Challenges and advances in computational docking: 2009 in review
Docking is a computational technique that places a small molecule (ligand) in the binding site of its macromolecular target (receptor) and estimates its binding affinity. This review addresses methodological developments that have occurred in the docking field in 2009, with a particular focus on the...
| Main Authors: | , , |
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| Format: | Journal Article |
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John Wiley & Sons Ltd.
2011
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| Online Access: | http://hdl.handle.net/20.500.11937/35703 |
| _version_ | 1848754567689273344 |
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| author | Yuriev, E. Agostino, Mark Ramsland, P. |
| author_facet | Yuriev, E. Agostino, Mark Ramsland, P. |
| author_sort | Yuriev, E. |
| building | Curtin Institutional Repository |
| collection | Online Access |
| description | Docking is a computational technique that places a small molecule (ligand) in the binding site of its macromolecular target (receptor) and estimates its binding affinity. This review addresses methodological developments that have occurred in the docking field in 2009, with a particular focus on the more difficult, and sometimes controversial, aspects of this promising computational discipline. These developments aim to address the main challenges of docking: receptor representation (such aspects as structural waters, side chain protonation, and, most of all, flexibility (from side chain rotation to domain movement)), ligand representation (protonation, tautomerism and stereoisomerism, and the effect of input conformation), as well as accounting for solvation and entropy of binding. This review is strongly focused on docking advances in the context of drug design, specifically in virtual screening and fragment-based drug design. |
| first_indexed | 2025-11-14T08:42:28Z |
| format | Journal Article |
| id | curtin-20.500.11937-35703 |
| institution | Curtin University Malaysia |
| institution_category | Local University |
| last_indexed | 2025-11-14T08:42:28Z |
| publishDate | 2011 |
| publisher | John Wiley & Sons Ltd. |
| recordtype | eprints |
| repository_type | Digital Repository |
| spelling | curtin-20.500.11937-357032017-09-13T15:32:01Z Challenges and advances in computational docking: 2009 in review Yuriev, E. Agostino, Mark Ramsland, P. receptor flexibility computational docking binding mode prediction protein-ligand complexes scoring Docking is a computational technique that places a small molecule (ligand) in the binding site of its macromolecular target (receptor) and estimates its binding affinity. This review addresses methodological developments that have occurred in the docking field in 2009, with a particular focus on the more difficult, and sometimes controversial, aspects of this promising computational discipline. These developments aim to address the main challenges of docking: receptor representation (such aspects as structural waters, side chain protonation, and, most of all, flexibility (from side chain rotation to domain movement)), ligand representation (protonation, tautomerism and stereoisomerism, and the effect of input conformation), as well as accounting for solvation and entropy of binding. This review is strongly focused on docking advances in the context of drug design, specifically in virtual screening and fragment-based drug design. 2011 Journal Article http://hdl.handle.net/20.500.11937/35703 10.1002/jmr.1077 John Wiley & Sons Ltd. restricted |
| spellingShingle | receptor flexibility computational docking binding mode prediction protein-ligand complexes scoring Yuriev, E. Agostino, Mark Ramsland, P. Challenges and advances in computational docking: 2009 in review |
| title | Challenges and advances in computational docking: 2009 in review |
| title_full | Challenges and advances in computational docking: 2009 in review |
| title_fullStr | Challenges and advances in computational docking: 2009 in review |
| title_full_unstemmed | Challenges and advances in computational docking: 2009 in review |
| title_short | Challenges and advances in computational docking: 2009 in review |
| title_sort | challenges and advances in computational docking: 2009 in review |
| topic | receptor flexibility computational docking binding mode prediction protein-ligand complexes scoring |
| url | http://hdl.handle.net/20.500.11937/35703 |