteiger, Gerhard Klebe. 1994

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Machine learning methods in chemoinformatics (2014, methodology): “This can be done from the molecular graph or connection table using a program such as CORINA, 7,8 from a crystal structure, or from a quantum chemical calculation.”
Kernels for small molecules and the prediction of mutagenicity, toxicity and anti-cancer activity (2005, background): “Programs exist, such as CORINA (Sadowski et al., 1994; Gasteiger et al., 1996) , that can derive fairly accurate 3D coordinates for small molecules starting from their 1D or 2D representations.”
ACPYPE - AnteChamber PYthon Parser interfacE (2012, methodology): “Two sets of files, one with the coordinates from the original PDB deposition and one with the ‘ideal’ CORINA coordinates [35,36] were written out in the MOL2 format via the CcpNmr FormatConverter [37] from the PDBe database [38,39], totalling 17900 input files.”
Artificial neural networks for computer-based molecular design. (1998, background): “For small molecules fast 3D structure generators based on 2D representations are at hand which allows 3D descriptors to be derived if no experimental spatial structures are available (Sadowski and Gasteiger, 1993, 1994).”
Force field optimization guided by small molecule crystal lattice data enables consistent sub-Angstrom protein-ligand docking (2021, methodology): “When testing ligand docking using a conformation directly built from its chemical connectivity, its initial conformation was generated by CORINA 37 with a few corrections to the protonation states in the output: carboxylic acids and protonated phosphates are deprotonated (as protonation overly prefe”
Calculation of molecular lipophilicity: state of the art and comparison of methods on more than 96000 compounds (2009, methodology): “For these methods 3D-structures were generated using CORINA.(137) 3D-geometries for GBLOGP were energy minimized using the MMFF94 force field as implemented in ICM.”