Nithin Chandran

Assistant Professor

2021 -  today - Assistant Professor,  Laboratory of Computational Biology, Biological and Chemical Research Centre, Faculty of Chemistry,  University of Warsaw
2018 - 2021 - Postdoctoral Researcher, Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw
2017 - 2018 - Research Associate, Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw
2012 - 2017 - Research Scholar, Computational Structural Biology Lab, Department of Biotechnology, Indian Institute of Technology Kharagpur

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Publications

26. Comparative analysis of RNA 3D structure prediction methods: towards enhanced modeling of RNA–ligand interactionsNucleic Acids Research, 52, 2024Chandran Nithin, Kmiecik Sebastian, Roman Błaszczyk, Julita Nowicka, Irina Tuszyńska
27. Exploring protein functions from structural flexibility using CABS-flex modelingProtein Science, 33(9): :e509, 2024Chandran Nithin, Fornari Rocco, Pilla Smita, Wróblewski Karol, Zalewski Mateusz, Rafał Madaj, Andrzej Kolinski, Joanna M. Macnar, Kmiecik Sebastian
28. RNA-Puzzles Round V: blind predictions of 23 RNA structuresNature Methods, 2024Fan Bu, Yagoub Adam, Ryszard W. Adamiak, Maciej Antczak, Belisa Rebeca H. de Aquino, Nagendar Goud Badepally, Robert T. Batey, Eugene F. Baulin, Pawel Boinski, Michał J. Boniecki, Janusz M. Bujnicki, Kristy A. Carpenter, Jose Chacon, Shi-Jie Chen, Wah Chiu, Pablo Cordero, Naba Krishna Das, Rhiju Das, Wayne K. Dawson, Frank DiMaio, Feng Ding, Anne-Catherine Dock-Bregeon, Nikolay V. Dokholyan, Ron O. Dror, Stanisław Dunin-Horkawicz, Stephan Eismann, Eric Ennifar, Reza Esmaeeli, Masoud Amiri Farsani, Adrian R. Ferré-D’Amaré, Caleb Geniesse, George E. Ghanim, Horacio V. Guzman, Iris V. Hood, Lin Huang, Dharm Skandh Jain, Farhang Jaryani, Lei Jin, Astha Joshi, Masha Karelina, Jeffrey S. Kieft, Wipapat Kladwang, Kmiecik Sebastian, Deepak Koirala, Markus Kollmann, Rachael C. Kretsch, Kurciński Mateusz, Jun Li, Shuang Li, Marcin Magnus, BenoÎt Masquida, S. Naeim Moafinejad, Arup Mondal, Sunandan Mukherjee, Thi Hoang Duong Nguyen, Grigory Nikolaev, Chandran Nithin, Grace Nye, Iswarya P. N. Pandaranadar Jeyeram, Alberto Perez, Phillip Pham, Joseph A. Piccirilli, Pilla Smita, Radosław Pluta, Simón Poblete, Almudena Ponce-Salvatierra, Mariusz Popenda, Lukasz Popenda, Fabrizio Pucci, Ramya Rangan, Angana Ray, Aiming Ren, Joanna Sarzynska, Congzhou Mike Sha, Filip Stefaniak, Zhaoming Su, Krishna C. Suddala, Marta Szachniuk, Raphael Townshend, Robert J. Trachman III, Jian Wang, Wenkai Wang, Andrew Watkins, Tomasz K. Wirecki, Yi Xiao, Peng Xiong, Yiduo Xiong, Jianyi Yang, Joseph David Yesselman, Jinwei Zhang, Yi Zhang, Zhenzhen Zhang, Yuanzhe Zhou, Tomasz Zok, Dong Zhang, Sicheng Zhang, Adriana Żyła, Eric Westhof, Zhichao Miao
29. Advanced computational tools for quantitative analysis of protein–nucleic acid interfaces In Advances in Protein Molecular and Structural Biology Methods : 163--180, 2022Sunandan Mukherjee, Chandran Nithin
30. Computational Pipeline for Reference-Free Comparative Analysis of RNA 3D Structures Applied to SARS-CoV-2 UTR Models Int. J. Mol. Sci., 23: 9630, 2022Julita Gumna, Maciej Antczak, Ryszard W. Adamiak, Janusz M. Bujnicki, Shi-Jie Chen, Feng Ding, Pritha Ghosh, Jun Li, Sunandan Mukherjee, Chandran Nithin, Katarzyna Pachulska-Wieczorek, Almudena Ponce-Salvatierra, Mariusz Popenda, Joanna Sarzynska, Tomasz Wirecki, Dong Zhang, Sicheng Zhang, Tomasz Zok, Eric Westhof, Marta Szachniuk, Zhichao Miao, Agnieszka Rybarczyk
31. MAPIYA contact map server for identification and visualization of molecular interactions in proteins and biological complexesNucleic Acids Research: gkac307, 2022Aleksandra E Badaczewska-Dawid, Chandran Nithin, Wróblewski Karol, Kurciński Mateusz, Kmiecik Sebastian
32. Molecular insights into RNA recognition and gene regulation by the TRIM-NHL protein Mei-P26Life Science Alliance, 5 (8) : e202201418, 2022Anna Salerno-Kochan, Andreas Horn, Pritha Ghosh, Chandran Nithin, Anna Kościelniak, Andreas Meindl, Daniela Strauss, Rościsław Krutyhołowa, Oliver Rossbach, Janusz M Bujnicki, Monika Gaik , Jan Medenbach, Sebastian Glatt
33. NCodR: A multi-class SVM classification to distinguish between non-coding RNAs in ViridiplantaeQuantitative Plant Biology, 3: E23, 2022Chandran Nithin, Sunandan Mukherjee, Jolly Basak, Ranjit Prasad Bahadur
34. Computational Modeling Methods for 3D Structure Prediction of RibozymesRibozymes: 861-881, 2021Ghosh Pritha, Chandran Nithin, Joshi Astha, Stefaniak Filip, Wirecki Tomasz K., Bujnicki Janusz M.
35. Constrained peptides mimic a viral suppressor of RNA silencingNucleic Acids Research, 2021Arne Kuepper, Niall McLoughlin, Saskia Neubacher, Alejandro Yeste-Vázquez, Estel Collado Camps, Chandran Nithin, Sunandan Mukherjee, Lucas Bethge, Janusz M Bujnicki, Roland Brock, Stefan Heinrichs, Tom N Grossmann
36. RNA and DNA G-quadruplexes bind to human Dicer and inhibit its activityCellular and Molecular Life Sciences, 2021Natalia Koralewska, Agnieszka Szczepanska, Kinga Ciechanowska, Marta Wojnicka, Maria Pokornowska, Marek C Milewski, Dorota Gudanis, Daniel Baranowski, Chandran Nithin, Janusz M Bujnicki, Zofia Gdaniec, Marek Figlerowicz, Anna Kurzynska-Kokorniak
37. Genome-wide mapping of SARS-CoV-2 RNA structures identifies therapeutically-relevant elementsNucleic Acids Research, 48: 12436–12452, 2020Ilaria Manfredonia, Chandran Nithin, Almudena Ponce-Salvatierra, Pritha Ghosh, Tomasz K Wirecki, Tycho Marinus, Natacha S Ogando, Eric J Snijder, Martijn J van Hemert, Janusz M Bujnicki, Danny Incarnato
38. Modeling of Three-Dimensional RNA Structures Using SimRNAProtein Structure Prediction (Part of the Methods in Molecular Biology book series), 2165: 103-125, 2020Tomasz K Wirecki, Chandran Nithin, Sunandan Mukherjee, Janusz M Bujnicki, Michał J Boniecki
39. A structure-based model for the prediction of protein-RNA binding affinityRNA, 25: 1628-1645, 2019Chandran Nithin, Sunandan Mukherjee, Ranjit Prasad Bahadur
40. Computational modeling of RNA 3D structure based on experimental dataBioscience Reports, 39(2): BSR20180430, 2019Almudena Ponce-Salvatierra, Astha, Katarzyna Merdas, Chandran Nithin, Pritha Ghosh, Sunandan Mukherjee, Janusz M Bujnicki

...And 11 more - see all publications of this author