Exploration of Empty Space among Spherical Obstacles via Additively Weighted Voronoi Diagram

Maňák, Martin

doi:10.1111/cgf.12980

Cited by 4 publications

(3 citation statements)

References 34 publications

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“…To overcome disconnected cases, the points of local maxima are connected to Voronoi vertices or to other extreme points by segments along which d aw is nondecreasing. These segments are called bridges and lie on Voronoi faces . Bridges for the situation in Figure c are depicted in Figure 4d.…”

Section: Methodsmentioning

confidence: 99%

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Voronoi‐based detection of pockets in proteins defined by large and small probes

Maňák

2019

J Comput Chem

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The function of enzymatic proteins is given by their ability to bind specific small molecules into their active sites. These sites can often be found in pockets on a hypothetical boundary between the protein and its environment. Detection, analysis, and visualization of pockets find its use in protein engineering and drug discovery. Many definitions of pockets and algorithms for their computation have been proposed. Kawabata and Go defined them as the regions of empty space into which a small spherical probe can enter but a large probe cannot and developed programs that can compute their approximate shape. In this article, this definition was slightly modified in order to capture the existence of large internal holes, and a Voronoi‐based method for the computation of the exact shape of these modified regions is introduced. The method first puts a finite number of large probes on the protein exterior surface and then, considering both large probes and atomic balls as obstacles for the small probe, the method computes the exact shape of the regions for the small probe. This is all achieved with Voronoi diagrams, which help with the safe navigation of spherical probes among spherical obstacles. Detected regions are internally represented as graphs of vertices and edges describing possible movements of the center of the small probe on Voronoi edges. The surface bounding each region is obtained from this representation and used for visualization, volume estimation, and comparison with other approaches. © 2019 Wiley Periodicals, Inc.

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Section: Methodsmentioning

confidence: 99%

“…These segments are called bridges and lie on Voronoi faces. [21,22] Bridges for the situation in Figure 4c are depicted in Figure 4d.…”

Section: Voronoi Diagrams and Related Conceptsmentioning

confidence: 99%

Voronoi‐based detection of pockets in proteins defined by large and small probes

Maňák

2019

J Comput Chem

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“…However, large cavities in macromolecular complexes may not be described by the voids of the molecular surface, because they often contain entrance holes. Manak, M. (2019) recently proposed a modified definition of Masuya-Doi-Kawabata-Go (MDKG) pocket [18], implementing it using a Voronoi-based method based on the sphere representation of molecules and probes [19,20]. In this study, we have designated the pocket defined by Manak as a "cave pocket", owing to the properties it shares with both closed cavities and pockets.…”

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confidence: 99%

Detection of cave pockets in large molecules: Spaces into which internal probes can enter, but external probes from outside cannot

Kawabata

2019

BIOPHYSICS

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Geometric features of macromolecular shapes are important for binding with other molecules. Kawabata, T. and Go, N. (2007) defined a pocket as a space into which a small probe can enter, but a large probe cannot. In 2010, mathematical morphology (MM) was introduced to provide a more rigorous definition, and the program GHECOM was developed using the grid-based representation of molecules. This method was simple, but effective in finding the binding sites of small compounds on protein surfaces. Recently, many 3D structures of large macromolecules have been determined to contain large internal hollow spaces. Identification and size estimation of these spaces is important for characterizing their function and stability. Therefore, we employ the MM definition of pocket proposed by Manak, M. (2019)-a space into which an internal probe can enter, but an external probe cannot enter from outside of the macromolecules. This type of space is called a "cave pocket", and is identified through molecular grid-representation. We define a "cavity" as a space into which a probe can enter, but cannot escape to the outside. Three types of spaces: cavity, pocket, and cave pocket were compared both theoretically and numerically. We proved that a cave pocket includes a pocket, and it is equal to a pocket if no cavity is found. We compared the three types of spaces for a variety of molecules with different-sized spherical probes; cave pockets were more sensitive than pockets for finding almost closed internal holes, allowing for more detailed representations of internal surfaces than cavities provide.

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Hybrid Voronoi diagrams, their computation and reduction for applications in computational biochemistry

Maňák

Zemek

Szkandera

et al. 2017

Journal of Molecular Graphics and Modelling

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Exploration of Empty Space among Spherical Obstacles via Additively Weighted Voronoi Diagram

Cited by 4 publications

References 34 publications

Voronoi‐based detection of pockets in proteins defined by large and small probes

Voronoi‐based detection of pockets in proteins defined by large and small probes

Detection of cave pockets in large molecules: Spaces into which internal probes can enter, but external probes from outside cannot

Hybrid Voronoi diagrams, their computation and reduction for applications in computational biochemistry

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