Protein-Ligand Komplekslerinin Konvolüsyenel Sinir Ağları ile Moleküler Tanınması

dc.contributor.advisor Aydın, Zafer
dc.contributor.author Güner, Hüseyin
dc.contributor.other 01. Abdullah Gül University
dc.contributor.other 02. 04. Bilgisayar Mühendisliği
dc.contributor.other 02. Mühendislik Fakültesi
dc.contributor.other 04. Yaşam ve Doğa Bilimleri Fakültesi
dc.contributor.other 04.02. Moleküler Biyoloji ve Genetik
dc.date.accessioned 2022-09-01T11:13:29Z
dc.date.available 2022-09-01T11:13:29Z
dc.date.issued 2022 en_US
dc.date.issued 2022
dc.date.submitted 2022-01
dc.description.abstract As a sub-discipline of Artificial Intelligence, deep neural networks have received enormous interest in research and industrial applications over the last decades owing to their highly successful performance in addressing and solving broad areas of problems. Hence, especially hitherto achievements in computer-aided drug design brought an extra impetus with the novel deep learning approaches in structure-based drug design etiology. Our group offers a novel convolutional neural network model, deepMLR, that casts insight into the molecular recognition of ligand molecules and a receptor protein molecule. Having compared our model and a few other existing models with a case study of a traditional approach, herein, we present the success story of a deep learning model straight. en_US
dc.description.abstract Yapay Zeka'nın bir alt disiplini olarak derin sinir ağları, geniş spektrumdaki problem alanlarını ele alma ve çözmedeki son derece başarılı performansları nedeniyle, son on yılda (özellikle) araştırma ve endüstriyel uygulamalarda büyük bir ilgi görmeye başladı. Özellikle son zamanlardaki, bilgisayar destekli ilaç tasarımındaki başarıları nedeniyle, yapı tabanlı ilaç tasarımı etiyolojislerindeki yeni derin öğrenme yaklaşımlarına karşı ekstra bir ivme kazanmıştır. Grubumuz, ligand moleküllerinin ve bir reseptör protein molekülünün moleküler olarak tanınması hakkında bir fikir veren yeni bir konvolüsyonel sinir ağı modeli sunmaktadır. Diğer mevcut modellerle ve modelimizle geleneksel bir yaklaşımın örnek çalışmasıyla karşılaştırıldığında, burada derin bir öğrenme modelinin başarı hikayesini sunuyoruz.
dc.description.tableofcontents 1. INTRODUCTION .................................................................................................... 1 2. STRUCTURE BASED DRUG DISCOVERY........................................................ 3 2.1 MOLECULAR RECOGNITION ..................................................................................... 5 2.1.1 Thermodynamic Entities.................................................................................. 6 2.2 LIGAND-PROTEIN AFFINITY SCORING FUNCTIONS................................................... 7 2.3 MOLECULAR DYNAMICS SIMULATIONS ................................................................... 8 2.3.1 Force fields in protein-ligand complexes ........................................................ 9 2.4 THE MM/PBSA AND MM/GBSA METHODS............................................................ 9 3. DEEP LEARNING METHODS............................................................................ 11 3.1 ARTIFICIAL INTELLIGENCE IN DRUG DISCOVERY................................................... 11 3.1.1 Feed-forward neural networks ...................................................................... 12 3.1.2 Convolutional Neural Networks .................................................................... 16 4. EXPERIMENTAL RESULTS............................................................................... 20 4.1 COMPUTATIONAL RESOURCES ............................................................................... 20 4.2 CONVENTIONAL/TRADITIONAL SBDD CAMPAIGN ................................................ 20 4.2.1 Structural Data Files and Preparation for Docking Experiments ................ 20 4.2.2 Docking experiments...................................................................................... 22 4.2.3 MD Experiments............................................................................................ 24 4.3 A 3D CNN MODEL BY PAFNUCY............................................................................ 25 4.3.1 Datasets ......................................................................................................... 26 4.3.2 Architecture of the network............................................................................ 27 4.3.3 Training with Back-propagation ................................................................... 27 4.3.4 Results and metrics of back-propagation ...................................................... 28 4.3.5 Binding affinity of 2SHP with the leads......................................................... 30 4.4 OUR MODEL DEEPMLR......................................................................................... 30 4.4.1 Architecture of DeepMLR.............................................................................. 32 4.4.2 Training and evaluation of DeepMLR........................................................... 34 4.4.3 Evaluation Metrics......................................................................................... 35 4.4.4 Results of experiments run by DeepMLR....................................................... 35 5. CONCLUSIONS AND FUTURE PROSPECTS ................................................. 40 5.1 CONCLUSIONS ........................................................................................................ 40 5.2 SOCIETAL IMPACT AND CONTRIBUTION TO GLOBAL SUSTAINABILITY................... 41 5.3 FUTURE PROSPECTS ............................................................................................... 42 6. BIBLIOGRAPHY................................................................................................... 43 en_US
dc.identifier.uri https://tez.yok.gov.tr/UlusalTezMerkezi/TezGoster?key=5XiSE4yCP_gmnukpMEp65Vo_kydwNinm2MylYLD2kZ44gZWfOA-YIr_4H7Myzveg
dc.identifier.uri https://hdl.handle.net/20.500.12573/1366
dc.language.iso eng en_US
dc.language.iso en
dc.publisher Abdullah Gül Üniversitesi Fen Bilimleri Enstitüsü en_US
dc.rights info:eu-repo/semantics/openAccess en_US
dc.subject Bilgisayar Mühendisliği Bilimleri-Bilgisayar Ve Kontrol
dc.subject Konvolüsyon
dc.subject Computer Engineering And Computer Science And Control en_US
dc.subject Moleküler Tanı
dc.subject Convolution en_US
dc.subject Protein Bağlama
dc.subject Molecular Identification en_US
dc.subject Sinir Ağları
dc.subject Protein Binding en_US
dc.subject İlaçlar
dc.subject Nerve Net en_US
dc.subject Drugs en_US
dc.title Protein-Ligand Komplekslerinin Konvolüsyenel Sinir Ağları ile Moleküler Tanınması
dc.title Molecular Recognition of Protein-Ligand Complexes Via Convolutional Neural Networks en_US
dc.title.alternative Protein-ligand komplekslerinin konvolüsyenel sinir ağları ile moleküler tanınması en_US
dc.type Master Thesis en_US
dspace.entity.type Publication
gdc.author.institutional Güner, Hüseyin
gdc.author.institutional Aydın, Zafer
gdc.description.department AGÜ, Fen Bilimleri Enstitüsü, Elektrik ve Bilgisayar Mühendisliği Ana Bilim Dalı en_US
gdc.description.endpage 62
gdc.description.publicationcategory Tez en_US
gdc.identifier.yoktezid 714262
relation.isAuthorOfPublication cf1c8c63-bd1c-4d84-9a09-a5c0b3c04d52
relation.isAuthorOfPublication a26c06af-eae3-407c-a21a-128459fa4d2f
relation.isAuthorOfPublication.latestForDiscovery cf1c8c63-bd1c-4d84-9a09-a5c0b3c04d52
relation.isOrgUnitOfPublication 665d3039-05f8-4a25-9a3c-b9550bffecef
relation.isOrgUnitOfPublication 52f507ab-f278-4a1f-824c-44da2a86bd51
relation.isOrgUnitOfPublication ef13a800-4c99-4124-81e0-3e25b33c0c2b
relation.isOrgUnitOfPublication 4eea69bf-e8aa-4e3e-ab18-7587ac1d841b
relation.isOrgUnitOfPublication f1a6e7de-5c27-471c-ada8-77b7e5558b19
relation.isOrgUnitOfPublication.latestForDiscovery 665d3039-05f8-4a25-9a3c-b9550bffecef

Files

Original bundle

Now showing 1 - 1 of 1
Loading...
Thumbnail Image
Name:
714262_hüseyingüner.pdf
Size:
3.02 MB
Format:
Adobe Portable Document Format
Description:
tez

License bundle

Now showing 1 - 1 of 1
No Thumbnail Available
Name:
license.txt
Size:
1.44 KB
Format:
Item-specific license agreed upon to submission
Description: