2010
DOI: 10.1186/1471-2105-11-99
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A new protein binding pocket similarity measure based on comparison of clouds of atoms in 3D: application to ligand prediction

Abstract: BackgroundPredicting which molecules can bind to a given binding site of a protein with known 3D structure is important to decipher the protein function, and useful in drug design. A classical assumption in structural biology is that proteins with similar 3D structures have related molecular functions, and therefore may bind similar ligands. However, proteins that do not display any overall sequence or structure similarity may also bind similar ligands if they contain similar binding sites. Quantitatively asse… Show more

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Cited by 85 publications
(151 citation statements)
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“…Some recent approaches have tried to escape from the positional bias of using atom coordinates. Among them, Baroni et al [86] use GRID force field analysis to locate minimal energy points, Hoffman et al [87] use of atomic densities, and Jalencas and Mestres [43] place pseudo-centres directly on the protein surface defining the binding site.…”
Section: Binding Site Representationmentioning
confidence: 99%
See 2 more Smart Citations
“…Some recent approaches have tried to escape from the positional bias of using atom coordinates. Among them, Baroni et al [86] use GRID force field analysis to locate minimal energy points, Hoffman et al [87] use of atomic densities, and Jalencas and Mestres [43] place pseudo-centres directly on the protein surface defining the binding site.…”
Section: Binding Site Representationmentioning
confidence: 99%
“…The binding site representation used in Cavbase [81,88] has been adopted by many other methods, such as MolLoc [89] or ProBiS [90] (see Table 1). In some cases, the features of the pseudo-centres have been expanded to include partial charges, [87] electrostatic potential, [85] positively (P) and negatively (N) charged regions, [91] or to differentiate between aromatic features in face and edge positions. [92] The use of pure geometric representations such as shape curvatures, spherical harmonics, wavelet coefficients or pocket frameworks has also been explored.…”
Section: Binding Site Representationmentioning
confidence: 99%
See 1 more Smart Citation
“…Other approaches employ the spherical harmonics description of the molecular surface [10] or concern the projection of the molecular surface on Zernike functions [11]. Further, there are techniques that utilise the convolution kernel [12] or consider the heat propagation on the molecular surface [13] and [14]. Yet, all of these methods have the same drawback in that they fail to put disconnected regions into relation.…”
Section: Introductionmentioning
confidence: 98%
“…In their respective papers, (Wang et al, 2007) and (Hoffmann et al, 2010) propose to find the best global alignment, in terms of rigid transformations, in between two macromolecules. Wang et al define a cost function which evaluates the local discrepancy in between the shape of two macromolecules.…”
Section: Alignment and Monte Carlo Based Methodsmentioning
confidence: 99%