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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  ...  We propose a novel numerical method able to determine efficiently and effectively the relationship of complementarity between portions of proteins surfaces.  ...  on the 2D Zernike polynomials, which allows the quantitative characterization of protein surface regions.  ... 
arXiv:2003.11107v2 fatcat:ggifx2fjjfgh3b6t26ugesivti

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  ...  We propose a novel numerical method able to determine efficiently and effectively the relationship of complementarity between portions of proteins surfaces.  ...  on the 2D Zernike polynomials, which allows the quantitative characterization of protein surface regions.  ... 
doi:10.1101/2020.03.24.006197 fatcat:gxdoejyxxbbc3ovglb5f2iqxmq

2D Zernike polynomial expansion: finding the protein-protein binding regions

Edoardo Milanetti, Mattia Miotto, Lorenzo Di Rienzo, Michele Monti, Giorgio Gosti, Giancarlo Ruocco
2020 Computational and Structural Biotechnology Journal  
Our method is able to rapidly and quantitatively measure the geometrical shape complementarity between interacting proteins, comparing their molecular iso-electron density surfaces expanding the surface  ...  patches in term of 2D Zernike polynomials.  ...  To quantitatively evaluate the level of complementarity these interacting regions exhibit, we measured how much the distance between the Zernike descriptors of a pair of interacting binding sites is smaller  ... 
doi:10.1016/j.csbj.2020.11.051 pmid:33363707 pmcid:PMC7750141 fatcat:5raw5xzlvzgxrb4gpjoig7jcke

Insights into the Interaction Mechanism of DTP3 with MKK7 by Using STD-NMR and Computational Approaches

Annamaria Sandomenico, Lorenzo Di Rienzo, Luisa Calvanese, Emanuela Iaccarino, Gabriella D'Auria, Lucia Falcigno, Angela Chambery, Rosita Russo, Guido Franzoso, Laura Tornatore, Marco D'Abramo, Menotti Ruvo (+2 others)
2020 Biomedicines  
Data gathered by fluorescence quenching and computational approaches consistently indicate that the N-terminal region of MKK7 is the optimal binding site explored by DTP3.  ...  These findings further the understanding of the selective mode of action of GADD45β/MKK7 inhibitors and inform potential mechanisms of drug resistance.  ...  Conflicts of Interest: M.R., G.F., and L.T. are listed as inventors in patents describing the use of DTP3 as a therapeutic agent against multiple myeloma.  ... 
doi:10.3390/biomedicines9010020 pmid:33396582 fatcat:fhice46oqjcs3cwvhg7zjalppi

In-Silico Evidence for a Two Receptor Based Strategy of SARS-CoV-2

Edoardo Milanetti, Mattia Miotto, Lorenzo Di Rienzo, Madhu Nagaraj, Michele Monti, Thaddeus W. Golbek, Giorgio Gosti, Steven J. Roeters, Tobias Weidner, Daniel E. Otzen, Giancarlo Ruocco
2021 Frontiers in Molecular Biosciences  
This innovative and general procedure, based on the representation of the molecular isoelectronic density surface in terms of 2D Zernike polynomials, allows the rapid and quantitative assessment of the  ...  In particular, we make use of our newly developed numerical method able to determine efficiently and effectively the relationship of complementarity between portions of protein surfaces.  ...  TW acknowledges support by the Novo Nordisk Foundation (Facility 307 Grant NanoScat, No. NNF18OC0032628). DO is grateful for support from the Innovation Fund Denmark (grant 0211-00066B).  ... 
doi:10.3389/fmolb.2021.690655 pmid:34179095 pmcid:PMC8219949 fatcat:5f2m5atkefgwllubw3ve2q2h3e

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.  ...  The 3DZD is a series expansion of mathematical threedimensional function, and thus a tertiary structure is represented compactly by a vector of coefficients of terms in the series.  ...  Acknowledgements This work is supported by the National Institute of General Medical Sciences of the National Institutes of Health (R01GM075004).  ... 
doi:10.2174/138920311796957612 pmid:21787306 fatcat:3nmgbp2dqfa65e74eb7bpx3hve

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  
However, defining their x-axes arbitrarily still produces robust descriptors: the mean AUC of shape-only descriptors of these pockets is only 0.7% lower than the mean dataset AUC.  ...  Quantitative computation of the area under the curve (AUC) of the ROC curve (upper half of Table II , results using the ''pocket shape only'' descriptor) shows that the p-Z, the 2D Zernike moments, and  ... 
doi:10.1002/prot.22715 pmid:20455259 pmcid:PMC3009464 fatcat:s5i56i7v3bfezonyio7zihqxyq

PL-PatchSurfer: A Novel Molecular Local Surface-Based Method for Exploring Protein-Ligand Interactions

Bingjie Hu, Xiaolei Zhu, Lyman Monroe, Mark Bures, Daisuke Kihara
2014 International Journal of Molecular Sciences  
Each patch is characterized by its geometrical shape and the electrostatic potential, which are represented using the 3D Zernike descriptor (3DZD).  ...  PL-PatchSurfer represents the protein binding pocket and the ligand molecular surface as a combination of segmented surface patches.  ...  L.M. measured computational time of software in Table 5 . M.B. analyzed ligand docking poses in Figure 6 . B.H., M.B., and D.K. wrote the manuscript. All authors read and approved the manuscript.  ... 
doi:10.3390/ijms150915122 pmid:25167137 pmcid:PMC4200761 fatcat:is4mlzb2qrhrjbhdh4vo75mnf4

Molecular Dynamics Simulations Reveal Canonical Conformations in Different pMHC/TCR Interactions

Josephine Alba, Lorenzo Di Rienzo, Edoardo Milanetti, Oreste Acuto, Marco D'Abramo
2020 Cells  
to different peptides, and modelled in the presence of a lipid bilayer.  ...  Our data suggest a correlation between the conformations explored by the β-chain constant regions and the T-cell response experimentally determined.  ...  Acknowledgments: The authors gratefully acknowledge PRACE, NVIDIA and CINECA for their computational support. Conflicts of Interest: The authors declare no conflict of interest.  ... 
doi:10.3390/cells9040942 pmid:32290289 pmcid:PMC7226950 fatcat:wfchs7kiczh25bisv7f7jteire

Local functional descriptors for surface comparison based binding prediction

Gregory M Cipriano, George N, Michael Gleicher
2012 BMC Bioinformatics  
Results: We present a new descriptor for protein functional surfaces and algorithms for using these descriptors to compare protein surface regions to identify ligand binding interfaces.  ...  Our approach uses descriptors of local regions of the surface, and assembles collections of matches to compare larger regions.  ...  Cipriano was supported in part by training grants from the National Institutes of Health (NIH) (NLM-5T15LM007359) and the US Department of Energy Genomics:GTL and SciDAC Programs (DE-FG02-04ER25627).  ... 
doi:10.1186/1471-2105-13-314 pmid:23176080 pmcid:PMC3585919 fatcat:puugpvm5pngwfmm7ryntzjqx7m

Pocket-Based Drug Design: Exploring Pocket Space

Xiliang Zheng, LinFeng Gan, Erkang Wang, Jin Wang
2012 AAPS Journal  
We have presented two case studies targeting the kinetic pockets generated by normal mode analysis and molecular dynamics method, respectively, in which we focus upon incorporating the pocket flexibility  ...  Herein, some recent progresses and developments of the computational analysis of pockets have been covered.  ...  To date, many properties and descriptors of binding pockets have been developed and refined to characterize the pockets.  ... 
doi:10.1208/s12248-012-9426-6 pmid:23180158 pmcid:PMC3535113 fatcat:7y65lisiyjbklnbbajbl6xzy7q

PROTEIN SURFACE SIMILARITIES EVALUATION FOR FUNCTIONAL ANNOTATION STUDIES [article]

PAOLO ALESSANDRO COZZI
2010
This method has been validated both in the search of similarities and in the search of complementarities.  ...  The search for similarities is then performed by indentifying correspondences between pairs of similar images, by filtering matches relying on geometrical criteria and then by clustering correspondences  ...  Another interesting solution can be the description of molecular surface with three dimensional Zernike descriptors (3DZD), by which each molecular surface is described by a vector of descriptors [63]  ... 
doi:10.13130/cozzi-paolo-alessandro_phd2010-12-09 fatcat:eakdov6th5cf5krb4y4c4gneuq

Kimdaejung Convention Center

2019 2019 IEEE 13th International Conference on Nano/Molecular Medicine & Engineering (NANOMED)  
He has extensive experience in fabricating, processing and characterizing inorganic, organic and biocompatible nanomaterials.  ...  Finally, sensing and therapeutic approaches can be harnessed by exploiting the optical properties of nanocrystals, including Quantum Dots and upconverting nanoparticles.  ...  The piezoelectric material deforms the crystal structure and generates an electrical moment by application of mechanical stress.  ... 
doi:10.1109/nanomed49242.2019.9130603 fatcat:wlmmq4uwyjablibepjnazw4fp4