Smita Pilla

Assistant Professor

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Publications

10. Blind Prediction of Complex Water and Ion Ensembles Around RNA in CASP16Proteins: Structure, Function, And Bioinformatics, n/a: 1–22, 2025Kretsch Rachael C., Posani Elisa, Baulin Eugene F., Bujnicki Janusz M., Bussi Giovanni, Cheatham Iii Thomas E., Chen Shi-Jie, Elofsson Arne, Farsani Masoud Amiri, Fisher Olivia N., Gromiha M. Michael, Gupta Ayush, Hamada Michiaki, Harini K., Hu Gang, Huang David, Iwakiri Junichi, Jain Anika, Kagaya Yuki, Kihara Daisuke, Kmiecik Sebastian, Krishnan Sowmya Ramaswamy, Kurisaki Ikuo, Languin-Cattoën Olivier, Li Jun, Li Shanshan, Malekzadeh Karim, Nakamura Tsukasa, Ni Wentao, Chandran Nithin, Palo Michael Z., Park Joon Hong, Pilla Smita, Poblete Simón, Pucci Fabrizio, Punuru Pranav, Saha Anouka, Sato Kengo, Srivastava Ambuj, Terashi Genki, Tugolukova Emilia, Verburgt Jacob, Wuyun Qiqige, Zerze Gül H., Zhang Kaiming, Zhang Sicheng, Zheng Wei, Zhou Yuanzhe, Chiu Wah, Case David A., Das Rhiju
11. RNA-Puzzles Round V: blind predictions of 23 RNA structuresNature Methods, 22: 399–411, 2025Fan 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
12. When does molecular dynamics improve RNA models? Insights from CASP15 and practical guidelinesComputational and Structural Biotechnology Journal, 27: 4201-4211, 2025Chandran Nithin, Pilla Smita, Kmiecik Sebastian
13. Are there double knots in proteins? Prediction and in vitro verification based on TrmD-Tm1570 fusion from C. nitroreducensFrontiers in Molecular Biosciences , 10, 2024 Agata P. Perlinska, Mai Lan Nguyen, Pilla Smita, Emilia Staszor, Iwona Lewandowska, Agata Bernat, Elżbieta Purta, Rafal Augustyniak, Janusz M. Bujnicki, Joanna I. Sulkowska
14. 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
15. Dissecting macromolecular recognition sites in ribosome: implication to its self-assemblyRna Biology, 16: 1300--1312, 2019Pilla Smita, Amal Thomas , Ranjit Prasad Bahadur
16. Dissecting protein-protein interactions in proteasome assembly: Implication to its self-assemblyJournal Of Molecular Recognition, 32, 2019Pilla Smita, Babu R, Ranjit Prasad Bahadur
17. Residue conservation elucidates the evolution of r-proteins in ribosomal assembly and functionInternational Journal Of Biological Macromolecules, 140: 323--329, 2019Pilla Smita, Ranjit Prasad Bahadur
18. Molecular architecture of protein-RNA recognition sitesJournal of Biomolecular Structure And Dynamics, 33: 2738 - 2751, 2015Amita Barik, Chandran Nithin, Pilla Smita, Ranjit Prasad Bahadur
19. Design of novel Geldanamycin analogue hsp90 alpha-inhibitor in silico for breast cancer therapyMedical Hypotheses, 81: 463--469, 2013Mahanta S, Pilla Smita, Paul S