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Real spherical harmonic expansion coefficients as 3D shape descriptors for protein binding pocket and ligand comparisons
2005
Bioinformatics
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The method uses the coefficients of a real spherical harmonics expansion to describe the shape of a protein's binding pocket. Shape similarity is computed as the L 2 distance in coefficient space. ...
Results: A novel technique is presented for the comparison of protein binding pockets. ...
Hierarchical clustering of 40 predicted binding pockets using their real spherical harmonic shape descriptors. ...
doi:10.1093/bioinformatics/bti337
pmid:15728116
fatcat:istd2npdufgivppedheiwi6iim
Protein Binding Ligand Prediction Using Moments-Based Methods
[chapter]
2011
Protein Function Prediction for Omics Era
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An advantage of moment-based methods is that the tertiary structure of pocket shapes is described compactly as a vector of coefficients of series expansion. ...
In this chapter, we introduce computational methods for describing and comparing ligand binding sites using two dimensional and three dimensional moments. ...
For the 3D descriptors of pockets, we introduce the spherical harmonics and the 3D Zernike descriptors. For the 2D descriptors, we introduce the p-Z moments. ...
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. ...
We further discuss recent advances covering aspects of shape and property-based comparison at both global and local levels and demonstrate their applicability through some of our studies. ...
Acknowledgments This work is supported by grants from the National Institutes of Health (R01 GM075004) and National Science Foundation (DMS0604776, DMS800568). ...
doi:10.1007/s12013-009-9051-x
pmid:19521674
fatcat:b3a4dmdl5zdmvpkiswdzpdpv3i
Real-time ligand binding pocket database search using local surface descriptors
2010
Proteins: Structure, Function, and Bioinformatics
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ACKNOWLEDGMENTS The authors are grateful to Gregg Thomas for proofreading the manuscript. ...
Here, we present two representations of ligand binding pockets and utilize them for ligand binding prediction by pocket shape comparison. ...
Note that the aforementioned spherical harmonics-based method needs pose normalization of pockets as a preprocessing step of shape comparison as the spherical harmonics vary when an object is placed in ...
doi:10.1002/prot.22715
pmid:20455259
pmcid:PMC3009464
fatcat:s5i56i7v3bfezonyio7zihqxyq
Molecular Surface Representation Using 3D Zernike Descriptors for Protein Shape Comparison and Docking
2011
Current protein and peptide science
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These two characteristics of the 3DZD allow rapid comparison of surface shapes, which is sufficient for real-time structure database screening. ...
We introduce the 3D Zernike descriptor (3DZD), an emerging technique to describe molecular surfaces. ...
The applications of the 3DZD, namely, protein global structure comparison, surface property comparison, local surface classification, binding ligand prediction by pocket shape comparison, and protein-protein ...
doi:10.2174/138920311796957612
pmid:21787306
fatcat:3nmgbp2dqfa65e74eb7bpx3hve
Advances in the Development of Shape Similarity Methods and Their Application in Drug Discovery
2018
Frontiers in Chemistry
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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. ...
In addition to methods assessing the similarity between small molecules, shape similarity approaches have been developed to compare shapes of protein structures and binding pockets. ...
Spherical harmonics expansion coefficients have also been employed in the approximation and comparison of binding pockets and ligand surfaces (Cai et al., 2002) . ...
doi:10.3389/fchem.2018.00315
pmid:30090808
pmcid:PMC6068280
fatcat:b2ieooqchfcepo7qe7u5cngtcy
Spherical Harmonics Coefficients for Ligand-Based Virtual Screening of Cyclooxygenase Inhibitors
2011
PLoS ONE
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They then use the coefficients of a real spherical harmonics expansion to describe and compare the molecular shape of binding pockets and ligands. ...
[38] highlights applications of spherical harmonics to protein structure comparison, ligand binding site similarity, protein-protein docking, and virtual screening. Jakobi et al. ...
doi:10.1371/journal.pone.0021554
pmid:21818259
pmcid:PMC3144885
fatcat:lsdt4r6ggfh43e3tjczqdzchbe
Predicting Drug Promiscuity Using Spherical Harmonic Surface Shape-Based Similarity Comparisons
2011
Open Conference Proceedings Journal
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Consensus shapes, drug promiscuity, ligand shape space, protein pocket space, protein sequence space, shape similarity, spherical harmonic shapes. ...
Here, we present a spherical harmonic (SH) surface shape-based approach to predict rapidly promiscuous ligands and targets by comparing sets of SH ligand and protein shapes, respectively. ...
ACKNOWLEDGEMENTS The authors thank Cepos Insilico Ltd. for providing an Academic Licence for PARASURF. VIPN is grateful for a Marie Curie IEF Fellowship, grant reference DOVSA ...
doi:10.2174/2210289201102010113
fatcat:3lnhzfwzyjfftmhzzcy7v7kaju
Predicting New Indications for Approved Drugs Using a Proteochemometric Method
2012
Journal of Medicinal Chemistry
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Over 58% of the known best ligands for each target were correctly predicted as top ranked, followed by 66%, 76%, 84% and 91% for agents ranked in the top 10, 20, 30 and 40, respectively, out of all 3,671 ...
The TMFS method combines shape, topology and chemical signatures, including docking score and functional contact points of the ligand, to predict potential drug-target interactions with remarkable accuracy ...
We acknowledge the Georgetown-Lombardi Cancer Center Grant Support Grant and the Surface Plasmon Resonance Shared Resource and Caliper Life Sciences for the kinase assay. ...
doi:10.1021/jm300576q
pmid:22780961
pmcid:PMC3419493
fatcat:5osemtappnawhmjx6h6ykrtbvq
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 ...
LBVS methods can be classified based on the complexity of ligand structure information utilized: one-dimensional (1D), twodimensional (2D), and three-dimensional (3D). ...
DK also acknowledges funding from the National Institute of General Medical Sciences of the National Institutes of Health (R01GM097528) and the National Science Foundation (IIS1319551, DBI1262189, IOS1127027 ...
doi:10.3390/molecules200712841
pmid:26193243
pmcid:PMC5005041
fatcat:ajzknqtl3jewfmxammsgr6ylhy
A new protein binding pocket similarity measure based on comparison of 3D atom clouds: application to ligand prediction
[article]
2009
arXiv
pre-print
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Results: We explore a new approach for ligand prediction in which binding pockets are represented by atom clouds. Each target pocket is compared to an ensemble of pockets of known ligands. ...
Motivation: Prediction of ligands for proteins of known 3D structure is important to understand structure-function relationship, predict molecular function, or design new drugs. ...
For example, methods based on real spherical harmonic expansion used in [MNKT05] for binding pocket comparison are also discussed by [PPPT07, SV01] in the context of general 3D shape matching. ...
arXiv:0907.1531v1
fatcat:oyaq42p6rnallapvzopgse3oke
Fast protein tertiary structure retrieval based on global surface shape similarity
2008
Proteins: Structure, Function, and Bioinformatics
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Related works, such as the multipole method 42 proposed for global protein shape comparison and an application of spherical harmonics for binding pocket and ligand comparisons by Morris et al., 43 need ...
descriptors mainly in comparison with the spherical harmonics descriptors (SHD), 46,47 which is a popular spherical harmonics-based projection techniques used for general 3D object comparison. ...
doi:10.1002/prot.22030
pmid:18361455
fatcat:pz532tthuvbfhk6vex3qsnvhxy
A new protein binding pocket similarity measure based on comparison of clouds of atoms in 3D: application to ligand prediction
2010
BMC Bioinformatics
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Predicting 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. ...
Pocket alignment and comparison is possible even when the corresponding proteins share no sequence or overall structure similarities. ...
Acknowledgements We thank Mines ParisTech and Cannot Mines for financial support to the project and funding of BH and MZ.
Author ...
doi:10.1186/1471-2105-11-99
pmid:20175916
pmcid:PMC2838872
fatcat:utynse6rurazvmeugtpxb5lase
Geometrical comparison of two protein structures using Wigner-D functions
[article]
2013
arXiv
pre-print
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In this paper, we develop a quantitative comparison method for two arbitrary protein structures. ...
We further demonstrate that the expansion coefficients for the shape function obtained with the help of the Wigner-D functions correspond to structure factors. ...
This method uses the expansion of the 3D density function in terms of radial and spherical harmonic functions and computes the correlation coefficients between two density function expansion coefficients ...
arXiv:1311.6771v2
fatcat:l2wefwcvtret5okkdjcpvtza3q
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. ...
Here, we developed an alignment free local surface comparison method for predicting a ligand molecule which binds to a query protein. ...
Acknowledgments The authors are grateful to David La for proofreading the manuscript. ...
doi:10.1002/prot.24018
pmid:22275074
pmcid:PMC3294165
fatcat:x4dny7aqsbevjo62muy77cjxxu
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