Show/Hide Menu
Hide/Show Apps
Logout
Türkçe
Türkçe
Search
Search
Login
Login
OpenMETU
OpenMETU
About
About
Open Science Policy
Open Science Policy
Communities & Collections
Communities & Collections
Help
Help
Frequently Asked Questions
Frequently Asked Questions
Guides
Guides
Thesis submission
Thesis submission
MS without thesis term project submission
MS without thesis term project submission
Publication submission with DOI
Publication submission with DOI
Publication submission
Publication submission
Supporting Information
Supporting Information
General Information
General Information
Copyright, Embargo and License
Copyright, Embargo and License
Contact us
Contact us
Predicting the effect of hydrophobicity surface on binding affinity of PCP-like compounds using machine learning methods
Download
index.pdf
Date
2011
Author
Yoldaş, Mine
Metadata
Show full item record
Item Usage Stats
211
views
74
downloads
Cite This
This study aims to predict the binding affinity of the PCP-like compounds by means of molecular hydrophobicity. Molecular hydrophobicity is an important property which aff ects the binding affinity of molecules. The values of molecular hydrophobicity of molecules are obtained on three-dimensional coordinate system. Our aim is to reduce the number of points on the hydrophobicity surface of the molecules. This is modeled by using self organizing maps (SOM) and k-means clustering. The feature sets obtained from SOM and k-means clustering are used in order to predict binding affinity of molecules individually. Support vector regression and partial least squares regression are used for prediction.
Subject Keywords
Support vector machines
,
Machine learning
URI
http://etd.lib.metu.edu.tr/upload/12613215/index.pdf
https://hdl.handle.net/11511/20556
Collections
Graduate School of Natural and Applied Sciences, Thesis
Suggestions
OpenMETU
Core
The effect of aromatic diboronic acid on characteristics of polybenzoxazine based on phenol and 4-aminomethylbenzoate
İPEK, HALİL; Hacaloğlu, Jale (2018-11-23)
In this study, a polybenzoxazine, (PPab) based on phenol and 4-aminomethyl benzoate and its composites containing various amounts of 1,4-benzene diboronic acid, (BDBA) were synthesized by stepwise curing. It has been determined that both thermal stability and char yield were increased as the amount of BDBA incorporated was increased. The improvements in thermal characteristics were associated with condensation reactions of B-OH of BDBA and not only with hydroxyl groups of polybenzoxazine but also ester grou...
The effect of 3-hydroxyphenylboronic acid on thermal characteristics of polybenzoxazine based on phenol and 4-aminomethylbenzoate
Ipek, Halil; Hacaloğlu, Jale (2020-07-01)
In this study, a polybenzoxazine, (PPab) based on phenol and 4-aminomethyl benzoate and its composites containing various amounts of 3-hydroxyphenylboronic acid, (HB) were prepared by stepwise curing. It has been found that thermal properties of composites were improved as the amount of HB introduced was increased. The improvements in thermal characteristics were associated with condensation reactions of hydroxyl groups of polybenzoxazine and ester groups on the aniline linkages yielding a highly cross-link...
Prediction of the effects of single amino acid variations on protein functionality with structural and annotation centric modeling
Cankara, Fatma; Tunçbağ, Nurcan; Department of Bioinformatics (2020)
Whole-genome and exome sequencing studies have indicated that genomic variations may cause deleterious effects on protein functionality via various mechanisms. Single nucleotide variations that alter the protein sequence, and thus, the structure and the function, namely non-synonymous SNPs (nsSNP), are associated with many genetic diseases in human. The current rate of manually annotating the reported nsSNPs cannot catch up with the rate of producing new sequencing data. To aid this process, automated compu...
Effects of oxidative functionalized and aminosilanized carbon nanotubes on the crystallization behaviour of polyamide-6 nanocomposites
Kaynak, Cevdet (2014-04-01)
The purpose of this study is to investigate effects of oxidative functionalized and aminosilanized carbon nanotubes on the (1) isothermal and (2) non-isothermal crystallization kinetics of polyamide-6 by DSC analyses, and (3) crystal structure of injection molded specimens by XRD analyses. Nanocomposites were compounded by using melt mixing technique via twin screw extrusion. Due to basically very effective heterogeneous nucleation effect, both increasing amount and surface functionalization of carbon nanot...
An application of CIFAP for predicting the binding affinity of Chk1 inhibitors derived from 2-aminothiazole-4-carboxamide
Konyar, Dilan; Erdas, Ozlem; Alpaslan, Ferda Nur; Buyukbingol, Erdem (2017-11-01)
Investigation of protein-ligand interactions obtained from experiments has a crucial part in the design of newly discovered and effective drugs. Analyzing the data extracted from known interactions could help scientists to predict the binding affinities of promising ligands before conducting experiments. The objective of this study is to advance the CIFAP (compressed images for affinity prediction) method, which is relevant to a protein-ligand model, identifying 2D electrostatic potential images by separati...
Citation Formats
IEEE
ACM
APA
CHICAGO
MLA
BibTeX
M. Yoldaş, “Predicting the effect of hydrophobicity surface on binding affinity of PCP-like compounds using machine learning methods,” M.S. - Master of Science, Middle East Technical University, 2011.
