caa a22 4500 467938865 CHVBK 20180406153006.0 cr unu---uuuuu 170328e20060301xx s 000 0 eng 10.1007/s10822-006-9044-4 doi (NATIONALLICENCE)springer-10.1007/s10822-006-9044-4 Permuting input for more effective sampling of 3D conformer space [Elektronische Daten] [Giorgio Carta, Valeria Onnis, Andrew Knox, Darren Fayne, David Lloyd] SMILES strings and other classic 2D structural formats offer a convenient way to represent molecules as a simplistic connection table, with the inherent advantages of ease of handling and storage. In the context of virtual screening, chemical databases to be screened are often initially represented by canonicalised SMILES strings that can be filtered and pre-processed in a number of ways, resulting in molecules that occupy similar regions of chemical space to active compounds of a therapeutic target. A wide variety of software exists to convert molecules into SMILES format, namely, Mol2smi (Daylight Inc.), MOE (Chemical Computing Group) and Babel (Openeye Scientific Software). Depending on the algorithm employed, the atoms of a SMILES string defining a molecule can be ordered differently. Upon conversion to 3D coordinates they result in the production of ostensibly the same molecule. In this work we show how different permutations of a SMILES string can affect conformer generation, affecting reliability and repeatability of the results. Furthermore, we propose a novel procedure for the generation of conformers, taking advantage of the permutation of the input strings—both SMILES and other 2D formats, leading to more effective sampling of conformation space in output, and also implementing fingerprint and principal component analyses step to post process and visualise the results. Springer Science+Business Media B.V., 2006 Conformers nationallicence Docking nationallicence Drug discovery nationallicence Fingerprints nationallicence Scoring nationallicence SMILES nationallicence Virtual screening nationallicence Carta Giorgio Molecular Design Group, School of Biochemistry and Immunology, Trinity College Dublin, Dublin 2, Ireland aut Onnis Valeria Molecular Design Group, School of Biochemistry and Immunology, Trinity College Dublin, Dublin 2, Ireland aut Knox Andrew School of Pharmacy and Pharmaceutical Sciences, Trinity College Dublin, Dublin 2, Ireland aut Fayne Darren Molecular Design Group, School of Biochemistry and Immunology, Trinity College Dublin, Dublin 2, Ireland aut Lloyd David Molecular Design Group, School of Biochemistry and Immunology, Trinity College Dublin, Dublin 2, Ireland aut Journal of Computer-Aided Molecular Design Kluwer Academic Publishers 20/3(2006-03-01), 179-190 0920-654X 20:3<179 2006 20 10822 https://doi.org/10.1007/s10822-006-9044-4 text/html Onlinezugriff via DOI 1 research-article jats NATIONALLICENCE 856 40 https://doi.org/10.1007/s10822-006-9044-4 text/html Onlinezugriff via DOI NATIONALLICENCE 700 1- Carta Giorgio Molecular Design Group, School of Biochemistry and Immunology, Trinity College Dublin, Dublin 2, Ireland aut NATIONALLICENCE 700 1- Onnis Valeria Molecular Design Group, School of Biochemistry and Immunology, Trinity College Dublin, Dublin 2, Ireland aut NATIONALLICENCE 700 1- Knox Andrew School of Pharmacy and Pharmaceutical Sciences, Trinity College Dublin, Dublin 2, Ireland aut NATIONALLICENCE 700 1- Fayne Darren Molecular Design Group, School of Biochemistry and Immunology, Trinity College Dublin, Dublin 2, Ireland aut NATIONALLICENCE 700 1- Lloyd David Molecular Design Group, School of Biochemistry and Immunology, Trinity College Dublin, Dublin 2, Ireland aut NATIONALLICENCE 773 0- Journal of Computer-Aided Molecular Design Kluwer Academic Publishers 20/3(2006-03-01), 179-190 0920-654X 20:3<179 2006 20 10822 Metadata rights reserved Springer special CC-BY-NC licence nationallicence BK010053 XK010053 XK010000 NATIONALLICENCE NATIONALLICENCE NL-springer