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A fast protein-ligand docking method
Högskolan i Skövde, Institutionen för kommunikation och information.
2006 (engelsk)Independent thesis Basic level (degree of Bachelor), 20 poäng / 30 hpOppgave
Abstract [en]

In this dissertation a novel approach to protein-ligand docking is presented. First an existing method to predict putative active sites is employed. These predictions are then used to cut down the search space of an algorithm that uses the fast Fourier transform to calculate the geometrical and electrostatic complementarity between a protein and a small organic ligand. A simplified hydrophobicity score is also calculated for each active site. The docking method could be applied either to dock ligands in a known active site or to rank several putative active sites according to their biological feasibility. The method was evaluated on a set of 310 protein-ligand complexes. The results show that with respect to docking the method with its initial parameter settings is too coarse grained. The results also show that with respect to ranking of putative active sites the method works quite well.

sted, utgiver, år, opplag, sider
2006. , s. 74
Emneord [en]
protein-ligand docking, molecular modelling, putative active sites ranking, fast Fourier transform
HSV kategori
Identifikatorer
URN: urn:nbn:se:his:diva-69OAI: oai:DiVA.org:his-69DiVA, id: diva2:3087
Presentation
(engelsk)
Uppsök
Physics, Chemistry, Mathematics
Veileder
Examiner
Tilgjengelig fra: 2007-06-13 Laget: 2007-06-13 Sist oppdatert: 2018-01-12

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