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Ligand Electron Density Shape Recognition Using 3D Zernike Descriptors [chapter]

Prasad Gunasekaran, Scott Grandison, Kevin Cowtan, Lora Mak, David M. Lawson, Richard J. Morris
2009 Lecture Notes in Computer Science  
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

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

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

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.  ...  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

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

Shuangye Yin, Nikolay V. Dokholyan
2011 Proteins: Structure, Function, and Bioinformatics  
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]

Edoardo Milanetti, Mattia Miotto, Lorenzo Di Rienzo, Michele Monti, Giorgio Gosti, Giancarlo Ruocco
2020 arXiv   pre-print
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

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  ...  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]

Edoardo Milanetti, Mattia Miotto, Lorenzo Di Rienzo, Michele Monti, Giorgio Gosti, Giancarlo Ruocco
2020 bioRxiv   pre-print
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

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.  ...  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

Yu-Shen Liu, Qi Li, Guo-Qin Zheng, Karthik Ramani, William Benjamin
2010 BMC Bioinformatics  
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

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

Woong-Hee Shin, Charles W. Christoffer, Jibo Wang, Daisuke Kihara
2016 Journal of Chemical Information and Modeling  
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

Juan Esquivel-Rodríguez, Daisuke Kihara
2013 Journal of Structural Biology  
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

Kovalenko
2015 Condensed Matter Physics  
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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