iBioProVis: Interactive Visualization and Analysis of Compound Bioactivity Space

Dönmez, Ataberk
Rifaioğlu, Ahmet Süreyya
Acar, Aybar Can
Doğan, Tunca
Martin, Maria Jesus
Atalay, Rengül
Atalay, Mehmet Volkan
Visualization and interpretation of high-dimensional chemical compound and target space is critical for better understanding of the mechanisms of bioactivity space and drug discovery process. Here, we describe iBioProVis, which projects and visualizes compounds on 2D space based on their structural features in the context of their cognate targets. The inputs are pairs of ChEMBL target identifiers and the output is the 2D projection plot of the active compounds of the input targets. By looking at the distribution of compounds(i.e.,points) in a projection, the user can infer that compounds that are close to each other may possess similar binding characteristics. One of the interesting additional feature is that the user can also provide a list of SMILES strings as input. By this way, the user can observe the projection of these compounds along with the projections of previously reported active compounds of the selected targets. iBioProVis provides an interactive environment where users can select different compounds and get several information about them. iBioProVis also provides cross-references to well-known databases so that users can easily relate the entities and navigate to those databases by clickable links. iBioProVis is freely available at http://ibioprovis.kansil.org/.


iBioProVis: interactive visualization and analysis of compound bioactivity space
Dönmez, Ataberk; Rifaioğlu, Ahmet Süreyya; Atalay, Rengül; Atalay, Mehmet Volkan (Oxford University Press (OUP), 2020-08-15)
SUMMARY: iBioProVis is an interactive tool for visual analysis of the compound bioactivity space in the context of target proteins, drugs and drug candidate compounds. iBioProVis tool takes target protein identifiers and, optionally, compound SMILES as input, and uses the state-of-the-art non-linear dimensionality reduction method t-Distributed Stochastic Neighbor Embedding (t-SNE) to plot the distribution of compounds embedded in a 2D map, based on the similarity of structural properties of compounds and i...
Nonlinear Finite Element Analysis Versus Ex Vivo Strain Gauge Measurements on Immediately Loaded Implants
Eser, Atilim; AKÇA, KIVANÇ; Eckert, Steven; Cehreli, Murat Cavit (2009-05-01)
Purpose: To evaluate the level of agreement between nonlinear finite element stress analysis (NL-FEA) and ex vivo strain gauge analysis (EV-SGA) on immediately loaded implants. Materials and Methods: Four 4.1-mm-diameter, 12-mm-long implants were placed bilaterally into the lateral and first premolar regions of completely edentulous maxillae of four human cadavers. Two-element 90-degree rosette strain gauges were bonded to the labial cortical bone around the implants, and 100 N maximal load was applied over...
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In this analytical study, free vibration analyses of a 3d mixed formulation beam element are performed by adopting force-based consistent mass matrix that incorporates shear and rotary inertia effects. The force-based approach takes into account the actual distribution of mass of an element in the derivation of the mass matrix. Moreover, the force-based approach enables accurate determination of free vibration frequencies of members with varying geometry and material distribution without any need for specif...
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Citation Formats
A. Dönmez et al., “iBioProVis: Interactive Visualization and Analysis of Compound Bioactivity Space,” 2019, Accessed: 00, 2021. [Online]. Available: https://www.iscb.org/cms_addon/conferences/ismbeccb2019/biovis.php.