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Real spherical harmonic expansion coefficients as 3D shape descriptors for protein binding pocket and ligand comparisons

R. J. Morris, R. J. Najmanovich, A. Kahraman, J. M. Thornton
2005 Bioinformatics  
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]

Rayan Chikhi, Lee Sael, Daisuke Kihara
2011 Protein Function Prediction for Omics Era  
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

Vishwesh Venkatraman, Lee Sael, Daisuke Kihara
2009 Cell Biochemistry and Biophysics  
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

Rayan Chikhi, Lee Sael, Daisuke Kihara
2010 Proteins: Structure, Function, and Bioinformatics  
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

Daisuke Kihara, Lee Sael, Rayan Chikhi, Juan Esquivel-Rodriguez
2011 Current protein and peptide science  
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

Ashutosh Kumar, Kam Y. J. Zhang
2018 Frontiers in Chemistry  
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

Quan Wang, Kerstin Birod, Carlo Angioni, Sabine Grösch, Tim Geppert, Petra Schneider, Matthias Rupp, Gisbert Schneider, Paul Wrede
2011 PLoS ONE  
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

Violeta I. Perez-Nueno
2011 Open Conference Proceedings Journal  
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

Sivanesan Dakshanamurthy, Naiem T. Issa, Shahin Assefnia, Ashwini Seshasayee, Oakland J. Peters, Subha Madhavan, Aykut Uren, Milton L. Brown, Stephen W. Byers
2012 Journal of Medicinal Chemistry  
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

Woong-Hee Shin, Xiaolei Zhu, Mark Bures, Daisuke Kihara
2015 Molecules  
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]

Brice Hoffmann, Jean-Philippe Vert
2009 arXiv   pre-print
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

Lee Sael, Bin Li, David La, Yi Fang, Karthik Ramani, Raif Rustamov, Daisuke Kihara
2008 Proteins: Structure, Function, and Bioinformatics  
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

Brice Hoffmann, Mikhail Zaslavskiy, Jean-Philippe Vert, Véronique Stoven
2010 BMC Bioinformatics  
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]

Seyed Majid S. M. Saberi Fathi, Jack A Tuszynski
2013 arXiv   pre-print
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

Lee Sael, Daisuke Kihara
2012 Proteins: Structure, Function, and Bioinformatics  
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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