Three-Dimensional Analysis of Binding Sites for Predicting Binding Affinities in Drug Design

Date

2019-11-01

Author

Erdas-Cicek, Ozlem
Atac, Ali Osman
Gurkan-Alp, A. Selen
Buyukbingol, Erdem
Alpaslan, Ferda Nur

Metadata

Show full item record

This work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License.

Item Usage Stats

234
views

0
downloads

Understanding the interaction between drug molecules and proteins is one of the main challenges in drug design. Several tools have been developed recently to decrease the complexity of the process. Artificial intelligence and machine learning methods offer promising results in predicting the binding affinities. It becomes possible to do accurate predictions by using the known protein-ligand interactions. In this study, the electrostatic potential values extracted from 3-dimensional grid cubes of the drug-protein binding sites are used for predicting binding affinities of related complexes. A new algorithm with a dynamic feature selection method was implemented, which is derived from Compressed Images For Affinity Prediction (CIFAP) study, to predict binding affinities of Checkpoint Kinase 1 and Caspase 3 inhibitors.

Subject Keywords

General Chemistry, General Chemical Engineering, Library and Information Sciences, Computer Science Applications

URI

https://hdl.handle.net/11511/36320

Journal

JOURNAL OF CHEMICAL INFORMATION AND MODELING

DOI

https://doi.org/10.1021/acs.jcim.9b00206

Collections

Department of Computer Engineering, Article

Suggestions

OpenMETU
Core

Amber-Compatible Parametrization Procedure for Peptide-like Compounds: Application to 1,4-and 1,5-Substituted Triazole-Based Peptidomimetics Marıon, Antoıne; Kracker, Oliver; Froehr, Tanja; Latajka, Rafal; Sewald, Norbert; Antes, Iris (American Chemical Society (ACS), 2018-01-01) Peptidomimetics are molecules of particular interest in the context of drug design and development. They are proteolytically and metabolically more stable than their natural peptide counterparts but still offer high specificity toward their biological targets. In recent years, 1,4- and 1,5-disubstituted 1,2,3-triazole-based peptidomimetics have emerged as promising lead compounds for the design of various inhibitory and tumor-targeting molecules as well as for the synthesis of peptide analogues. The growing...
3D analysis of the binding sites for predicting binding affinities in drug design Ataç, Ali Osman; Alpaslan, Ferda Nur; Büyükbingöl, Erdem; Department of Computer Engineering (2014) Understanding the interaction between drug molecules and proteins is one of the main challenges in drug design. Several tools have been developed recently to decrease the complexity of the process. Artificial intelligence and machine learning methods have promising results in predicting the affinities. Recently, accurate estimations have been performed by extracting the electrostatic potentials from images of the drug-protein binding sites which were generated by autodocking simulator. In this study, a new ...
Development of a synthetic strategy for Water soluble tripodal receptors: Two novel fluorescent receptors for highly selective and sensitive detections of Fe3+ and Cu2+ ions and biological evaluation USLU, AYLİN; Ozcan, Elif; TÜMAY, SÜREYYA OĞUZ; Kazan, Hasan Huseyin; YEŞİLOT, SERKAN (Elsevier BV, 2020-04-01) A general synthetic strategy is developed to synthesize water soluble receptors by employing tripodal system based on a cyclotriphosphaze platform. The developed model is successfully synthesized and characterized by using elemental analysis, FT-IR, MALDI-TOF, H-1 NMR, C-13 NMR and P-31 NMR techniques. The fluorescence sensing performance of prepared water soluble tripodal systems were evaluated by UV/Vis and fluorescence spectroscopies. According to obtained results, two novel water-soluble sensing platfor...
Dynamic analysis of changes in diffusion and sorption parameters in the reaction of SO2with activated soda ash Doǧu, Gülsen; Keskin, Alne; Doǧu, Timur (Wiley, 1988-8) Variations in pore structure cause significant changes in diffusion resistance and adsorption characteristics during the reaction of SO2 with activated soda. Breakthrough and moment analysis of the SO2‐activated soda ash reaction showed that the effective diffusion coefficient of SO2 in the solid product (mostly Na2SO3) was about three times smaller than its value in the original activated soda. About 30% of the diffusion flux of SO2 in the solid product was found to be due to surface diffusion. The adsorpt...
A novel synthesis of optically active alpha-amino acids Demir, Ayhan Sıtkı (Walter de Gruyter GmbH, 1997-01-01) A new enantioselective synthesis of alpha- amino acids are described in which the key step is the enantioselective reduction of E, and Z furyl ketone oxime ethers with chiral boron complexes. The chirality of amino acid is fully controlled by appropriate choice of geometrical isomer of the oxime ether.

Citation Formats

O. Erdas-Cicek, A. O. Atac, A. S. Gurkan-Alp, E. Buyukbingol, and F. N. Alpaslan, “Three-Dimensional Analysis of Binding Sites for Predicting Binding Affinities in Drug Design,” JOURNAL OF CHEMICAL INFORMATION AND MODELING, pp. 4654–4662, 2019, Accessed: 00, 2020. [Online]. Available: https://hdl.handle.net/11511/36320.