Publications and professional activities

Peer-reviewed articles:

1. Ognjen Perišić, Willy Wriggers, “Mechanism for the Unfolding of the TOP7 Protein in Steered Molecular Dynamics Simulations as Revealed by Mutual Information Analysis”, Frontiers in Molecular Biosciences, 8, 2021; doi: 10.3389/fmolb.2021.696609

2. Ognjen Perišić, “Recognition of Potential COVID-19 Drug Treatments through the Study of Existing Protein–Drug and Protein-Protein Structures: An Analysis of Kinetically Active Residues”, MDPI – Biomolecules, (2020), 10, 1346; doi:10.3390/biom10091346

3. Ognjen Perišić, Stephanie Portillo-Ledesma, Tamar Schlick, “Sensitive effect of linker histone binding mode and subtype on chromatin condensation”, Nucleic Acids Research journal, June 2019, 47(10), pp 4948–4957, https://doi.org/10.1093/nar/gkz234.

4. Ognjen Perišić, "“Heterodimer binding scaffolds recognition via the analysis of kinetically hot residues", Pharmaceuticals, 2018, 11(1), 29; DOI:10.3390/ph11010029.

5. Ognjen Perišić, Tamar Schlick, "Dependence of the Linker Histone and Chromatin Condensation on the Nucleosome Environment", Journal of Physical Chemistry B, 2017, 121 (33), pp 7823-7832, DOI: 10.1021/acs.jpcb.7b04917.

6. Irena Marjanovic, Jelena Kostic, Bojana Stanic, Nadja Pejanovic, Bojana Lucic, Teodora Karan-Djurasevic, Dragana Janic, Lidija Dokmanovic, Srdja Jankovic, Nada Suvajdzic Vukovic, Dragica Tomin, Ognjen Perisic, Goran Rakocevic, Milos Popovic, Sonja Pavlovic, Natasa Tosic, "Parallel targeted next generation sequencing of childhood and adult acute myeloid leukemia patients reveals uniform genomic profile of the disease", Tumor Biology (2016), doi:10.1007/s13277-016-5142-7.

7. Ognjen Perišić, Tamar Schlick, "Computational strategies to address chromatin structure problems", Physical Biology (2016), Volume 13, Number 3, 035006.

8. Milena Todorovic Balint, JelenaJelicic, Biljana Mihaljevic, Jelena Kostic, Bojana Stanic, Bela Balint, Nadja Pejanovic, Bojana Lucic, Natasa Tosic, Irena Marjanovic, Maja Stojiljkovic, Teodora Karan-Djurasevic, Ognjen Perisic, Goran Rakocevic, Milos Popovic, Sava Raicevic, Jelena Bila, Darko Antic, Bosko Andjelic, Sonja Pavlovic, "Gene Mutation Profiles in Primary Diffuse Large B Cell Lymphoma of Central Nervous System: Next Generation Sequencing Analyses", International Journal of Molecular Sciences (2016), Vol. 17, 683.

9. Ognjen Perišić, Hui Lu, (2014), On the Improvement of Free-Energy Calculation from Steered Molecular Dynamics Simulations Using Adaptive Stochastic Perturbation Protocols. PLoS ONE 9(9): e101810.doi:10.1371/journal.pone.0101810 -> http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0101810

10. Ognjen Perišić, "Pulling-spring modulation as a method for improving the potential of mean-force reconstruction in single-molecule manipulation experiments", Physical Review E, Vol. 87, 013303 (2013).

11. Ognjen Perišić, Hui Lu, "Efficient free-energy-profile reconstruction using adaptive stochastic perturbation protocols", Physical Review E, Vol. 84, 056705 (2011).

12. Ognjen Perišić, Rosana Collepardo-Guevara, Tamar Schlick, "Modeling studies of chromatin fiber structure as a function of DNA linker length", Journal of Molecular Biology (2010), Vol. 403, Issue 5, 777-802.

13. Cele Abad-Zapatero, Ognjen Perišić, John Wass, A. Patricia Bento, John Overington, Bissan Al-Lazikani and Michael E. Johnson,  "Ligand Efficiency Indices for an Effective Mapping of Chemico-Biological Space: The concept of and Atlas-like representation",  Drug Discovery Today (2010), Vol. 15, Issues 19-20, 804-811.

14. Tamar Schlick, Ognjen Perišić, "Mesoscale Simulations of Two Nucleosome-Repeat Length Oligonucleosomes", Physical Chemistry Chemical Physics (2009), Vol. 11, 10729-10737.

15. Georgi Z. Genchev, Morten Källberg, Gamze Gürsoy, Anuradha Mittal, Lalit Dubey, Ognjen Perišić, Gang Feng, Robert Langlois and Hui Lu, "Mechanical Signaling on the Single Protein Level Studied Using Steered Molecular Dynamics",  Cell Biochemistry Biophysics (2009), Vol. 55, 141-152.

16. Deepak Sharma, Ognjen Perisic, Qing Peng, Yi Cao, Canaan Lam, Hui Lu and Hongbin Li, "Single Molecule Force Spectroscopy Reveals a Novel Mechanically Stable Protein Fold and the Rational Tuning of its Mechanical Stability", Proceedings of the National Academy of Sciences (2007), Vol. 104, no.22, 9278-9283. Highlighted in SCIENCE vol. 316, (1395), 8 JUNE 2007!

17. Robert E. Langlois, Alice Diec, Ognjen Perisic, Yang Dai, Hui Lu, "Improved protein fold assignment using support vector machines", International Journal of Bioinformatics Research and Applications, (2005), Vol. 1(3), 319.

Book chapter :

• • 1. Hui Lu, Ognjen Perišić and Dong Xu, "Physical and Chemical Basis for Structural Bioinformatics", Book: Computational Methods for Protein Structure Prediction and Modeling: Volume 2, Pages 267-297, 2007,. edited by Ying Xu, Dong Xu, and Jie Liang. Springer-Verlag, ISBN-10: 0387333215, ISBN-13: 978-0387333212.

Membership:

• AAAS – awarded a free membership and subscription to Science after participating in the AAAS/Science Program for Excellence in Science (2018-2019)

  • • 1. Professional activities:

      2. Challenges in Data Science : a complex systems perspective - International Conference, October 14-17 2015, Castello del Valentino, Torino, Italy                                                                                                                                                                  

      3. Lipari School on BioInformatics and Computational Biology - Computational Dynamic Analysis of Biological Processes,  July 19 - July 25, 2015, Lipari Island, Italy.                                                                                                                                                                  

      4. International Conference on Statistical Physics - SigmaPhi, 7-12 July 2014, Rhodes, Greece. An Advisory Committee member.