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Ligand Electron Density Shape Recognition Using 3D Zernike Descriptors
[chapter]
2009
Lecture Notes in Computer Science
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We present a novel approach to crystallographic ligand density interpretation based on Zernike shape descriptors. ...
Electron density for a bound ligand is expanded in an orthogonal polynomial series (3D Zernike polynomials) and the coefficients from this expansion are employed to construct rotation-invariant descriptors ...
Acknowledgments The idea to this piece of work is based on discussions with Dr Victor S Lamzin (EMBL Hamburg) about using spherical harmonics to interpret ligand density shapes. ...
doi:10.1007/978-3-642-04031-3_12
fatcat:cdvh72dqx5cw5dyeeu7gruiyfi
Molecular Surface Representation Using 3D Zernike Descriptors for Protein Shape Comparison and Docking
2011
Current protein and peptide science
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We introduce the 3D Zernike descriptor (3DZD), an emerging technique to describe molecular surfaces. ...
These two characteristics of the 3DZD allow rapid comparison of surface shapes, which is sufficient for real-time structure database screening. ...
Here, we review application of protein surface representation using moment-based descriptors, namely, the 3D Zernike descriptors (3DZD) [9;10] . ...
doi:10.2174/138920311796957612
pmid:21787306
fatcat:3nmgbp2dqfa65e74eb7bpx3hve
Protein Binding Ligand Prediction Using Moments-Based Methods
[chapter]
2011
Protein Function Prediction for Omics Era
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A new development of pocket comparison method is also mentioned, which allows partial matching of pockets by using local patch descriptors. ...
In this chapter, we introduce computational methods for describing and comparing ligand binding sites using two dimensional and three dimensional moments. ...
electron density maps [49] .
2D Pocket Model with Pseudo-Zernike Moments We have also developed a new computational pocket model using two dimensional moments [50] . ...
doi:10.1007/978-94-007-0881-5_8
fatcat:mqowzldesvfdzksjnmvzar4fam
Potential for Protein Surface Shape Analysis Using Spherical Harmonics and 3D Zernike Descriptors
2009
Cell Biochemistry and Biophysics
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In this article, we present an overview of some commonly used representations with specific focus on two schemes namely spherical harmonics and their extension, the 3D Zernike descriptors. ...
To this end, moment-based representations provide a compact and nonredundant description of molecular shape and other associated properties. ...
As a result, the original shape cannot be reconstructed from the calculated descriptors.
3D Zernike Descriptors 2D Zernike moments have been used in a wide range of applications in image analysis [32 ...
doi:10.1007/s12013-009-9051-x
pmid:19521674
fatcat:b3a4dmdl5zdmvpkiswdzpdpv3i
Advances in the Development of Shape Similarity Methods and Their Application in Drug Discovery
2018
Frontiers in Chemistry
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Additionally, shape comparisons between atomic models and 3D density maps allowed the fitting of atomic models into cryo-electron microscopy maps. ...
The most widely used methods include atom distance-based methods, surface-based approaches such as spherical harmonics and 3D Zernike descriptors, atom-centered Gaussian overlay based representations. ...
Pocket-Surfer utilizes pseudo-Zernike descriptors and 3D Zernike descriptors to represent and compare properties and 3D shapes of binding pockets (Chikhi et al., 2010) . ...
doi:10.3389/fchem.2018.00315
pmid:30090808
pmcid:PMC6068280
fatcat:b2ieooqchfcepo7qe7u5cngtcy
Fingerprint-based structure retrieval using electron density
2011
Proteins: Structure, Function, and Bioinformatics
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All structural alignments are calculated using the TMalign program. 28 The figures are prepared using UCSF Chimera 25 and Pymol. 29 The datasets are available for downloading at http://faust.med.unc.edu ...
Novotni and Klein first used 3D Zernike invariants for shape retrieval, and find better performance than spherical harmonic descriptors. 12 In this study, we demonstrate the feasibility of using electron ...
RESULTS AND DISCUSSIONS
Zernike invariants as fingerprints for electron density Our fingerprint of any 3D electron density is constructed using 3D Zernike moments. 10,12,23,24 A detailed introduction ...
doi:10.1002/prot.22941
pmid:21287628
pmcid:PMC3072439
fatcat:nc7xjindqzhfhnhnwiy2dfrkuq
In-Silico evidence for two receptors based strategy of SARS-CoV-2
[article]
2020
arXiv
pre-print
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This innovative and general procedure, based on the representation of the molecular iso-electron density surface in terms of 2D Zernike polynomials, allows the rapid and quantitative assessment of the ...
geometrical shape complementarity between interacting proteins, that was unfeasible with previous methods. ...
overcome such performances in shape complementarity recognition. ...
arXiv:2003.11107v2
fatcat:ggifx2fjjfgh3b6t26ugesivti
Three-Dimensional Compound Comparison Methods and Their Application in Drug Discovery
2015
Molecules
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Keywords Ligand-based virtual screening; Three-dimensional similarity; ROCS; USR; 3D Zernike descriptors; Patch-Surfer; PL-PatchSurfer; molecular shape; molecular surface licensee MDPI, Basel, Switzerland ...
Virtual screening has been widely used in the drug discovery process. Ligand-based virtual screening (LBVS) methods compare a library of compounds with a known active ligand. ...
Every vertex has charge and shape density information. ...
doi:10.3390/molecules200712841
pmid:26193243
pmcid:PMC5005041
fatcat:ajzknqtl3jewfmxammsgr6ylhy
In-Silico evidence for two receptors based strategy of SARS-CoV-2
[article]
2020
bioRxiv
pre-print
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This innovative and general procedure, based on the representation of the molecular iso-electron density surface in terms of 2D Zernike polynomials, allows the rapid and quantitative assessment of the ...
geometrical shape complementarity between interacting proteins, that was unfeasible with previous methods. ...
Therefore, each binding site is associated with a one dimensional vector, allowing us to easily compare the shape of protein regions with the euclidean distance between their Zernike descriptors. ...
doi:10.1101/2020.03.24.006197
fatcat:gxdoejyxxbbc3ovglb5f2iqxmq
Detecting local ligand-binding site similarity in nonhomologous proteins by surface patch comparison
2012
Proteins: Structure, Function, and Bioinformatics
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The shape and the physicochemical properties of surface patches are represented using the 3D Zernike descriptor, which is a series expansion of mathematical 3D function. ...
Surface patch representation using the 3D Zernike descriptor normalized local 3DZDs, lzd P i"shape , lzd P i"hyd , lzd P i ,ele , and lzd P i"vis , which are computed for the four features, shape, hydrophobicity ...
the comparison of low-resolution electron density maps 45, 46 . ...
doi:10.1002/prot.24018
pmid:22275074
pmcid:PMC3294165
fatcat:x4dny7aqsbevjo62muy77cjxxu
Using diffusion distances for flexible molecular shape comparison
2010
BMC Bioinformatics
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Results: In this paper, we present a new shape descriptor, named Diffusion Distance Shape Descriptor (DDSD), for comparing 3D shapes of flexible molecules. ...
to incorrect shape recognition. ...
KR identified the underlying opportunity and basis for connecting diffusion to shape analysis. WB helped YL with the understanding of diffusion maps. ...
doi:10.1186/1471-2105-11-480
pmid:20868474
pmcid:PMC2949899
fatcat:3tbgklffsvfatdspi6plyc2uou
Spherical Harmonics Coefficients for Ligand-Based Virtual Screening of Cyclooxygenase Inhibitors
2011
PLoS ONE
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(ultrafast shape recognition, based on statistical moments) [14] , ROCS (rapid overlay of chemical structures, based on Gaussian densities) [15] , VolSurf (volumes and surfaces of 3D molecular fields ...
., Erlangen, Germany) in a virtual screening study on the directory of useful decoys (DUD) data set [39] , which motivates 3D shape-property combinations specifically for flexible ligands [40] . ...
doi:10.1371/journal.pone.0021554
pmid:21818259
pmcid:PMC3144885
fatcat:lsdt4r6ggfh43e3tjczqdzchbe
PL-PatchSurfer2: Improved Local Surface Matching-Based Virtual Screening Method That Is Tolerant to Target and Ligand Structure Variation
2016
Journal of Chemical Information and Modeling
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In PL-PatchSurfer2, protein and ligand surfaces are represented by a set of overlapping local patches, each of which are represented by 3D Zernike descriptors (3DZDs). ...
By using 3DZDs, shape and physicochemical complementarity of local surface regions of a pocket surface and a ligand molecule can be concisely and effectively computed. ...
density maps from electron microscopy 27 , and protein structure similarity search 28 . ...
doi:10.1021/acs.jcim.6b00163
pmid:27500657
pmcid:PMC5037053
fatcat:2xpyxb6ic5euznbsc4yo24trui
Computational methods for constructing protein structure models from 3D electron microscopy maps
2013
Journal of Structural Biology
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from a 3D EM density map that is constructed from two-dimensional (2D) maps. ...
Protein structure determination by cryo-electron microscopy (EM) has made significant progress in the past decades. ...
Our group has shown that the 3D Zernike descriptors (3DZD), a mathematical series expansion of a 3D function, is effective for fast comparison of isosurfaces derived from EM density maps (Sael and Kihara ...
doi:10.1016/j.jsb.2013.06.008
pmid:23796504
pmcid:PMC3795986
fatcat:mr3lorsn75akriotpmzs4be3ki
Molecular theory of solvation: Methodology summary and illustrations
2015
Condensed Matter Physics
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structure in terms of 3D maps of correlation functions, including density distributions, of solvent interaction sites around a solute (supra)molecule with full consistent account for the effects of chemical ...
Beginning with a molecular interaction potential force field, it uses diagrammatic analysis of the solvation free energy to derive integral equations for correlation functions between molecules in solution ...
) quantum chemistry methods for multiscale description of electronic structure in solution [9, 12, [14] [15] [16] , (ii) using 3D maps of potentials of mean force as scoring functions for molecular recognition ...
doi:10.5488/cmp.18.32601
fatcat:zuw67sq465d77lpzduqgrj5onm
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