2001
DOI: 10.1002/jcc.1165
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Docking of small ligands to low‐resolution and theoretically predicted receptor structures

Abstract: Abstract:We have developed a simple docking procedure that is able to utilize low-resolution models of proteins created by structure prediction algorithms such as threading or ab initio folding to predict the conformation of receptor-small ligand complexes. In our approach, using only approximate, discretized models of both molecules, we search for the steric and quasi-chemical complementarity between a ligand and the receptor molecules. This averaging procedure allows for the compensation of numerous structur… Show more

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Cited by 31 publications
(41 citation statements)
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“…12 In Figure 9, we plot the percent of correct specific contacts for 298 proteins (native structures) for the new program versus Dolores (the test set is described in more detail in the section "test sets," it is there denoted as set "3"). The number of cases in which more than 50% of the specific contacts are correctly predicted is very different for the two algorithms: the Dolores program only achieves this level of accuracy for 27 out of 298 protein-ligand pairs.…”
Section: Known Ligand and Unknown Binding Site: Results For Unconstramentioning
confidence: 99%
See 2 more Smart Citations
“…12 In Figure 9, we plot the percent of correct specific contacts for 298 proteins (native structures) for the new program versus Dolores (the test set is described in more detail in the section "test sets," it is there denoted as set "3"). The number of cases in which more than 50% of the specific contacts are correctly predicted is very different for the two algorithms: the Dolores program only achieves this level of accuracy for 27 out of 298 protein-ligand pairs.…”
Section: Known Ligand and Unknown Binding Site: Results For Unconstramentioning
confidence: 99%
“…A set of 298 proteins, derived from the set of 318 proteins, for which results of the Dolores method are published. 12 We term this the Dolores test set. We used the program Reduce 22 to place hydrogen atoms on the PDB structures of the proteins.…”
Section: Test Setsmentioning
confidence: 99%
See 1 more Smart Citation
“…When the atomic potential is used, the number of correct predictions increases to 50 of 65. The resulting structure can be used for further analyses such as functional annotation by matching three-dimensional active-site motifs (24) or for low-resolution ligand docking (25).…”
Section: Discussionmentioning
confidence: 99%
“…High resolution structures seem not necessary for docking experiments [53], and several reports describe the successful use of homology models [54]. Even if a close protein homologue is not experimentally available, docking proved to be efficient in virtual screening, as demonstrated with GPCR for which the only template is bovine rhodopsin.…”
Section: Resultsmentioning
confidence: 97%