Publications

2017

  • 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 22;121(24):5917-5927.
  • 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.
  • 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.

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.
  • 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 Nov;1860(11 Pt B):2646-55.
  • 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.
  • Keskin O, Tuncbag N, Gursoy A., Keskin O, Tuncbag N, Gursoy A., Chem Rev. 2016 Apr 27;116(8):4884-909.
  • 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.
  • Chavan TS, Muratcioglu S, Marszalek R, Jang H, Keskin O, Gursoy A, Nussinov R, Gaponenko V.,  Plasma membrane regulates Ras signaling networks. Cell Logist. 2016 Feb 18;5(4):e1136374.
  • 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.
  • 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.

2015

  • Muratcioglu S, Guven-Maiorov E, Keskin O, Gursoy A., Advances in template-based protein docking by utilizing interfaces towards completing structural interactome. Curr Opin Struct Biol. 2015 Nov 2;35:87-92.
  • Muratcioglu S, Presman DM, Pooley JR, Grntved 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.
  • 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.
  • 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.
  • 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
  • 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 Jul 7;23(7):1325-35.
  • Cavga AD, Karahan N, Keskin O, Gursoy A., Taming Oncogenic Signaling at Protein Interfaces: Challenges and Opportunities, Curr Top Med Chem. 2015;15(20):2005-18.
  • Nussinov R, Tsai CJ, Muratcioglu S, Jang H, Gursoy A, Keskin O., Principles of K-Ras effector organization and the role of oncogenic K-Ras in cancer initiation through G1 cell cycle deregulation. Expert Rev Proteomics. 2015 Dec;12(6):669-82

2014

  • 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.
  • Acuner Ozbabacan SE, Gursoy A, Nussinov R, Keskin O. 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).
  • Cukuroglu E, Gursoy A, Nussinov R, Keskin O. Non-redundant unique interface structures as templates for modeling protein interactions. PLoS One. 2014 Jan 27;9(1).
  • Kuzu G, Keskin O, Nussinov R, Gursoy A. Modeling protein assemblies in the proteome. Mol Cell Proteomics. 2014 Mar;13(3):887-96.
  • 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.
  • Acuner-Ozbabacan ES, Engin BH, 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. doi: 10.1186/1471-2164-15-S4-S2.
  • Cukuroglu E, Engin HB, Gursoy A, Keskin O., Hot spots in protein-protein interfaces: towards drug discovery. Prog Biophys Mol Biol. 2014 Nov-Dec;116(2-3):165-73
  • Demircioglu D, Keskin O, Gursoy A., Modeling structural protein interaction networks for betweenness analysis. ISCIS2014 LCNS. 2014:367-76

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)
  • Maiorov EG, Keskin O, Ng OH, Ozbek U, Gursoy A.,  Identification of interconnected markers for T-cell acute lymphoblastic leukemia. Biomed Res Int. 2013;2013:210253.
  • 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. 2013 May 22.
  • Guven Maiorov E, Keskin O, Gursoy A, Nussinov R. , The structural network of inflammation and cancer: merits and challenges. Semin Cancer Biol. 2013 Aug;23(4):243-51.
  • An O, Gursoy A, Gurgey A, Keskin O. , Structural and functional analysis of perforin mutations in association with clinical data of familial hemophagocytic lymphohistiocytosis type 2 (FHL2) patients. Protein Sci. 2013 Jun;22(6):823-39.
  • Kuzu G, Gursoy A, Nussinov R, Keskin O. , Exploiting conformational ensembles in modeling protein-protein interactions on the proteome scale. J Proteome Res. 2013 Jun 7;12(6):2641-53.
  • Kar G, Keskin O, Fraternali F, Gursoy A. , Emerging role of the ubiquitin-proteasome system as drug targets. Curr Pharm Des. 2013;19(18):3175-89.

2012

  • Engin HB, Keskin O, Nussinov R, Gursoy A., 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
  • Kar G, Kuzu G, Keskin O, Gursoy A. , Protein-protein interfaces integrated into interaction networks: implications on drug design. Curr Pharm Des. 2012 May 29.
  • Kuzu G, Keskin O, Gursoy A, Nussinov R. Constructing structural networks of signaling pathways on the proteome scale. Curr Opin Struct Biol. 2012 Jun;22(3):367-77.
  • Acuner Ozbabacan SE, Keskin O, Nussinov R, Gursoy A. , Enriching the human apoptosis pathway by predicting the structures of protein-protein complexes. J Struct Biol. 2012 Sep;179(3):338-46
  • Tuncbag N, Keskin O, Nussinov R, Gursoy A. Fast and accurate modeling of protein-protein interactions by combining template-interface-based docking with flexible refinement. Proteins. 2012 Apr;80(4):1239-49.
  • Kuzu G, Keskin O, Gursoy A, Nussinov R. Expanding the conformational selection paradigm in protein-ligand docking. Methods Mol Biol. 2012;819:59-74.
  • Kar G, Keskin O, Nussinov R, Gursoy A. Human proteome-scale structural modeling of E2-E3 interactions exploiting interface motifs. J Proteome Res. 2012; Feb 3;11(2):1196-207.

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, Nature Protocol, 2011 vol. 6 (9) pp. 1341-54.
  • Cukuroglu E, Gursoy A, Keskin O. HotRegion: a database of predicted hot spot clusters. Nucleic Acids Res. 2012 Jan;40(Database issue):D829-33.
  • Sanli D, Keskin O, Gursoy A, Erman B. Structural cooperativity in histone H3 tail modifications. Protein Sci. 2011 Dec;20(12):1982-90. doi: 10.1002/pro.745.
  • O. Ulucan, O. Keskin, B. Erman, A. Gursoy, A Comparative Molecular Dynamics Study of Methylation State Specificity of JMJD2A, PLos ONE, 2011 vol. 6 (9) pp. e24664
  • S.E.A. Ozbabacan, H.B. Engin, A. Gursoy, O. Keskin, Transient protein-protein interactions, Protein Engineering Design & Selection, 2011 vol. 24 (9) pp. 635-48.
  • N. Tuncbag, A. Gursoy, O. Keskin, Prediction of protein-protein interactions: unifying evolution and structure at protein interfaces, Phys Biol, 2011 vol. 8 (3) pp. 035006.
  • 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 vol. 6 (3) pp. e14765.

2010

  • G. Kar, O. Keskin, A. Gursoy, N. Nussinov, Allostery and population shift in drug discovery, Current Opinion in Pharmacology, Sep, 2010.
  • S.E.A Ozbabacan, A. Gursoy, O. Keskin, R. Nussinov, Conformational ensembles, signal transduction and residue hot spots: Application to drug discovery, Current Opinion in Drug Discovery and Development, 13(5), pp. 527-537, 2010
  • S. Kalyoncu, O. Keskin, A. Gursoy,Interaction prediction and classification of PDZ domains, BMC Bioinformatics, 11(357), 2010.
  • N. Tuncbag, FS. Salman, O. Keskin, A. Gursoy, Analysis and network representation of hotspots in protein interfaces using minimum cut trees, Protein-Structure Function and Bioinformatics, 78(10), pp. 2283-2294, 2010.
  • EB. Unal, A. Gursoy, B. Erman,VitAL: Viterbi algorithm for de novo peptide design, PLOS One, 5(6), e10926, 2010.
  • N. Tuncbag, O.Keskin, A. Gursoy, HotPoint: hotspot prediction server for protein interfaces, Nucl. Acids. Res. (38) Web Server Issue, W402-W406, 2010.
  • E. Cukuroglu, A. Gursoy, O. Keskin, Analysis of Hot Region Organization in Hub Proteins, Annals of Biomedical Engineering, 38(6), pp. 2068-2078, 2010.

2009

  • G. Kar, A. Gursoy, O. Keskin, Human cancer protein-protein interaction network: a structural perspective, PLOS Computational Biology, 5(12) , e1000601, Dec 2009
  • Tuncbag N, Kar G, Gursoy A, Keskin O,  Nussinov R, Towards inferring time dimensionality in protein_protein interaction networks by integrating structures: the p53 example, Molecular BioSystems, 2009
  • Unal B, Gursoy A, Erman B, Conformational energies and entropies of peptides, and the peptide-protein binding problem, Physical Biology 6, 2009
  • Tuncbag N, Gursoy A, Keskin O, Identification of computational hot spots in protein interfaces: combining solvent accessibility and inter-residue potentials improves the accuracy, Bioinformatics, Volume: 25 Issue: 12 Pages: 1513-1520 , 2009
  • Tuncbag N, Kar G, Keskin O, Gursoy A, Nussinov R, A survey of available tools and web servers for analysis of protein-protein interactions and interfaces, Briefings in Bioinformatics, Volume: 10 Issue: 3 Pages: 217-232, 2009

2008

  • Gursoy A, Keskin O, Nussinov R., Topological properties of protein interaction networks from a structural perspective, Biochemical Society Transactions, Volume: 36 Pages: 1398-1403, 2008
  • Tuncbag N, Gursoy A, Guney E, Keskin O, Nussinov R, Architectures and functional coverage of protein-protein interfaces, Journal of Molecular Biology, Volume: 381 Issue: 3 Pages: 785-802, 2008
  • Keskin, O,  Tuncbag, N,  Gursoy, A, Characterization and prediction of protein interfaces to infer protein-protein interaction networks, Current Pharmaceutical Biotechnology, (9)2, 67-76, 2008.
  • Guney, E, Tuncbag, N, Keskin, O, Gursoy, A, HotSprint: database of computational hot spots in protein interfaces, Nucleic Acid Research, (36)  D662-D666, 2008.
  • O. Keskin, A. Gursoy,, B. Ma, R. Nussinov, Principles of protein-protein interactions: What are the preferred ways for proteins to interact?,Chemical Reviews, (108) 4, 1225-1244, 2008.

2007

  • Keskin O, Gursoy A, Ma B, Nussinov R. Towards drugs targeting multiple proteins in a systems biology approach,  Current Topics in Medicinal Chemistry 7 (10): 943-951 2007
  • O. Sonmez and A. Gursoy, A Novel Economic-based Scheduling Heuristic for Computational Grids, International Journal of High Performance Computing Applications, 21(1), 21-29, 2007.
  • L. Ormeci, A. Gursoy, G. Tunca, B. Erman, Computational Basis of Knowledge-Based Conformational Probabilities Derived from Local and Long-Range Interactions in Proteins, Proteins: Structure, Function, and Bioinformatics, 66(1):29-40 , 2007.

2006

  • A. Gursoy, O. Keskin, M. Turkay, B. Erman, Relationships between Unfolded Configurations of Proteins and Dynamics of Folding to the Native State, Journal of Polymer Science Part B: Polymer Physics, Vol. 44, 3667-3678, 2006
  • O. Yogurtcu, E. Erzin, and A. Gursoy, Extracting Gene Regulation Information from Microarray Time-Series Data Using Hidden Markov Model, LNCS Vol.:4263 , Pages:144-153 , 2006, Springer-Verlag

2005

  • O. Sonmez and A. Gursoy, Comparison of Pricing Policies for a Computational Grid Market, LNCS Vol. 3911 pp. 766-773, 2006 (PPAM 2005).
  • U. Ogmen, O. Keskin, S. Aytuna, R.Nussinoiv, A.Gursoy, PRISM: Protein interactions by Structural Matching, Nucleic Acids Research, Vol. 33, Web server issue, pp.W331-W336, (2005). PRISM Web Server
  • A.S. Aytuna, A.Gursoy, O.Keskin, Predictions of protein-protein interactions by combining structure and sequence conservation in protein interfaces, Bioinformatics, Vol. 21. No. 12, pp. 2850-2855, 2005.
  • A.K. Sinop, T. Abaci, U. Akkus, A. Gursoy, U. Gudukbay, PHR: A Paralllel Hierarchical Radiosity System with Dynamic Load Balancing, Journal of Supercomputing, Vol 31, pp. 249-263, 2005

2004

  • A. Palazoglu, A. Gursoy, Y. Arkun and  B. Erman, Folding Dynamics of Proteins from Denatured to Native State: Principal Component Analysis, Journal of Computational Biology Dec 2004, Vol. 11, No. 6: 1149-1168.
  • O. Keskin, D. Yuret, A. Gursoy, M. Turkay and B. Erman, Relationships between amino acid sequence and backbone torsion angle preferences, Proteins: Structure, Function, and Bioinformatics, Vol 55 No 4 pp. 992-998, 2004.
  • A, Gursoy, L.V. Kale, Performance and Modularity Benefits of Message-Driven Execution, Journal of Parallel and Distributed Computing, 64(2004) 461-480
  • E. Demir, O. Babur, U. Dogrusoz, A. Gursoy, A. Ayaz, G. Gulesir, G. Nisanci and R. Cetin-Atalay, An Ontology for Collaborative Construction and Analysis of Cellular Pathways,  Bioinformatics, Vol  20 No 3 pp. 349-356, 2004.

2003

  • A. Gursoy, Data Decomposition for K-Means Parallel Clustering, LNCS Vol 3019 pp. 241-248,  2003 (PPAM 2003)
  • A. Kocatas, A. Gursoy, R. Cetin-Atalay, Application of Data Mining Techniques to Protein-Protein Interactions“, LNCS Vol 2869 pp. 316-323, 2003  (ISCIS 2003)

2002

  • E. Demir, O. Babur, U. Dogrusoz, A. Gursoy, G. Nisanci, R. Cetin-Atalay, M. Ozturk, PATIKA: An Integrated Visual Environment for Collaborative Construction and Analysis of Cellular Pathways, Bioinformatics, Vol 18., No 7., pp. 996-1003 (2002)
  • A. Erdem, A. Gursoy, Time Domain Based Web Usage Mining, Proceedings of the IASTED Artificial and Computational Intelligence 2002, Pages:273-279 , Sep , 2002, Tokyo, Japan

2001

2000

1999-

  • A. Gursoy and I. Cengiz Mechanism for Programming SMP Clusters‘, Proc. of Intl Conf. Parallel and Distributed Processing Techniques and Applications, PDPTA’99, Ed. H.R. Arabnia, Las Vegas, June 28- July 1, 1999 , Vol IV pp. 1723-1729
  • I. Cengiz and A. Gursoy, Node-level Replicated Objects in SMP Clusters, Proc. of the 14th Intl. Symp. on Computer and Information Sciences, ISCISXIV, Ed. M Turksever et al. October 18-20, 1999, Kusadasi – Turkey, pp. 296-303
  • M. Atun and A. Gursoy, A New Load Balancing Algorithm Using Self-Organizing Maps, Proc. of the 14th Intl. Symp. on Computer and Information Sciences, ISCISXIV, Ed. M Turksever et al. October 18-20, 1999, Kusadasi – Turkey, pp. 787-794
  • R. Sireli and A. Gursoy, Parallel Hierarchical Radiosity‘, Proc. of Intl Conf. Parallel and Distributed Processing Techniques and Applications, PDPTA’99, Ed. H.R. Arabnia, Las Vegas, June 28- July 1, 1999 , Vol III pp. 1634-1640 Las Vegas, June 28- July 1, 1999,
  • L. Kale, R. Skeel, M. Bhandarkar, R. Brunner, A. Gursoy, N. Krawetz, J. Phillips, A. Shinozaki, K. Varadarajan, and K. Schulten. NAMD2: Greater scalability for parallel molecular dynamics. Journal of Computational Physics, 151, 283-312, (1999)
  • J.C. Phillips, R. Brunner, A. Shinozaki, M. Bhandarkar, N. Krawetz, A. Gursoy, L. Kale, R.D. Skeel, and K. Schulten, Avoiding Algorithmic Obfuscation in a Message-Driven Parallel MD Code, Computational Molecular Dynamics: Challenges, Methods, Ideas, Lecture Notes in Computational Science and Enginering, Springer, Berlin, 1999.
  • A. Gursoy and L.V. Kale, Simulating Message Driven Programs, Proc. of ICPP, Chicago, Aug 1996, Vol. III pp. 223-230
  • M. Nelson, W. Humphrey, A. Gursoy, A. Dalke, L.V. Kale, B. Skeel, K. Schulten, NAMD- A Paralel Object-Oriented Molecular Dynamics Program, International Journal of Supercomputing Applications, Vol. 10, No. 4, Winter 1996, pp. 251-268
  • M. Nelson, W. Humphrey, A. Gursoy, A. Dalke, L.V. Kale, B. Skeel, K. Schulten, R.Kuffrin, MDScope – A Visual Computing Environment for Structural Biology, Computer Physics Communications, Volume 91, Oct 1995, pages 111-134.
  • L.V. Kale, A. Gursoy, Modularity, reuse, and efficiency with message-driven libraries, Proceedings of the Seventh SIAM Conference on Parallel Processing For Scientific Computing, San Fransisco, California, Feb 15-17 1995, pages 738-743.
  • M. Nelson, W. Humphrey, A. Gursoy, A. Dalke, L.V. Kale, B. Skeel, K. Schulten, R.Kuffrin, MDScope – A Visual Computing Environment for Structural Biology, Proc. of the Intl. Conf. on Computational Engineering Science, July 30 – August 3 , 1995, Hawaii, 1995, Volume 1, pages .476-481 Editors: S.N.Atluri, G.Yagawa, T.A.Cruse, Springer-Verlag.
  • A. Gursoy and L.V. Kale, Dagger: combining the benefits of synchronous and asynchronous communication styles, Proceedings of IPPS’94, April 1994, Cancun, pages 590-596.
  • A. Gursoy, L.V. Kale, and S.P. Vanka. Unsteady fluid flow calculations using a machine independent parallel programming environment, In R. B. Pelz, A. Ecer, and J.Hauser, editors, Parallel Computational Fluid Dynamics ’92, pages 175-185. North-Holland, 1993.
  • L.V. Kale, A. Gursoy, Performance Benefits of Message Driven Executions, Intel Supercomputer User’s Group, Annual North America Users’ Conference, October 3-6, 1993, pages 209-129
  • A. Gursoy and L.V. Kale, Tolerating Latency with Dagger, International Symposium on Computer and Information Sciences, ISCIS VIII, November 1-3, 1993, Istanbul, Turkey, pages 354-361
  • L.V. Kale, A. Sinha, A. Gursoy, A Portable Software Support System for Irregular Computations, DIMACS93
  • A. Gursoy and L.V. Kale, High-Level Support for Divide-and-Conquer Parallelism, Proceedings of Supercomputing’91, Albuquerque, NM., November 1991, pages 283-282.