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Sirugue L, Langenfeld F, Lagarde N, Montes M. PLO3S: Protein LOcal Surficial Similarity Screening. Comput Struct Biotechnol J 2024; 26:1-10. [PMID: 38189058 PMCID: PMC10770625 DOI: 10.1016/j.csbj.2023.12.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 12/01/2023] [Accepted: 12/03/2023] [Indexed: 01/09/2024] Open
Abstract
The study of protein molecular surfaces enables to better understand and predict protein interactions. Different methods have been developed in computer vision to compare surfaces that can be applied to protein molecular surfaces. The present work proposes a method using the Wave Kernel Signature: Protein LOcal Surficial Similarity Screening (PLO3S). The descriptor of the PLO3S method is a local surface shape descriptor projected on a unit sphere mapped onto a 2D plane and called Surface Wave Interpolated Maps (SWIM). PLO3S allows to rapidly compare protein surface shapes through local comparisons to filter large protein surfaces datasets in protein structures virtual screening protocols.
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Affiliation(s)
- Léa Sirugue
- Laboratoire GBCM, EA7528, Conservatoire National des Arts et Métiers, Hesam Université, 2, rue Conté, Paris, 75003, France
| | - Florent Langenfeld
- Laboratoire GBCM, EA7528, Conservatoire National des Arts et Métiers, Hesam Université, 2, rue Conté, Paris, 75003, France
| | - Nathalie Lagarde
- Laboratoire GBCM, EA7528, Conservatoire National des Arts et Métiers, Hesam Université, 2, rue Conté, Paris, 75003, France
| | - Matthieu Montes
- Laboratoire GBCM, EA7528, Conservatoire National des Arts et Métiers, Hesam Université, 2, rue Conté, Paris, 75003, France
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Molecular fingerprints based on Jacobi expansions of electron densities. Theor Chem Acc 2021. [DOI: 10.1007/s00214-020-02708-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Dokholyan NV. Experimentally-driven protein structure modeling. J Proteomics 2020; 220:103777. [PMID: 32268219 PMCID: PMC7214187 DOI: 10.1016/j.jprot.2020.103777] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Revised: 03/17/2020] [Accepted: 04/02/2020] [Indexed: 11/25/2022]
Abstract
Revolutions in natural and exact sciences started at the dawn of last century have led to the explosion of theoretical, experimental, and computational approaches to determine structures of molecules, complexes, as well as their rich conformational dynamics. Since different experimental methods produce information that is attributed to specific time and length scales, corresponding computational methods have to be tailored to these scales and experiments. These methods can be then combined and integrated in scales, hence producing a fuller picture of molecular structure and motion from the "puzzle pieces" offered by various experiments. Here, we describe a number of computational approaches to utilize experimental data to glance into structure of proteins and understand their dynamics. We will also discuss the limitations and the resolution of the constraints-based modeling approaches. SIGNIFICANCE: Experimentally-driven computational structure modeling and determination is a rapidly evolving alternative to traditional approaches for molecular structure determination. These new hybrid experimental-computational approaches are proving to be a powerful microscope to glance into the structural features of intrinsically or partially disordered proteins, dynamics of molecules and complexes. In this review, we describe various approaches in the field of experimentally-driven computational structure modeling.
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Affiliation(s)
- Nikolay V Dokholyan
- Department of Pharmacology, Penn State University College of Medicine, Hershey, PA 17033, USA; Department of Biochemistry & Molecular Biology, Penn State College of Medicine, Hershey, PA 17033, USA.; Department of Chemistry, Pennsylvania State University, University Park, PA 16802, USA.; Department of Biomedical Engineering, Pennsylvania State University, University Park, PA 16802, USA.
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Urquiza-Carvalho GA, Rocha GB, López R. Efficient algorithm for expanding theoretical electron densities in canterakis-zernike functions. J Comput Chem 2018; 39:2022-2032. [PMID: 30315586 DOI: 10.1002/jcc.25376] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Revised: 05/11/2018] [Accepted: 05/15/2018] [Indexed: 12/18/2022]
Abstract
An algorithm for the efficient computation of Canterakis-Zernike moments of theoretically computed molecular electron densities and rotationally invariant Fingerprint indices derived from them is reported. The algorithm is suitable for any density expressed in terms of Gaussian- or Slater-type functions within the Linear Combination of Atomic Orbitals framework at any level of computation. Electron density is expressed as a one-center expansion of real regular spherical harmonics times radial factors by means of translation techniques, which facilitates the efficient computation of the moments in terms of a single one-dimension numerical integration. The performance of the algorithm is analyzed showing that the computation of radial factors in the quadrature points is responsible for almost all computational time. The procedure is applicable to any density obtained with standard packages for molecular structure calculations. © 2018 Wiley Periodicals, Inc.
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Affiliation(s)
| | - Gerd B Rocha
- Departamento de Química, Universidade Federal da Paraíba, João Pessoa, Brazil
| | - Rafael López
- Departamento de Química Física Aplicada, Universidad Autónoma de Madrid, Madrid, Spain
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Kumar A, Zhang KYJ. Advances in the Development of Shape Similarity Methods and Their Application in Drug Discovery. Front Chem 2018; 6:315. [PMID: 30090808 PMCID: PMC6068280 DOI: 10.3389/fchem.2018.00315] [Citation(s) in RCA: 81] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Accepted: 07/09/2018] [Indexed: 12/21/2022] Open
Abstract
Molecular similarity is a key concept in drug discovery. It is based on the assumption that structurally similar molecules frequently have similar properties. Assessment of similarity between small molecules has been highly effective in the discovery and development of various drugs. Especially, two-dimensional (2D) similarity approaches have been quite popular due to their simplicity, accuracy and efficiency. Recently, the focus has been shifted toward the development of methods involving the representation and comparison of three-dimensional (3D) conformation of small molecules. Among the 3D similarity methods, evaluation of shape similarity is now gaining attention for its application not only in virtual screening but also in molecular target prediction, drug repurposing and scaffold hopping. A wide range of methods have been developed to describe molecular shape and to determine the shape similarity between small molecules. 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. Several of these methods demonstrated excellent virtual screening performance not only retrospectively but also prospectively. 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. Additionally, shape comparisons between atomic models and 3D density maps allowed the fitting of atomic models into cryo-electron microscopy maps. This review aims to summarize the methodological advances in shape similarity assessment highlighting advantages, disadvantages and their application in drug discovery.
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Affiliation(s)
| | - Kam Y. J. Zhang
- Laboratory for Structural Bioinformatics, Center for Biosystems Dynamics Research, RIKEN, Yokohama, Japan
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Esquivel-Rodríguez J, Xiong Y, Han X, Guang S, Christoffer C, Kihara D. Navigating 3D electron microscopy maps with EM-SURFER. BMC Bioinformatics 2015; 16:181. [PMID: 26025554 PMCID: PMC4448178 DOI: 10.1186/s12859-015-0580-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2014] [Accepted: 04/20/2015] [Indexed: 03/18/2023] Open
Abstract
BACKGROUND The Electron Microscopy DataBank (EMDB) is growing rapidly, accumulating biological structural data obtained mainly by electron microscopy and tomography, which are emerging techniques for determining large biomolecular complex and subcellular structures. Together with the Protein Data Bank (PDB), EMDB is becoming a fundamental resource of the tertiary structures of biological macromolecules. To take full advantage of this indispensable resource, the ability to search the database by structural similarity is essential. However, unlike high-resolution structures stored in PDB, methods for comparing low-resolution electron microscopy (EM) density maps in EMDB are not well established. RESULTS We developed a computational method for efficiently searching low-resolution EM maps. The method uses a compact fingerprint representation of EM maps based on the 3D Zernike descriptor, which is derived from a mathematical series expansion for EM maps that are considered as 3D functions. The method is implemented in a web server named EM-SURFER, which allows users to search against the entire EMDB in real-time. EM-SURFER compares the global shapes of EM maps. Examples of search results from different types of query structures are discussed. CONCLUSIONS We developed EM-SURFER, which retrieves structurally relevant matches for query EM maps from EMDB within seconds. The unique capability of EM-SURFER to detect 3D shape similarity of low-resolution EM maps should prove invaluable in structural biology.
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Affiliation(s)
| | - Yi Xiong
- Department of Biological Sciences, Purdue University, West Lafayette, IN, 47907, USA.
| | - Xusi Han
- Department of Biological Sciences, Purdue University, West Lafayette, IN, 47907, USA.
| | - Shuomeng Guang
- Department of Biological Sciences, Purdue University, West Lafayette, IN, 47907, USA.
| | - Charles Christoffer
- Department of Computer Science, Purdue University, West Lafayette, IN, 47907, USA.
- Department of Mathematics, Purdue University, West Lafayette, IN, 47907, USA.
| | - Daisuke Kihara
- Department of Computer Science, Purdue University, West Lafayette, IN, 47907, USA.
- Department of Biological Sciences, Purdue University, West Lafayette, IN, 47907, USA.
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Esquivel-Rodríguez J, Kihara D. Computational methods for constructing protein structure models from 3D electron microscopy maps. J Struct Biol 2013; 184:93-102. [PMID: 23796504 DOI: 10.1016/j.jsb.2013.06.008] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2012] [Revised: 06/11/2013] [Accepted: 06/13/2013] [Indexed: 12/31/2022]
Abstract
Protein structure determination by cryo-electron microscopy (EM) has made significant progress in the past decades. Resolutions of EM maps have been improving as evidenced by recently reported structures that are solved at high resolutions close to 3Å. Computational methods play a key role in interpreting EM data. Among many computational procedures applied to an EM map to obtain protein structure information, in this article we focus on reviewing computational methods that model protein three-dimensional (3D) structures from a 3D EM density map that is constructed from two-dimensional (2D) maps. The computational methods we discuss range from de novo methods, which identify structural elements in an EM map, to structure fitting methods, where known high resolution structures are fit into a low-resolution EM map. A list of available computational tools is also provided.
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Affiliation(s)
- Juan Esquivel-Rodríguez
- Department of Computer Science, College of Science, Purdue University, West Lafayette, IN 47907, USA
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Sael L, Kihara D. Detecting local ligand-binding site similarity in nonhomologous proteins by surface patch comparison. Proteins 2012; 80:1177-95. [PMID: 22275074 DOI: 10.1002/prot.24018] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2011] [Revised: 11/27/2011] [Accepted: 12/13/2011] [Indexed: 11/06/2022]
Abstract
Functional elucidation of proteins is one of the essential tasks in biology. Function of a protein, specifically, small ligand molecules that bind to a protein, can be predicted by finding similar local surface regions in binding sites of known proteins. Here, we developed an alignment free local surface comparison method for predicting a ligand molecule which binds to a query protein. The algorithm, named Patch-Surfer, represents a binding pocket as a combination of segmented surface patches, each of which is characterized by its geometrical shape, the electrostatic potential, the hydrophobicity, and the concaveness. Representing a pocket by a set of patches is effective to absorb difference of global pocket shape while capturing local similarity of pockets. 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. Two pockets are compared using a modified weighted bipartite matching algorithm, which matches similar patches from the two pockets. Patch-Surfer was benchmarked on three datasets, which consist in total of 390 proteins that bind to one of 21 ligands. Patch-Surfer showed superior performance to existing methods including a global pocket comparison method, Pocket-Surfer, which we have previously introduced. Particularly, as intended, the accuracy showed large improvement for flexible ligand molecules, which bind to pockets in different conformations.
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Affiliation(s)
- Lee Sael
- Department of Computer Science, Purdue University, West Lafayette, Indiana 47907, USA
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