Publications

Google Scholar Citations

2023

  • Ozcan A, Keskin O, Akbulut BS, Ozbek P. Piperidine-based natural products targeting type IV pili antivirulence: A computational approach. Journal of Molecular Graphics and Modelling, 2023 Mar;119:108382, doi: 10.1016/j.jmgm.2022.108382
  • Picón-Pagès P,  Bosch-Morató M,  Subirana L, Francisca Rubio-Moscardó, Biuse Guivernau, Hugo Fanlo-Ucar, Melisa Ece Zeylan, Simge Senyuz, Víctor Herrera-Fernández, Rubén Vicente, José M Fernández-Fernández, Jordi García-Ojalvo, Attila Gursoy, Ozlem Keskin, Baldomero Oliva, Francesc Posas, Eulàlia de Nadal, Francisco J Muñoz. A Genome-Wide Functional Screen Identifies Enhancer and Protective Genes for Amyloid Beta-Peptide Toxicity. International Journal of Molecular Sciences 24 (2), 1278 3. 2023
  • Ebru Celik, Gulin Ozcan, Cansel Vatansever, Erxiati Paerhati, Mert A Kuşkucu, Ozlem Dogan, Sebile Guler Cekic, Onder Ergonul, Attila Gürsoy, Özlem Keskin, Fusun Can. Alterations in vaginal microbiota among pregnant women with COVID‐19, Journal of Medical Virology, 2023,  95 (1), e28132 5.

2022

  • Lim H, Tsai CJ, Keskin O, Nussinov R, Gursoy A. HMI-PRED 2.0: a biologist-oriented web application for prediction of host-microbe protein-protein interaction by interface mimicry Bioinformatics 38 (21), 4962-4965. 2022 Sep 19:btac633. doi: 10.1093/bioinformatics/btac633.
  • Ovek D, Taweel A, Abali Z, Tezsezen E, Koroglu YE, Tsai CJ, Nussinov R, Keskin O, Gursoy A. SARS-CoV-2 Interactome 3D: A Web interface for 3D visualization and analysis of SARS-CoV-2–human mimicry and interactions. Bioinformatics, 2022, 38 (5), 1455-1457 doi: 10.1093/bioinformatics/btab799.
  • Özkan E, Ayaz Ö, Keskin O, Gursoy A, Gürsoy-Özdemir Y. Is persistent post-COVID headache associated with protein-protein interactions between antibodies against viral spike protein and CGRP receptor?: A case report. Frontiers in Pain Research, 2022 Apr 1;3:858709; 35 doi: 10.3389/fpain.2022.858709.
  • Celik E, Ozcan G, Vatansever C, Paerhati E, Kuşkucu MA, Dogan O, Cekic SG, Ergonul O, Gürsoy A, Keskin Ö, Can F. Alterations in vaginal microbiota among pregnant women with COVID-19. .J Med Virol. 2022 Sep 6:10.1002/jmv.28132. doi: 10.1002/jmv.28132.
  • Lim H, Cankara F, Tsai CJ, Keskin O, Nussinov R, Gursoy A. Artificial intelligence approaches to human-microbiome protein-protein interactions. Curr Opin Struct Biol. 2022 Apr;73:102328. doi: 10.1016/j.sbi.2022.102328.
  • Ovek D, Abali Z, Zeylan ME, Keskin O, Gursoy A, Tuncbag N. Artificial intelligence based methods for hot spot prediction. Curr Opin Struct Biol. 2022 Feb;72:209-218. doi: 10.1016/j.sbi.2021.11.003.

2021

  • Can ND, Basturk E, Kizilboga T, Akcay IM, Dingiloglu B, Tatli O, Acar S, Ozfiliz Kilbas P, Elbeyli E, Muratcioglu S, Jannuzzi AT, Gursoy A, Keskin O, Doganay HL, Karademir Yilmaz B, Dinler Doganay G. Interactome analysis of Bag-1 isoforms reveals novel interaction partners in endoplasmic reticulum-associated degradation. PLoS One. 2021 Aug 24;16(8):e0256640. doi: 10.1371/journal.pone.0256640.
  • Nussinov R, Jang H, Gursoy A, Keskin O , Gaponenko V. Inhibition of nonfunctional Ras. Cell Chem Biol. 2021 Jan 6;S2451-9456(20)30521-3.
  • Keskin O, Miller Y, Liu J, Lu S. Tribute to Ruth Nussinov. J Phys Chem B. 2021 Jul 1;125(25):6733-6734. doi: 10.1021/acs.jpcb.1c04721.
  • Eren M, Tuncbag N, Jang H, Nussinov R, Gursoy A, Keskin O. Normal Mode Analysis of KRas4B Reveals Partner Specific Dynamics. J Phys Chem B. 2021 May 27;125(20):5210-5221. doi: 10.1021/acs.jpcb.1c00891.
  • Senyuz S, Jang H, Nussinov R, Keskin O, Gursoy A. Mechanistic Differences of Activation of Rac1P29S and Rac1A159V. J Phys Chem B. 2021 Apr 22;125(15):3790-3802. doi: 10.1021/acs.jpcb.1c00883.
  • Weako J, Jang H, Keskin O, Nussinov R, Gursoy A.The structural basis of Akt PH domain interaction with calmodulin. Biophys J. 2021 May 18;120(10):1994-2008. doi: 10.1016/j.bpj.2021.03.018.
  • Yapici-Eser H, Koroglu YE, Oztop-Cakmak O, Keskin O, Gursoy A, Gursoy-Ozdemir Y. Neuropsychiatric Symptoms of COVID-19 Explained by SARS-CoV-2 Proteins’ Mimicry of Human Protein Interactions. Front Hum Neurosci. 2021 Mar 23;15:656313. doi: 10.3389/fnhum.2021.656313. eCollection 2021
  • Nussinov R, Jang H, Gursoy A, Keskin O , Gaponenko V. Inhibition of nonfunctional Ras. Cell Chem Biol. 2021 Jan 6;S2451-9456(20)30521-3.

2020

  • Weako J, Uba AI, Keskin Ö, Gürsoy A, Yelekçi K. Identification of potential inhibitors of human methionine aminopeptidase (type II) for cancer therapy: Structure-based virtual screening, ADMET prediction and molecular dynamics studies. Comput Biol Chem. 2020 Jun;86:107244. doi: 10.1016/j.compbiolchem.2020.107244.
  • Guven-Maiorov E, Hakouz A, Valjevac S, Keskin O, Tsai CJ, Gursoy A, Nussinov HMI-PRED: A Web Server for Structural Prediction of Host-Microbe Interactions  Based on Interface Mimicry. J Mol Biol. 2020 Feb 13. pii: S0022-2836(20)30089-9.  doi: 10.1016/j.jmb.2020.01.025.
  • Morova T, McNeill DR, Lallous N, Gönen M, Dalal K, Wilson DM 3rd, Gürsoy A, Keskin Ö, Lack NA. Androgen receptor-binding sites are highly mutated in prostate Nat Commun. 2020 Feb 11;11(1):832. doi: 10.1038/s41467-020-14644-y.
  • Muratcioglu S, Aydin C, Odabasi E, Ozdemir ES, Firat-Karalar EN, Jang H, Tsai CJ, Nussinov R, Kavakli IH, Gursoy A, Keskin O. Oncogenic K-Ras4B Dimerization Enhances Downstream Mitogen-activated Protein Kinase Signaling. J Mol Biol. 2020  Jan 10. pii: S0022-2836(20)30018-8. doi: 10.1016/j.jmb.2020.01.002. [Epub ahead of print] PubMed PMID: 31931009.
  • Pooley JR, Rivers CA, Kilcooley MT, Paul SN, Cavga AD, Kershaw YM, Muratcioglu S, Gursoy A, Keskin O, Lightman SL. Beyond the heterodimer model for mineralocorticoid and glucocorticoid receptor interactions in nuclei and at DNA. PLoS One. 2020 Jan 10;15(1):e0227520. doi: 10.1371/journal.pone.0227520. eCollection 2020. PubMed PMID: 31923266; PubMed Central PMCID: PMC6953809.

2019

  • Yang X, Cheng H, Chen J, Wang R, Saleh A, Si H, Lee S, Guven-Maiorov E, Keskin O, Gursoy A, Nussinov R, Fang J, Van Waes C, Chen Z. Head and Neck Cancers Promote an Inflammatory Transcriptome through Coactivation of Classic and Alternative NF-κB Pathways. Cancer Immunol Res. 2019 Nov;7(11):1760-1774. doi: 1158/2326-6066.CIR-18-0832. Epub 2019 Oct 17.
  • Halakou F, Gursoy A, Keskin O. Embedding Alternative Conformations of Proteins in Protein-Protein Interaction Networks. Methods Mol Biol. 2020;2074:113-124. doi: 10.1007/978-1-4939-9873-9_9. PubMed PMID: 31583634.
  • Dincer C, Kaya T, Keskin O, Gursoy A, Tuncbag N. 3D spatial organization and network-guided comparison of mutation profiles in Glioblastoma reveals similarities across patients. PLoS Comput Biol. 2019 Sep 17;15(9):e1006789. doi: 1371/journal.pcbi.1006789. eCollection 2019 Sep. PubMed PMID: 31527881; PubMed Central PMCID: PMC6782092.
  • Uba AI, Weako J, Keskin Ö, Gürsoy A, Yelekçi K. Examining the stability of binding modes of the co-crystallized inhibitors of human HDAC8 by molecular dynamics simulation. J Biomol Struct Dyn. 2019 May 5:1-10. doi: 10.1080/07391102.2019.1615989.
  • Cavga AD, Tardu M, Korkmaz T, Keskin O, Ozturk N, Gursoy A, Kavakli IH. Cryptochrome deletion in p53 mutant mice enhances apoptotic and anti-tumorigenic responses to UV damage at the transcriptome level. Funct Integr Genomics. 2019 Sep;19(5):729-742. doi: 10.1007/s10142-019-00680-5. Epub 2019 May 1. PubMed PMID: 31044344.
  • Ozdemir ES, Halakou F, Nussinov R, Gursoy A, Keskin O. Methods for Discovering and Targeting Druggable Protein-Protein Interfaces and Their Application to Repurposing. Methods Mol Biol. 2019;1903:1-21. doi: 10.1007/978-1-4939-8955-3_1. PubMed PMID: 30547433.

2018

  • Ozdemir ES, Nussinov R, Gursoy A, Keskin O. Developments in integrative modeling with dynamical interfaces. Curr Opin Struct Biol. 2019 Jun;56:11-17. doi: 10.1016/j.sbi.2018.10.007. Epub 2018 Nov 12. Review. PubMed PMID: 30439586.
  • Ozdemir ES, Gursoy A, Keskin O. Analysis of single amino acid variations in singlet hot spots of protein-protein interfaces. Bioinformatics. 2018 Sep 1;34(17):i795-i801. doi: 10.1093/bioinformatics/bty569. PubMed PMID: 30423104.
  • Ozdemir ES, Jang H, Gursoy A, Keskin O, Nussinov R. Arl2-Mediated Allosteric Release of Farnesylated KRas4B from Shuttling Factor PDEδ. J Phys Chem B. 2018 Aug 2;122(30):7503-7513. doi: 10.1021/acs.jpcb.8b04347. Epub 2018 Jul 18. PubMed PMID: 29961325.
  • Kuzu G, Keskin O, Nussinov R, Gursoy A. PRISM-EM: template interface-based modelling of multi-protein complexes guided by cryo-electron microscopy density maps. Corrigendum. Acta Crystallogr D Struct Biol. 2018 Jan 1;74(Pt 1):65-66. doi: 10.1107/S2059798317017739. Epub 2018 Jan 1. PubMed PMID: 29372900.
  • Ozdemir ES, Jang H, Gursoy A, Keskin O, Li Z, Sacks DB, Nussinov R. Unraveling the molecular mechanism of interactions of the Rho GTPases Cdc42 and Rac1 with the scaffolding protein IQGAP2. J Biol Chem. 2018 Jan 22. pii: jbc.RA117.001596. doi: 10.1074/jbc.RA117.001596. [Epub ahead of print] PubMed PMID: 29358323.

2017

  • Halakou F, Kilic ES, Cukuroglu E, Keskin O, Gursoy A. Enriching Traditional Protein-protein Interaction Networks with Alternative Conformations of Proteins. Sci Rep. 2017 Aug 3;7(1):7180. doi: 10.1038/s41598-017-07351-0. PubMed PMID:28775330; PubMed Central PMCID: PMC5543104.
  • Muratcioglu S, Jang H, Gursoy A, Keskin O, Nussinov R. PDEδ Binding to Ras Isoforms Provides a Route to Proper Membrane Localization. J Phys Chem B. 2017 Jun 7. doi: 10.1021/acs.jpcb.7b03035. [Epub ahead of print] PubMed PMID: 28540724.
  • Ozgur B, Ozdemir ES, Gursoy A, Keskin O. Relation between Protein Intrinsic Normal Mode Weights and Pre-Existing Conformer Populations. J Phys Chem B. 2017 Apr 20;121(15):3686-3700. doi: 10.1021/acs.jpcb.6b10401. Epub 2017 Feb 22. PubMed PMID: 28181436.
  • Tuncbag N, Keskin O, Nussinov R, Gursoy A. Prediction of Protein Interactions by Structural Matching: Prediction of PPI Networks and the Effects of Mutations on PPIs that Combines Sequence and Structural Information. Methods Mol Biol. 2017;1558:255-270. doi: 10.1007/978-1-4939-6783-4_12. PubMed PMID: 28150242.

2016

  • Kuzu G, Keskin O, Nussinov R, Gursoy A. PRISM-EM: template interface-based modelling of multi-protein complexes guided by cryo-electron microscopy density maps. Acta Crystallogr D Struct Biol. 2016 Oct 1;72(Pt 10):1137-1148. Epub 2016 Sep 20. PubMed PMID: 27710935; PubMed Central PMCID: PMC5053140.
  • Nussinov R, Muratcioglu S, Tsai CJ, Jang H, Gursoy A, Keskin O. K-Ras4B/calmodulin/PI3Kα: A promising new adenocarcinoma-specific drug target? Expert Opin Ther Targets. 2016 Jul;20(7):831-42. doi: 10.1517/14728222.2016.1135131.
  • Jang H, Muratcioglu S, Gursoy A, Keskin O, Nussinov R. Membrane-associated Ras dimers are isoform-specific: K-Ras dimers differ from H-Ras dimers. Biochem J. 2016 Jun 15;473(12):1719-32. doi: 10.1042/BCJ20160031.
  • Guven-Maiorov E, Keskin O, Gursoy A, VanWaes C, Chen Z, Tsai CJ, Nussinov R. TRAF3 signaling: Competitive binding and evolvability of adaptive viral molecular mimicry. Biochim Biophys Acta. 2016 May 18. pii: S0304-4165(16)30163-5. doi: 10.1016/j.bbagen.2016.05.021.
  • Keskin O, Tuncbag N, Gursoy A. Predicting Protein-Protein Interactions from the Molecular to the Proteome Level. Chem Rev. 2016 Apr 27;116(8):4884-909. doi: 10.1021/acs.chemrev.5b00683
  • Tuncbag N, Gursoy A, Keskin O, Nussinov R. The potential impact of recent developments in three-dimensional quantitative interaction proteomics on structural biology. Expert Rev Proteomics. 2016 May;13(5):447-9. doi: 10.1080/14789450.2016.1182023.
  • Lu S, Jang H, Muratcioglu S, Gursoy A, Keskin O, Nussinov R, Zhang J. Ras Conformational Ensembles, Allostery, and Signaling. Chem Rev. 2016 Jun 8;116(11):6607-65. doi: 10.1021/acs.chemrev.5b00542.

2015

  • Muratcioglu S, Chavan TS, Freed BC, Jang H, Khavrutskii L, Freed RN, Dyba MA, Stefanisko K, Tarasov SG, Gursoy A, Keskin O, Tarasova NI, Gaponenko V, Nussinov R. GTP-Dependent K-Ras Dimerization. Structure. 2015 Jun 1. pii:S0969-2126(15)00178-1. doi: 10.1016/j.str.2015.04.019. [Epub ahead of print]PubMed PMID: 26051715.
  • Guven-Maiorov E, Keskin O, Gursoy A, Nussinov R. A Structural View of Negative Regulation of the Toll-like Receptor-Mediated Inflammatory Pathway. Biophys J. 2015 Sep 15;109(6):1214-26. doi: 10.1016/j.bpj.2015.06.048. Epub 2015 Aug 11. PubMed PMID: 26276688.
  • Cavga AD, Karahan N, Keskin O, Gursoy A. Taming Oncogenic Signaling at Protein Interfaces: Challenges and Opportunities. Curr Top Med Chem. 2015 May 18. [Epub ahead of print] PubMed PMID: 25986691.
  • Muratcioglu S, Presman DM, Pooley JR, Grøntved L, Hager GL, Nussinov R, Keskin O, Gursoy A. Structural Modeling of GR Interactions with the SWI/SNF Chromatin Remodeling Complex and C/EBP. Biophys J. 2015 Sep 15;109(6):1227-39. doi:10.1016/j.bpj.2015.06.044. Epub 2015 Aug 13. PubMed PMID: 26278180.
  • Keskin O, Dyson HJ, Bahar I. Biomolecular Systems Interactions, Dynamics, and Allostery: Reflections and New Directions. Biophys J. 2015 Sep 15;109(6):E01-2.doi: 10.1016/j.bpj.2015.08.005. PubMed PMID: 26377787.
  • Guven-Maiorov E, Keskin O, Gursoy A, VanWaes C, Chen Z, Tsai CJ, Nussinov R. The Architecture of the TIR Domain Signalosome in the Toll-like Receptor-4 Signaling Pathway. Sci Rep. 2015 Aug 21;5:13128. doi: 10.1038/srep13128. PubMed PMID: 26293885; PubMed Central PMCID: PMC4544004.
  • Özoğuz A, Uyan Ö, Birdal G, Iskender C, Kartal E, Lahut S, Ömür Ö, Agim ZS, Eken AG, Sen NE, Kavak P, Saygı C, Sapp PC, Keagle P, Parman Y, Tan E, Koç F, Deymeer F, Oflazer P, Hanağası H, Gürvit H, Bilgiç B, Durmuş H, Ertaş M, Kotan D, Akalın MA, Güllüoğlu H, Zarifoğlu M, Aysal F, Döşoğlu N, Bilguvar K, Günel M, Keskin Ö, Akgün T, Özçelik H, Landers JE, Brown RH, Başak AN. The distinct genetic pattern of ALS in Turkey and novel mutations. Neurobiol Aging. 2015 Apr;36(4):1764.e9-1764.e18. doi: 10.1016/j.neurobiolaging.2014.12.032. Epub 2015 Jan 10. PubMed PMID: 25681989.
  • Nussinov R, Muratcioglu S, Tsai CJ, Jang H, Gursoy A, Keskin O. The Key Role of Calmodulin in KRAS-Driven Adenocarcinomas. Mol Cancer Res. 2015 Sep;13(9):1265-73. doi: 10.1158/1541-7786.MCR-15-0165. Epub 2015 Jun 17. Review. PubMed PMID: 26085527; PubMed Central PMCID: PMC4572916.

2014

  • Acuner-Ozbabacan E.S., Engin B.H., Guven-Maiorov E, Kuzu G, Muratcioglu S, Baspinar A, Chen Z, Van Waes C, Gursoy A, Keskin O, Nussinov R. The structural network of Interleukin-10 and its implications in inflammation and cancer. BMC Genomics.2014;15 Suppl 4:S2. pdf
  • Cukuroglu E, Engin HB, Gursoy A, Keskin O. Hot spots in protein-protein interfaces: Towards drug discovery. Prog Biophys Mol Biol. 2014 Jul 2. pii:S0079-6107(14)00045-5. pdf
  • Baspinar A, Cukuroglu E, Nussinov R, Keskin O, Gursoy A. PRISM: a web server and repository for prediction of protein-protein interactions and modeling their 3D complexes. Nucleic Acids Res. 2014 Jul;42(Web Server issue):W285-9. pdf
  • Guven-Maiorov E, Acuner-Ozbabacan SE, Keskin O, Gursoy A, Nussinov R. Structural pathways of cytokines may illuminate their roles in regulation of cancer development and immunotherapy. Cancers (Basel). 2014 Mar 25;6(2):663-83.pdf
  • G. Kuzu, O. Keskin, R. Nussinov, A. Gursoy. Modeling protein assemblies in the proteome. Mol Cell Proteomics. 2014 Mar;13(3):887-96. pdf
  • S.E. Acuner Ozbabacan, A. Gursoy, R. Nussinov, O. Keskin. The Structural Pathway of Interleukin 1 (IL-1) Initiated Signaling Reveals Mechanisms of Oncogenic Mutations and SNPs in Inflammation and Cancer. PLoS Comput Biol. 2014 Feb 13;10(2):e1003470. pdf
  • E Cukuroglu, A. Gursoy, R.Nussinov, O. Keskin. Non-redundant unique interface structures as templates for modeling protein interactions. PLoS One. 2014 Jan 27;9(1):e86738. pdf
  • Engin HB, Gursoy A, Nussinov R, Keskin O. Network-Based Strategies Can Help Mono- and Poly-pharmacology Drug Discovery: A Systems Biology View. Curr Pharm Des. 2014. pdf

2013

  • Engin HB, Guney E, Keskin O, Oliva B, Gursoy A. Integrating structure to protein-protein interaction  networks that drive metastasis to brain and lung in breast cancer. PLoS One. 2013 Nov 22;8(11):e81035. pdf
  • Guven Maiorov E, Keskin O, Gursoy A, Nussinov R. The structural network of inflammation and cancer: Merits and challenges. Semin Cancer Biol. 2013. pdf
  • Guven Maiorov, E, O. Keskin, O. Hatirnaz Ng, U. Ozbek, A. Gursoy. Identification of interconnected markers for T-cell acute lymphoblastic leukemia. Biomed Res Int. 210253, 2013. pdf
  • Kuzu, G, A. Gursoy, R. Nussinov, O. Keskin. Exploiting conformational ensembles in modeling protein-protein interactions on the proteome scale. J Proteome Res. 2013 Jun 7;12(6):2641-53. pdf
  • O. An, A. Gursoy, A. Gurgey, O. Keskin. Structural and functional analysis of perforin mutations in association with clinical data of familial hemophagocytic lymphohistiocytosis type 2 (FHL2) patients. pdf Protein Sci. 22(6):823-39, 2013.pdf
  • G. Kar, O. Keskin, F. Fraternali, A. Gursoy. Emerging role of the ubiquitin-proteasome system as drug targets. Curr Pharm Des. 19(18):3175-89, 2013. pdf

2012

  • H.B. Engin, O. Keskin, R. Nussinov, A. Gursoy. A strategy based on protein-protein interface motifs may help in identifying drug off-targets. J Chem Inf Model. 2012 Aug 27;52(8):2273-86.2012. pdf
  •  S.E. Acuner Ozbabacan, O. Keskin, R. Nussinov, A. Gursoy. Enriching the human apoptosis pathway by predicting the structures of protein-protein complexes. J Struct Biol. 179(3):338-46, 2012. pdf
  • Kar G, Kuzu G, Keskin O, Gursoy A. Protein-protein interfaces integrated into interaction networks: implications on drug design. Curr Pharm Des. 2012 . pdf
  • Kuzu G, Keskin O, Gursoy A, Nussinov R. Constructing structural networks of signaling pathways on the proteome scale. Curr Opin Struct Biol. 22(3):367-77. 2012. pdf
  • N. Tuncbag, O. Keskin, R. Nussinov, A. Gursoy. Fast and accurate modeling of protein-protein interactions by combining template-interface-based docking with flexible refinement. Proteins. 80(4):1239-49, 2012. pdf
  • A. Bolia, Z.N. Gerek, O. Keskin, S.B. Ozkan, K.K. Dev. The binding affinities of proteins interacting with the PDZ domain of PICK1. Proteins. 2012 80(5):1393-408.2012. pdf
  • G. Kuzu, O. Keskin, A. Gursoy, R. Nussinov. Expanding the conformational selection paradigm in protein-ligand docking. Methods Mol Biol. 819:59-74, 2012. pdf
  • G. Kar, O. Keskin, R. Nussinov, A. Gursoy. Human proteome-scale structural modeling of E2-E3 interactions exploiting interface motifs. J Proteome Res. 11(2):1196-207, 2012. pdf
  • E. Cukuroglu, A. Gursoy, O. Keskin. HotRegion: a database of predicted hot spot clusters. Nucleic Acids Res. 40(1):D829-33, 2012. pdf

2011

  • N. Tuncbag, A. Gursoy, R. Nussinov, O. Keskin. Predicting protein-protein interactions on a proteome scale by matching evolutionary and structural similarities at interfaces using PRISM. Nat Protoc. 6(9):1341-54, 2011. pdf
  • O. Ulucan, O. Keskin, B. Erman, A. Gursoy. A Comparative Molecular Dynamics Study of Methylation State Specificity of JMJD2A. PLoS One. 6(9):e24664, 2011. pdf
  • D. Sanli, O. Keskin, A. Gursoy, B. Erman. Structural Cooperativity in Histone H3 Tail Modifications. Protein Sci. 20(12):1982-90, 2011. pdf
  •  SE. Acuner Ozbabacan, HB. Engin, A. Gursoy, O.  Keskin. Transient protein-protein interactions. Protein Eng Des Sel. 24(9):635-48, 2011. pdf
  • M. Ozboyaci,  A. Gursoy, B. Erman, O. Keskin. Molecular Recognition of H3/H4 Histone Tails by the Tudor Domains of JMJD2A: A Comparative Molecular Dynamics Simulations Study. PLoS One. 2011 Mar 25;6(3):e14765. pdf
  • N.Tuncbag, A.Gursoy, O.Keskin, Prediction of protein-protein interactions: Unifying evolution and structure at protein interfaces, Phys Biol., 8(3):035006, 2011. pdf

2010

  • G. Kar, O. Keskin, A. Gursoy, R. Nussinov. Allostery and population shift in drug design. Curr Opin Pharmacol. 10(6):715-22,  2010. pdf   “included in ScieTopics in the field of Structural Biology <http://www.scitopics.com/categories.jsp?domain=1315> and Drug Discovery <http://www.scitopics.com/categories.jsp?domain=3002>. “
  • A. Zen , C. Micheletti, O. Keskin, R. Nussinov. Comparing interfacial dynamics inprotein-protein complexes: an elastic network approach. BMC Struct Biol. 10(1):26, 2010. pdf
  • S.E. Ozbabacan, A. Gursoy, O. Keskin, R. Nussinov. Conformational ensembles, signal transduction and residue hot spots: Application to drug discovery. Curr Opin Drug Discov Devel. 2010 Sep;13(5):527-37. pdf
  • S. Kalyoncu, O. Keskin, A. Gursoy. Interaction prediction and classification of PDZ domains. BMC Bioinformatics. 11(1):357, 2010. pdf
  • N. Tuncbag, O. Keskin, A. Gursoy. HOTPOINT: Hot Spot Prediction Server For Protein Interfaces, Nucleic Acids Res., 38 Suppl:W402-6, 2010. pdf
  • S. Ahmad, O. Keskin, R. Nussinov, K. Mizuguchi, A. Sarai, R. Nussinov. CCRXP: Exploring Clusters of Conserved Residues in Protein Structures,  Nucleic Acids Res., 38 Suppl:W398-401, 2010. pdf
  • E. Cukuroglu, A. Gursoy, O. Keskin. Analysis of hot region organization in hub proteins. Annals of Biomedical Engineering, 38(6):2068-78, 2010. pdf
  • N. Tuncbag, S. Salman, O. Keskin, A. Gursoy. Analysis and Network Representation of Hot Spots in Protein Interfaces Using Minimum Cut Trees. Proteins, 78(10):2283-94, 2010. pdf

2009

  • G. Kar, A. Gursoy, O. Keskin. Human cancer protein-protein interaction network: a structural perspective, Plos Comp Biol. 5(12):e1000601, 2009. pdf
  • I. Baris, A. Tuncel, N. Ozber, O. Keskin, H. Kavakli. Free energy decomposition of the potato ADPglucose Pyrophosphorylase identifies critical residues in the heterotetramer interface, Plos Comp Biol. 5(10):e1000546, 2009. pdf
  • Z.N. Gerek, O. Keskin, B. Ozkan. Identification of Specificity and Promiscuity of PDZ Domain Interactions through their Dynamic Behavior, Proteins, 77(4):796-811, 2009. pdf
  • N. Tuncbag, G Kar, O. Keskin, A. Gursoy, R. Nussinov. Inferring Time Dimensionality in Protein – Protein Interaction Networks by Integrating Structures: The p53 Example,  Mol Biosyst. 5(12):1770-8, 2009. pdf
  • N. Tuncbag, A. Gursoy, O. Keskin. Identification of Computational Hot Spots in Protein Interfaces: Combining Solvent Accessibility and Inter-Residue Potentials Improves the Accuracy. Bioinformatics, 25(12):1513-20, 2009. pdf

SELECTED AS THE FAST BREAKING PAPER at  Thomson Reuters (http://sciencewatch.com/dr/fbp/2010/10decfbp/10decfbpGursET/ )

  • N. Tuncbag, G Kar, O. Keskin, A. Gursoy, R. Nussinov. A Survey of available tools and web servers for analysis of protein-protein interactions and interfaces, Brief Bioinform, 10(3):217-32, 2009. pdf

 2008

  • A. Gursoy, O. Keskin, R. Nussinov. Topological Properties of Protein Interaction Networks from a Structural Perspective, Biochem Soc Trans, 2008 Dec;36(Pt 6):1398-403. pdf
  • S. Ahmad, O. Keskin, A. Sarai, R. Nussinov. Protein-DNA interactions: structural, thermodynamic and clustering patterns of conserved residues in DNA-binding proteins. Nucleic Acids Res. 36(18):5922-32, 2008. pdf
  • A. Tuncel, I.H. Kavakli, O. Keskin. Insights into Subunit Interactions in the Heterotetrameric Structure of Potato ADP-glucose Pyrophosphorylase. Biophysical J, 95(8):3628-39, 2008. pdf
  • N. Tuncbag, E. Guney, R. Nussinov , A. Gursoy, O. Keskin. Architectures and Functional Coverage of Protein-Protein Interfaces, J. Mol. Biol. 381(3):785-802, 2008. pdf
  • O. Keskin, N. Tuncbag, A. Gursoy,  Characterization and Prediction of Protein Interfaces to Infer Protein-Protein Interaction Networks, Curr Pharmacet Biotech, 9(2):67-76, 2008. pdf
  • O. Keskin, A. Gursoy, B. Ma, R. Nussinov, What is the preferred ways for proteins to interact, Chemical Rev., 108(4):1225-1244, 2008. pdf
  • O.N. Yogurtcu, B. Erdemli, R. Nussinov, M. Turkay, O. Keskin, Restricted mobility of conserved residues in protein-protein interfaces in molecular simulations, Biophysical J, 94(9):3475-85, 2008. pdf
  • E. Guney, N. Tuncbag, O. Keskin, A. Gursoy. HotSprint: database of computational hot spots in protein interfaces. Nucleic Acids Res. 2008 Jan;36(Database issue):D662-6. pdf

        2007

  • O. Keskin. Binding induced experimental conformational changes of proteins correlate with their intrinsic fluctuations: A case study of antibodies. BMC Struct. Biol.  7: 31, 2007. pdf
  • O. Keskin, A. Gursoy, B. Ma, R.Nussinov. Towards Drugs Targetıng Multıple Proteıns In A Systems Biology Approach. Curr. Top. Med. Chem,  7 (10): 943-951, 2007. pdf
  • O. Keskin, R.Nussinov. Similar Binding Sites and Different Partners: Implications to Shared Proteins in Cellular Pathways. Structure, 15 (3):341-354, 2007. pdf

  2006

  • A. Gursoy, O. Keskin, M. Turkay, B. Erman. Relationships between Unfolded Configurations of Proteins and Dynamics of Folding to the Native State. J. Polym. Sci., Part B: Polym. Phys. 44 (24): 3667-3678, 2006. pdf

2005

  • U. Ogmen, O. Keskin, A.S. Aytuna, R. Nussinov, A. Gursoy.  PRISM: protein interactions by structural matching. Nucleic Acids Res. 33 (Web Server issue):W331-6, 2005. pdf
  • AS Aytuna, A Gursoy, O Keskin. Prediction of protein-protein interactions by combining structure and sequence conservation in protein interfaces Bioinformatics. 21(12):2850-5. 2005. pdf
  • O. Keskin, B. Ma, K. Rogale, K. Gunasekaran, R. Nussinov. Protein-protein interactions: organization, cooperativity and mapping in a bottom-up systems biology approach,  Phys. Biol. 2  S24-S35, 2005. pdf
  • B. Ma, Y. Pan, K. Gunasekaran, O. Keskin, R.B. Venkataraghavan, A.J. Levine, R. Nussinov. The contribution of the Trp/Met/Phe residues to physical interactions of p53 with cellular proteins Phys. Biol. 2, 2005. pdf
  • O Keskin, R Nussinov. Favorable scaffolds: proteins with different sequence, structure and function may associate in similar ways. Protein Eng Des Sel. 18(1):11-24, 2005.  pdf
  • O. Keskin, B. Ma, R. Nussinov, Hot regions in protein–protein interactions: the organization and contribution of structurally conserved hot spot residues. J Mol Biol. 345(5):1281-94, 2005. pdf
  • T. Haliloglu, O. Keskin, B. Ma, R. Nussinov.  How similar are protein folding and protein binding nuclei? Examination of vibrational motions of energy hot spots and conserved residues. Biophys J. 88(3):1552-9, 2005. pdf
  • M. C. Demirel, O. Keskin. Protein Interactions and Fluctuations in a Proteomic Network using an Elastic Network Model. J Biomol Struct Dyn. 2005 Feb;22(4):381-6.  pdf

 2004

  • X. Li, O.Keskin, B. Ma, R. Nussinov, J. Liang.  Protein-protein interactions: hot spots and structurally conserved residues often locate in complemented pockets that pre-organized in the unbound states: implications for docking.  J Mol Biol,  2004 Nov 26;344(3):781-95. pdf
  • O. Keskin, C.J. Tsai, H. Wolfson, R. Nussinov, A new, structurally non-redundant, diverse dataset of protein-protein interfaces and its implications. Protein Sci. 13(4):1043-1055, 2004.pdf
  • Y Pan, B Ma, O Keskin, R Nussinov. Characterization of the conformational state and flexibility of HIV-1 glycoprotein gp120 core domain. J Biol Chem. 279(29):30523-30, 2004. pdf
  • O. Keskin, D. Yuret, A. Gursoy, M. Turkay, B. Erman. Relationships between amino acid sequence and backbone torsion angle preferences. Proteins. 55(4): 992-998, 2004. pdf

2002

  • O. Keskin. Comparison of Full-atomic and Coarse-grained Models to Examine the Molecular Fluctuations of c-AMP Dependent Protein Kinase. J Biomol Struct Dyn. 20(3):333-46, 2002. pdf
  • O. Keskin, X. Ji, J. Blaszcyk, D.G. Covell. Molecular motions and conformational changes of HPPK. Protein, 49(2):191-205, 2002. pdf
  • O. Keskin, S. Durell, I. Bahar, R.L. Jernigan, and D.G. Covell. Relating global motions of tubulin to its function. Biophys J. 83(2):663-80, 2002. pdf
  • O. Keskin, I. Bahar, D. Flatow, D.G. Covell, and R.L. Jernigan. Dynamics of GroEL/GroES complex. Biochemistry, 41(2):491-501, 2002. pdf

 2001

  • A.R. Atilgan, S.R. Durell, R.L. Jernigan, M.C. Demirel, O. Keskin and I. Bahar, Anisotropy of Fluctuation Dynamics of Proteins with an elastic network model. Biophysical Journal. Vol 80, pg. 505-515, 2001.pdf

2000

  • O. Keskin, R. L. Jernigan & I. Bahar, Proteins with similar architecture exhibit common large-scale dynamic behavior. Biophysical Journal, Vol. 78, pg. 2093-2106, 2000.pdf
  • O. Keskin, I. Bahar, R.L. Jernigan, T.G. Myers, J.A. Beutler, R.H. Shoemaker, E.A. Sausville and D.G. Covell, Characterization of Anticancer Agents by their Growth-Inhibitory Activity and Relationships to Mechanism of Action and Structure, Anti-Cancer Drug Design, Vol 15, pg. 79-98, 2000. pdf
  • G. Duman, O. Keskin,I. Bahar, J. R. Robinson, Stabilization of Molten Globular State of Hen Egg Lysozyme with Solutions Containing Polyvinyl Pyrrolidone. J Controlled Release, Vol 64 (1-3), pg. 331-333, 2000. pdf

1998

  • O. Keskin, I. Bahar, A. Ya. Badretdinov, O. B. Ptitsyn, & R. L. Jernigan. Solvent-mediated inter-residue potentials at protein-protein interfaces exhibit close similarity to those in protein monomers. Protein Science, Vol 7, Number 12- pg. 2578-2586, 1998. pdf
  • O. Keskin, I. Bahar, Packing of sidechains in low resolution models for proteins. Folding & Design, Vol 3, pg. 469-479, 1998. pdf

BOOK CHAPTERS

·         Ozlem Keskin, Attila Gursoy, and Ruth Nussinov.. Principles of protein recognition and properties of protein-protein interfaces. (2008)  In Protein-protein Interactions and Networks: Identification, Computer Analysis, and Prediction (Computational Biology) (ed. In Protein-protein Interactions and Networks: Identification, Computer Analysis, and Prediction (Computational Biology),) Springer.

·         Ozlem Keskin, Ruth Nussinov and Attila Gursoy. PRISM: Protein-protein  Interaction prediction  by Structural Matching. (2008) In Functional Proteomics: Methods and Protocols (Methods in Molecular Biology) (ed. J. D. Thompson, C. Schaeffer-Reiss, M. Ueffing. Humana Press.

  • SerminSunol, Ozlem Keskin, Ozge Guney, Aydın Sunol, “Supercritical Fluid Aided Preparation of aerogels and their Characterization”, (1995). ACS Symposium Series, Chap.17, Vol. 608, pg. 258-268, San Francisco.

CONFERENCE PUBLICATIONS (not updated)

  1. Keskin, T. Haliloglu, B. Ma, R. Nussinov. “Protein-protein interactions: Structurally conserved residues at protein-protein interfaces“,BiophysicalJournal, Vol. 86 (1): 267A-267A, 2004.
  2. Li, O. Keskin, B. Ma, R. Nussinov. “Interfacial pockets, structurally conserved residues, and energetic hot spots in protein-protein interactions“, Biophysical Journal, Vol. 86 (1): 301A-301A, 2004.

O.Keskin,  CJ Tsai, H. Wolfson, R. Nussinov. “A new dataset of non-redundant protein/protein interfaces”, Biophysical Journal, Vol. 84, pg. 42a, 2003.

  1. Keskin, X. Ji, J. Blaszcyk, D.G. Covell. “Molecular motions and conformational changes of HPPK”, Biophysical Journal, Vol. 82, pg. 319a, 2002.
  2. Keskin, I. Bahar, D.G. Covell, A.R. Atilgan, S. Durell, R.L. Jernigan. “Large functional motions of proteins” Biophysical Journal.Vol 80, pg. 173A-173A, 2001.
  3. Keskin, I. Bahar, R.L. Jernigan, D.G. Covell, “Characterization of Anticancer Agents and their Growth Inhibitory Potency: Relationships between Potency and Chemical Substructure”, Biophysical Journal, Vol76, pg. A384-A384, 1999.

S.G. Sunol, Keskin, O., Guney, O., Sunol A.K., Supercritical fluid aided preparation of aerogels and their characterization, Proceedings of the 3rd International Symposium on Supercritical Fluids, Tome 3, Reactions, Material Science, Chromatography and Analytical SFE, I.N.P.L. A.R., Nancy, France (1994) p. 387-392.

 

POSTER PRESENTATIONS/TALKS AT CONFERENCES

  1. Keskin, D. Yuret, A. Gursoy, M. Turkay, B. Erman. “Determination of protein folding trajectories by montecarlo simulation based on go-type potentials”. AICHE Annual Meeting, November 2003, San Francisco, USA.

 

O.Keskin, T. Haliloglu, B. Ma, R. Nussinov. “A new dataset of non-redundant protein/protein interfaces”, 5th ICSMB, September 2003, Vienna, Austria.

 

  1. Keskin, “Tubulindynamics”, Protein Structure Prediction Workshop, November, 2002, Antalya, Turkey

 

  1. Keskin, C.J. Tsai, H. Wolfson, R. Nussinov. “A New Dataset of Non-Redundant Protein/Protein Interfaces”, 47th Annual Meeting of Biophysical Society Meeting, San Antonio, Texas, USA, 1-5 March 2003.

 

  1. Keskin. “Assessing Global Molecular Motions Of Large Mole Cules: Relating TubulinFlexibility To Its Functions” Protein Structure Prediction Workshop – November 1-3, 2002, Antalya, Turkey.

 

Yilmaz, O., M. Türkay, S. Savas, E. Kaya. S.B. Sonuc, M. E. Coskun, and O. Keskin. A Novel Branch and Bound Algorithm for Determining Secondary Structures of Proteins, INFORMS Annual Meeting, San Jose, CA, November, 2002.

 

  1. Keskin, R. Munshiand I. Bahar. Genes in cocaine addiction, RECOMB2002, 17-21 April, 2002,Washington DC, USA, Published in the Proceedings of the Conference. 2002.

 

  1. Keskin, X. Ji, J. Blaszcyk, and D.G. Covell. “Molecular motions and conformational changes of HPPK”,46th Annual Meeting of Biophysical Society Meeting, San Francisco, CA, USA. 23-27 Feb. 2002.

 

  1. Doruker, O. Keskin, R. L. Jernigan, I. Bahar. “Calculation of protein motions with extremely coarse grained models”.  4thEuropean Symposium of the Protein Society, 18-22 April 2001, Paris, France.Protein Sci. Vol. Pp. 2001.

 

  1. Keskin, I. Bahar, D.G. Covell, A.R. Atilgan, S. Durell, R.L. Jernigan. “Large functional motions of proteins”.Biophysical Society Meeting, Boston, MA, USA. 17-21 Feb. 2001.

 

  1. Keskin, S. Durell, R.L. Jernigan, and D. G. Covell, “Relating Global Molecular Motions of Microtubule to its Function”, 5-9 August, 2000, 14thAnnual Symposium of the Protein Society, San Diego, CA, USA. Protein Sci. Vol. 9(1), pp.122, 2000.

 

  1. Keskin, S. Durell, R. L. Jernigan, and D. G. Covell, “Global Motions: Relating of Tubulin”, 13-15 June 2000, Computational Biophysics, Nice, France.

 

  1. Keskin, S. Durell, R. L. Jernigan, and D. G.  Covell, “Assessing Global Molecular Motions: Relating TubulinFlexibility to Function”, 18-21 March 2000, 5th Johns Hopkins Protein Folding Meeting, VA, USA.

 

  1. Keskin, I. Bahar, R. L. Jernigan, D.G. Covell, “Characterization of Anticancer Agents and their Growth Inhibitory Potency: Relationships between Potency and Chemical Substructure”, 24-28 July.1999, 13thAnnual Symposium of the Protein Society, Boston, Massachusetts, USA.

 

  1. Keskin, R. L. Jernigan & I. Bahar, “Proteins with similar architecture exhibit common large-scale dynamic behavior. Specificity resides in local differences”, 24-28 July.1999, 13thAnnual Symposium of the Protein Society, Boston, Massachusetts, USA.

 

  1. Keskin, I. Bahar, R. L. Jernigan, D.G. Covell, “Characterization of Anticancer Agents and their Growth Inhibitory Potency: Relationships between Potency and Chemical Substructure”, 13-17 Feb.1999, Biophysical Society Meeting, Baltimore, USA.

 

  1. Duman, O. Keskin, I. Bahar, J. R. Robinson, “Stabilization of Hen Egg Lysozyme with Solutions Containing Polyvinyl Pyrrolidone” presented as poster in the Fifth European Symposium on Controlled Drug Delivery, 1-3 April 1998, Noordwijk aan Zee, The Netherlands.

 

  1. Keskin, B. Ozkan, I. Bahar, “Side Chain Packing in Protein Structures”, presented as poster in 8th European Congress on Biotechnology, 17-21 August 1997, Budapest, Hungary. Published in the Proceedings of the Symposium.

 

  1. Ozkan, O. Keskin, I. Bahar, “Identification of Native Conformations of Proteins Using a Low Resolution Model”, presented as poster in 8th European Congress on Biotechnology, 17-21 August 1997, Budapest, Hungary. Published in the Proceedings of the Symposium.

 

  1. Keskin, I.Bahar, “Side Chain Packing in Protein Structures in Low Resolution Model”, 4th Statistical Physics Days, June 17-18,1997, Istanbul Technical Univesity, Istanbul.

 

  1. Sunol, O. Keskin, O. Guney, A. Sunol, “Supercritical Fluid Aided Preparation of Aerogelsand their Characterization” presented as poster in 3rd International Symposium on Supercritical Fluids, 17-19 October, 1994, Strasbourg, France. Published in the Proceedings of the Symposium.

 

  1. Sunol, O. Keskin, O. Guney, A. Sunol, “Supercritical Fluid Aided Preparation of Aerogelsand their Characterization” AICHE Annual Meeting, San Francisco, CA, 13-18 November, 1994. Published in the Proceedings of the Symposium.