Voronota: A fast and reliable tool for computing the vertices of the Voronoi diagram of atomic balls

Olechnovič, Kliment; Venclovas, C̆eslovas

doi:10.1002/jcc.23538

Cited by 70 publications

(75 citation statements)

References 34 publications

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“…We also used a more permissive version, the binding site CAD‐score, as an analog to IPS to evaluate binding site prediction. The CAD‐score values were calculated using a new version of CAD‐score implemented in the Voronota package …”

Section: Methodsmentioning

confidence: 99%

Structural modeling of protein complexes: Current capabilities and challenges

2019

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Proteins frequently interact with each other, and the knowledge of structures of the corresponding protein complexes is necessary to understand how they function. Computational methods are increasingly used to provide structural models of protein complexes. Not surprisingly, community‐wide Critical Assessment of protein Structure Prediction (CASP) experiments have recently started monitoring the progress in this research area. We participated in CASP13 with the aim to evaluate our current capabilities in modeling of protein complexes and to gain a better understanding of factors that exert the largest impact on these capabilities. To model protein complexes in CASP13, we applied template‐based modeling, free docking and hybrid techniques that enabled us to generate models of the topmost quality for 27 of 42 multimers. If templates for protein complexes could be identified, we modeled the structures with reasonable accuracy by straightforward homology modeling. If only partial templates were available, it was nevertheless possible to predict the interaction interfaces correctly or to generate acceptable models for protein complexes by combining template‐based modeling with docking. If no templates were available, we used rigid‐body docking with limited success. However, in some free docking models, despite the incorrect subunit orientation and missed interface contacts, the approximate location of protein binding sites was identified correctly. Apparently, our overall performance in docking was limited by the quality of monomer models and by the imperfection of scoring methods. The impact of human intervention on our results in modeling of protein complexes was significant indicating the need for improvements of automatic methods.

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Section: Methodsmentioning

confidence: 99%

Structural modeling of protein complexes: Current capabilities and challenges

2019

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“…The algorithm computes a component of the Voronoi 1‐skeleton by tracing edges incident to already discovered vertices. It can be extended to find all components, space‐filtering techniques improve its efficiency and implementations are available …”

Section: Methodsmentioning

confidence: 99%

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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“…With crystal structures of protein complexes for which experimental mutation data is available, the protein–protein interface is calculated using Voronoï decomposition and the total surface area of each surface type is determined. The mutant form is modeled and the surface type composition of the mutant is calculated.…”

Section: Methodsmentioning

confidence: 99%

“…Interactions between the four atom types give rise to ten interaction types. Intermolecular atomic contact areas for each interaction type were determined using Voronoï diagrams, calculated using the CAD‐score program . Interface areas for each interaction type are given in Supporting Information Table S1.…”

Section: Methodsmentioning

confidence: 99%