Investigating the Effect of GLU283 Protonation State on the Conformational Heterogeneity of CCR5 by Molecular Dynamics Simulations
Journal of Chemical Information and Modeling, Vol. 64, Ekim 2024, ISSN: 1549-9596
DOĞAN BERNA,DURDAĞI SERDAR
@article{article,
author = {DOĞAN BERNA,DURDAĞI SERDAR},
title = {Investigating the Effect of GLU283 Protonation State on the Conformational Heterogeneity of CCR5 by Molecular Dynamics Simulations},
journal = {Journal of Chemical Information and Modeling},
year = 2024,
month = 10,
volume = 64
}
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Efficient, rapid, and high-yield synthesis of aryl Schiff base derivatives and their in vitro and in silico inhibition studies of hCA I, hCA II, AChE, and BuChE
ARCHIV DER PHARMAZIE, Vol. 357, No. 7, Temmuz 2024, s. 2300266, ISSN: 0365-6233
ÖZİL MUSA,BALAYDIN HALİS TÜRKER,DOĞAN BERNA,ŞENTÜRK MURAT,DURDAĞI SERDAR
@article{article,
author = {ÖZİL MUSA,BALAYDIN HALİS TÜRKER,DOĞAN BERNA,ŞENTÜRK MURAT,DURDAĞI SERDAR},
title = {Efficient, rapid, and high-yield synthesis of aryl Schiff base derivatives and their in vitro and in silico inhibition studies of hCA I, hCA II, AChE, and BuChE},
journal = {ARCHIV DER PHARMAZIE},
year = 2024,
number = 7,
pages = {2300266},
month = 7,
volume = 357
}
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Machine Learning Approaches to Predict the Selectivity of Compounds against HDAC1 and HDAC6
JOURNAL OF COMPUTATIONAL BIOPHYSICS AND CHEMISTRY, Vol. 23, No. 6, Haziran 2024, s. 837-850, ISSN: 2737-4165
DOĞAN BERNA
@article{article,
author = {DOĞAN BERNA},
title = {Machine Learning Approaches to Predict the Selectivity of Compounds against HDAC1 and HDAC6},
journal = {JOURNAL OF COMPUTATIONAL BIOPHYSICS AND CHEMISTRY},
year = 2024,
number = 6,
pages = {837-850},
month = 6,
volume = 23
}
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Quantitative prediction of compound selectivity against HDAC1 and HDAC6 isoforms
ordon Research Conference on Computer Aided Drug Design, Vermont/AMERİKA BİRLEŞİK DEVLETLERİ, 16 Temmuz 2023
DOĞAN BERNA
@inproceedings{inproceedings,
author = {DOĞAN BERNA},
title = {Quantitative prediction of compound selectivity against HDAC1 and HDAC6 isoforms},
year = 2023,
month = 7
}
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Investigating the Conformational Heterogeneity of CCR5
by Molecular Dynamics Simulations
11th Visegrad Symposium on Biomolecular Interactions, Röjtökmuzsaj/MACARİSTAN, 20 Haziran 2023
DOĞAN BERNA, DURDAĞI SERDAR
@inproceedings{inproceedings,
author = {DOĞAN BERNA, DURDAĞI SERDAR},
title = {Investigating the Conformational Heterogeneity of CCR5
by Molecular Dynamics Simulations},
year = 2023,
month = 6
}
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Prediction of HIV-1 protease resistance using genotypic, phenotypic, and molecular information with artificial neural networks
PeerJ, Vol. 11, Mart 2023, ISSN: 2167-8359
TUNÇ HÜSEYİN, DOĞAN BERNA, DARENDELİ KİRAZ BÜSRA NUR, SARI MURAT, DURDAĞI SERDAR, KOTİL ENES SEYFULLAH
@article{article,
author = {TUNÇ HÜSEYİN, DOĞAN BERNA, Darendeli Kiraz Büsra Nur, SARI MURAT, DURDAĞI SERDAR, KOTİL ENES SEYFULLAH},
title = {Prediction of HIV-1 protease resistance using genotypic, phenotypic, and molecular information with artificial neural networks},
journal = {PeerJ},
year = 2023,
month = 3,
volume = 11
}
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First MD Simulations of Full Structure HIV1/GP120 in Complex with CD4 and CCR5
7th International Bau Drug Design Congress: Recent Developments in Structure- and Ligand-based Drug Design Methodologies, İstanbul/TÜRKİYE, 19 Aralık 2022
DOĞAN BERNA, DURDAĞI SERDAR
@inproceedings{inproceedings,
author = {DOĞAN BERNA, DURDAĞI SERDAR},
title = {First MD Simulations of Full Structure HIV1/GP120 in Complex with CD4 and CCR5},
year = 2022,
month = 12
}
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A novel BH3 mimetic Bcl-2 inhibitor promotes autophagic cell death and reduces in vivo Glioblastoma tumor growth
Springer Science and Business Media LLC, Vol. 8, Ekim 2022, ISSN: 2058-7716
CALİS SEYMA, DOĞAN BERNA, DURDAĞI SERDAR, CELEBİ CELEBİ, YAPICIER ÖZLEM, KILIÇ TÜRKER, TAHİR TURANLI EDA, AVŞAR TİMUÇİN
@article{article,
author = {Calis Seyma, DOĞAN BERNA, DURDAĞI SERDAR, Celebi Celebi, YAPICIER ÖZLEM, KILIÇ TÜRKER, TAHİR TURANLI EDA, AVŞAR TİMUÇİN},
title = {A novel BH3 mimetic Bcl-2 inhibitor promotes autophagic cell death and reduces in vivo Glioblastoma tumor growth},
journal = {Springer Science and Business Media LLC},
year = 2022,
month = 10,
volume = 8
}
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Design and synthesis of novel caffeic acid phenethyl ester (CAPE) derivatives and their biological activity studies in glioblastoma multiforme (GBM) cancer cell lines
JOURNAL OF MOLECULAR GRAPHICS & MODELLING, Vol. 113, Haziran 2022, ISSN: 1093-3263
SUCU BİLGESU ONUR, KOÇ ELİF BEYZA, SAVLUĞ İPEK ÖZGECAN, MİRAT AFRANUR, ALMAS FURKAN, GÜZEL MELİKE AYBALA, DOĞAN BERNA, ULUDAĞ DAMLA, KARAKAŞ NİHAL, DURDAĞI SERDAR, GÜZEL MUSTAFA
@article{article,
author = {SUCU BİLGESU ONUR, Koç Elif Beyza, Savluğ İpek Özgecan, Mirat Afranur, Almas Furkan, Güzel Melike Aybala, DOĞAN BERNA, Uludağ Damla, Karakaş Nihal, DURDAĞI SERDAR, GÜZEL MUSTAFA},
title = {Design and synthesis of novel caffeic acid phenethyl ester (CAPE) derivatives and their biological activity studies in glioblastoma multiforme (GBM) cancer cell lines},
journal = {JOURNAL OF MOLECULAR GRAPHICS & MODELLING},
year = 2022,
month = 6,
volume = 113
}
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Applications Of Molecular Modeling Approaches For The Identification Of Novel Sars-Cov-2 Rdrp Inhibitors
2. Computer-Aided Drug Design Symposium and Workshop - Linking Design, Biology, Chemistry and Medicine, İstanbul/TÜRKİYE, 11 Mayıs 2022
DOĞAN BERNA, DURDAĞI SERDAR, MOTAPANYANE, NTSOAKİ BAİTHEDİ
@inproceedings{inproceedings,
author = {DOĞAN BERNA, DURDAĞI SERDAR, Motapanyane, Ntsoaki Baithedi},
title = {Applications Of Molecular Modeling Approaches For The Identification Of Novel Sars-Cov-2 Rdrp Inhibitors},
year = 2022,
month = 5
}
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Screening of Clinically Approved and Investigation Drugs as Potential Inhibitors of SARS-CoV-2: A Combined in silico and in vitro Study
MOLECULAR INFORMATICS, Vol. 41, No. 2, Şubat 2022, ISSN: 1868-1743
DURDAĞI SERDAR, ORHAN MÜGE DİDEM, AKSOYDAN BUSECAN, CALİS SEYMA, DOĞAN BERNA, ŞAHİN KADER, SHAHRAKİ AİDA, IYİSON NECLA BİRGÜL, AVŞAR TİMUÇİN
@article{article,
author = {DURDAĞI SERDAR, Orhan Müge Didem, Aksoydan Busecan, Calis Seyma, DOĞAN BERNA, ŞAHİN KADER, Shahraki Aida, Iyison Necla Birgül, AVŞAR TİMUÇİN},
title = {Screening of Clinically Approved and Investigation Drugs as Potential Inhibitors of SARS-CoV-2: A Combined in silico and in vitro Study},
journal = {MOLECULAR INFORMATICS},
year = 2022,
number = 2,
month = 2,
volume = 41
}
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Near-physiological-temperature serial crystallography reveals conformations of SARS-CoV-2 main protease active site for improved drug repurposing
STRUCTURE, Vol. 29, No. 12, Aralık 2021, s. 1382, ISSN: 0969-2126
DURDAĞI SERDAR, DOĞAN BERNA, DEMİRCİ HASAN
@article{article,
author = {DURDAĞI SERDAR, DOĞAN BERNA, DEMİRCİ HASAN},
title = {Near-physiological-temperature serial crystallography reveals conformations of SARS-CoV-2 main protease active site for improved drug repurposing},
journal = {STRUCTURE},
year = 2021,
number = 12,
pages = {1382},
month = 12,
volume = 29
}
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Synthesis, molecular docking and molecular dynamics studies of novel tacrine-carbamate derivatives as potent cholinesterase inhibitors
BIOORGANIC CHEMISTRY, Vol. 115, Ekim 2021, ISSN: 0045-2068
ÖZTEN ÖZGE, ZENGİN KURT BELMA, SÖNMEZ FATİH, DOĞAN BERNA, DURDAĞI SERDAR
@article{article,
author = {Özten Özge, ZENGİN KURT BELMA, SÖNMEZ FATİH, DOĞAN BERNA, DURDAĞI SERDAR},
title = {Synthesis, molecular docking and molecular dynamics studies of novel tacrine-carbamate derivatives as potent cholinesterase inhibitors},
journal = {BIOORGANIC CHEMISTRY},
year = 2021,
month = 10,
volume = 115
}
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Investigation of supramolecular interaction of quercetin with N,N-dimethylamine-functionalized p-sulfonated calix[4,8]arenes using molecular modeling and their in vitro cytotoxic response towards selected cancer cells
NEW JOURNAL OF CHEMISTRY, Vol. 45, No. 39, Ekim 2021, s. 18443-18452, ISSN: 1144-0546
MEHMET OĞUZ, DOĞAN BERNA, DURDAĞI SERDAR, KARAKURT SERDAR, YILMAZ MUSTAFA
@article{article,
author = {Mehmet Oğuz, DOĞAN BERNA, DURDAĞI SERDAR, KARAKURT SERDAR, Yılmaz Mustafa},
title = {Investigation of supramolecular interaction of quercetin with N,N-dimethylamine-functionalized p-sulfonated calix[4,8]arenes using molecular modeling and their in vitro cytotoxic response towards selected cancer cells},
journal = {NEW JOURNAL OF CHEMISTRY},
year = 2021,
number = 39,
pages = {18443-18452},
month = 10,
volume = 45
}
|
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Discovery of promising antineoplastic drugs against the USP7 deubiquitinating enzyme: A pharmacophore-based FDA-approved and investigational drugs repurposing study
Proceedings of the American Association for Cancer Research Annual Meeting 2021, 17 Mayıs 2021
KANAN DUAA, DOĞAN BERNA, DURDAĞI SERDAR, KANAN TAREK
@inproceedings{inproceedings,
author = {Kanan Duaa, DOĞAN BERNA, DURDAĞI SERDAR, Kanan Tarek},
title = {Discovery of promising antineoplastic drugs against the USP7 deubiquitinating enzyme: A pharmacophore-based FDA-approved and investigational drugs repurposing study},
year = 2021,
month = 5
}
|
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An Integrated in silico Approach and in vitro Study for the Discovery of Small-Molecule USP7 Inhibitors as Potential Cancer Therapies
CHEMMEDCHEM, Vol. 16, No. 3, Şubat 2021, s. 555-567, ISSN: 1860-7179
KANAN DUAA, KANAN TARIK, DOĞAN BERNA, ORHAN MÜGE DİDEM, AVŞAR TİMUÇİN, DURDAĞI SERDAR
@article{article,
author = {Kanan Duaa, Kanan Tarık, DOĞAN BERNA, Orhan Müge Didem, AVŞAR TİMUÇİN, DURDAĞI SERDAR},
title = {An Integrated in silico Approach and in vitro Study for the Discovery of Small-Molecule USP7 Inhibitors as Potential Cancer Therapies},
journal = {CHEMMEDCHEM},
year = 2021,
number = 3,
pages = {555-567},
month = 2,
volume = 16
}
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Drug Re-Positioning Studies for Novel HIV-1 Inhibitors Using Binary QSAR Models and Multi-Target-DrivenIn SilicoStudies
MOLECULAR INFORMATICS, Vol. 40, No. 2, Şubat 2021, ISSN: 1868-1743
DOĞAN BERNA, DURDAĞI SERDAR
@article{article,
author = {DOĞAN BERNA, DURDAĞI SERDAR},
title = {Drug Re-Positioning Studies for Novel HIV-1 Inhibitors Using Binary QSAR Models and Multi-Target-DrivenIn SilicoStudies},
journal = {MOLECULAR INFORMATICS},
year = 2021,
number = 2,
month = 2,
volume = 40
}
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Structural and Functional Characterization of Allatostatin Receptor Type-C of Thaumetopoea pityocampa, a Potential Target for Next-Generation Pest Control Agents
Journal of Chemical Information and Modeling, Vol. 61, Ocak 2021, ISSN: 1549-9596","1549-960X
SHAHRAKİ AİDA, İŞBİLİR ALİ, DOĞAN BERNA, DURDAGİ SERDAR, BİRGÜL NECLA
@article{article,
author = {Shahraki Aida, İşbilir Ali, DOĞAN BERNA, Durdagi Serdar, BİRGÜL NECLA},
title = {Structural and Functional Characterization of Allatostatin Receptor Type-C of Thaumetopoea pityocampa, a Potential Target for Next-Generation Pest Control Agents},
journal = {Journal of Chemical Information and Modeling},
year = 2021,
month = 1,
volume = 61
}
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Integrating Ligand and Target-Driven Based Virtual Screening Approaches With in vitro Human Cell Line Models and Time-Resolved Fluorescence Resonance Energy Transfer Assay to Identify Novel Hit Compounds Against BCL-2
FRONTIERS IN CHEMISTRY, Vol. 8, Nisan 2020, ISSN: 2296-2646
TUTUMLU GURBET,DOĞAN BERNA,AVSAR TİMUCİN,ORHAN MUGE DİDEM,CALİS SEYMA,DURDAGİ SERDAR
@article{article,
author = {Tutumlu Gurbet,DOĞAN BERNA,Avsar Timucin,Orhan Muge Didem,Calis Seyma,Durdagi Serdar},
title = {Integrating Ligand and Target-Driven Based Virtual Screening Approaches With in vitro Human Cell Line Models and Time-Resolved Fluorescence Resonance Energy Transfer Assay to Identify Novel Hit Compounds Against BCL-2},
journal = {FRONTIERS IN CHEMISTRY},
year = 2020,
month = 4,
volume = 8
}
|
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Formation of the inclusion complex of water soluble fluorescent calix[4]arene and naringenin: solubility, cytotoxic effect and molecular modeling studies
Journal of Biomolecular Structure and Dynamics, Ekim 2019, s. 3801-3813, ISSN: 0739-1102
OGUZ MEHMET,BHATTİ ASİF ALİ,DOĞAN BERNA,KARAKURT SERDAR,DURDAGİ SERDAR,YİLMAZ MUSTAFA
@article{article,
author = {Oguz Mehmet,Bhatti Asif Ali,DOĞAN BERNA,KARAKURT SERDAR,Durdagi Serdar,Yilmaz Mustafa},
title = {Formation of the inclusion complex of water soluble fluorescent calix[4]arene and naringenin: solubility, cytotoxic effect and molecular modeling studies},
journal = {Journal of Biomolecular Structure and Dynamics},
year = 2019,
pages = {3801-3813},
month = 10
}
|
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Synthesis, biological activity and multiscale molecular modeling studies of bis-coumarins as selective carbonic anhydrase IX and XII inhibitors with effective cytotoxicity against hepatocellular carcinoma
BIOORGANIC CHEMISTRY, Vol. 87, Haziran 2019, s. 838-850, ISSN: 0045-2068
ZENGİN KURT BELMA,DAĞ AYDAN,DOĞAN BERNA,DURDAĞI SERDAR,ANGELİ ANDREA,NOCENTİNİ ALESSİO,SUPURAN CLAUDİU T,SÖNMEZ FATİH
@article{article,
author = {ZENGİN KURT BELMA,DAĞ AYDAN,DOĞAN BERNA,DURDAĞI SERDAR,Angeli Andrea,Nocentini Alessio,Supuran Claudiu T,SÖNMEZ FATİH},
title = {Synthesis, biological activity and multiscale molecular modeling studies of bis-coumarins as selective carbonic anhydrase IX and XII inhibitors with effective cytotoxicity against hepatocellular carcinoma},
journal = {BIOORGANIC CHEMISTRY},
year = 2019,
pages = {838-850},
month = 6,
volume = 87
}
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Current status of multiscale simulations on GPCRs
CURRENT OPINION IN STRUCTURAL BIOLOGY, Vol. 55, No. null, Nisan 2019, s. 93-103, ISSN: 0959-440X
DURDAGİ SERDAR,DOĞAN BERNA,EROL ISMAİL,KAYİK GULRU,AKSOYDAN BUSECAN
@article{article,
author = {Durdagi Serdar,DOĞAN BERNA,Erol Ismail,Kayik Gulru,Aksoydan Busecan},
title = {Current status of multiscale simulations on GPCRs},
journal = {CURRENT OPINION IN STRUCTURAL BIOLOGY},
year = 2019,
number = null,
pages = {93-103},
month = 4,
volume = 55
}
|
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Integration of Text Mining and Binary QSAR Models for Novel Anti-Hypertensive Antagonist Scaffolds
63rd Annual Meeting of the Biophysical-Society, Baltımore/AMERİKA BİRLEŞİK DEVLETLERİ, 15 Şubat 2019
DOĞAN BERNA, DURDAĞI SERDAR, EROL İSMAİL, SEN TAHA BERKAY
@inproceedings{inproceedings,
author = {DOĞAN BERNA, DURDAĞI SERDAR, Erol İsmail, Sen Taha Berkay},
title = {Integration of Text Mining and Binary QSAR Models for Novel Anti-Hypertensive Antagonist Scaffolds},
year = 2019,
month = 2
}
|
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Integration of Text Mining and Binary QSAR Models for Novel Anti-Hypertensive Antagonist Scaffolds
BIOPHYSICAL JOURNAL, Vol. 116, No. 3, Ocak 2019, ISSN: 0006-3495
EROL İSMAİL, DURDAĞI SERDAR, DOĞAN BERNA, SEN BERKEY TAHA
@article{article,
author = {Erol İsmail, DURDAĞI SERDAR, DOĞAN BERNA, Sen Berkey Taha},
title = {Integration of Text Mining and Binary QSAR Models for Novel Anti-Hypertensive Antagonist Scaffolds},
journal = {BIOPHYSICAL JOURNAL},
year = 2019,
number = 3,
month = 1,
volume = 116
}
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In silico dissolution rates of pharmaceutical ingredients
CHEMICAL PHYSICS LETTERS, Vol. 662, No. null, 2016, s. 52-55, ISSN: 0009-2614
DOĞAN BERNA,SCHNEİDER JULİAN,REUTER KARSTEN
@article{article,
author = {DOĞAN BERNA,Schneider Julian,Reuter Karsten},
title = {In silico dissolution rates of pharmaceutical ingredients},
journal = {CHEMICAL PHYSICS LETTERS},
year = 2016,
number = null,
pages = {52-55},
volume = 662
}
|
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Free radical polymerization of ethyl methacrylate and ethyl alpha-hydroxy methacrylate: A computational approach to the propagation kinetics
POLYMER, Vol. 53, No. 15, 2012, s. 3211-3219, ISSN: 0032-3861
DOĞAN BERNA,ÇATAK ŞARON,VAN SPEYBROECK VERONİQUE,WAROQUİER MİCHEL,AVİYENTE VİKTORYA
@article{article,
author = {DOĞAN BERNA,ÇATAK ŞARON,Van Speybroeck Veronique,Waroquier Michel,Aviyente Viktorya},
title = {Free radical polymerization of ethyl methacrylate and ethyl alpha-hydroxy methacrylate: A computational approach to the propagation kinetics},
journal = {POLYMER},
year = 2012,
number = 15,
pages = {3211-3219},
volume = 53
}
|
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