Publications by authors named "Nithin C"

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Blind Prediction of Complex Water and Ion Ensembles Around RNA in CASP16.
Rachael C Kretsch, Elisa Posani, Eugene F Baulin, Janusz M Bujnicki, Giovanni Bussi

Proteins· January 2026

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Blind prediction of complex water and ion ensembles around RNA in CASP16.
Rachael C Kretsch, Elisa Posani, Eugene F Baulin, Janusz M Bujnicki, Giovanni Bussi

bioRxiv· November 2025

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When does molecular dynamics improve RNA models? Insights from CASP15 and practical guidelines.
Chandran Nithin, Smita P Pilla, Sebastian Kmiecik

Comput Struct Biotechnol J· October 2025

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Protein-RNA Docking Benchmark v3.0 Integrated With Binding Affinity.
Shri Kant, Chandran Nithin, Sunandan Mukherjee, Atanu Maity, Ranjit Prasad Bahadur

Proteins· September 2025

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Computational methods for modeling protein-protein interactions in the AI era: Current status and future directions.
Hao Li, Chandran Nithin, Sebastian Kmiecik, Sheng-You Huang

Drug Discov Today· June 2025

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RNA-Puzzles Round V: blind predictions of 23 RNA structures.
Fan Bu, Yagoub Adam, Ryszard W Adamiak, Maciej Antczak, Belisa Rebeca H de Aquino

Nat Methods· February 2025

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Exploring protein functions from structural flexibility using CABS-flex modeling.
Chandran Nithin, Rocco Peter Fornari, Smita P Pilla, Karol Wroblewski, Mateusz Zalewski

Protein Sci· September 2024

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Comparative analysis of RNA 3D structure prediction methods: towards enhanced modeling of RNA-ligand interactions.
Chandran Nithin, Sebastian Kmiecik, Roman Błaszczyk, Julita Nowicka, Irina Tuszyńska

Nucleic Acids Res· July 2024

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NCodR: A multi-class support vector machine classification to distinguish non-coding RNAs in Viridiplantae.
Chandran Nithin, Sunandan Mukherjee, Jolly Basak, Ranjit Prasad Bahadur

Quant Plant Biol· October 2022

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Molecular insights into RNA recognition and gene regulation by the TRIM-NHL protein Mei-P26.
Anna Salerno-Kochan, Andreas Horn, Pritha Ghosh, Chandran Nithin, Anna Kościelniak

Life Sci Alliance· August 2022

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Computational Pipeline for Reference-Free Comparative Analysis of RNA 3D Structures Applied to SARS-CoV-2 UTR Models.
Julita Gumna, Maciej Antczak, Ryszard W Adamiak, Janusz M Bujnicki, Shi-Jie Chen

Int J Mol Sci· August 2022

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MAPIYA contact map server for identification and visualization of molecular interactions in proteins and biological complexes.
Aleksandra E Badaczewska-Dawid, Chandran Nithin, Karol Wroblewski, Mateusz Kurcinski, Sebastian Kmiecik

Nucleic Acids Res· July 2022

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Constrained peptides mimic a viral suppressor of RNA silencing.
Arne Kuepper, Niall M McLoughlin, Saskia Neubacher, Alejandro Yeste-Vázquez, Estel Collado Camps

Nucleic Acids Res· December 2021

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RNA and DNA G-quadruplexes bind to human dicer and inhibit its activity.
Natalia Koralewska, Agnieszka Szczepanska, Kinga Ciechanowska, Marta Wojnicka, Maria Pokornowska

Cell Mol Life Sci· April 2021

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Modeling of Three-Dimensional RNA Structures Using SimRNA.
Tomasz K Wirecki, Chandran Nithin, Sunandan Mukherjee, Janusz M Bujnicki, Michał J Boniecki

Methods Mol Biol· March 2021

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Genome-wide mapping of SARS-CoV-2 RNA structures identifies therapeutically-relevant elements.
Ilaria Manfredonia, Chandran Nithin, Almudena Ponce-Salvatierra, Pritha Ghosh, Tomasz K Wirecki

Nucleic Acids Res· December 2020

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Identification and characterization of differentially expressed Phaseolus vulgaris miRNAs and their targets during mungbean yellow mosaic India virus infection reveals new insight into Phaseolus-MYMIV interaction.
Nisha Patwa, Chandran Nithin, Ranjit Prasad Bahadur, Jolly Basak

Genomics· December 2019

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A structure-based model for the prediction of protein-RNA binding affinity.
Chandran Nithin, Sunandan Mukherjee, Ranjit Prasad Bahadur

RNA· December 2019

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Dissecting water binding sites at protein-protein interfaces: a lesson from the atomic structures in the Protein Data Bank.
Sunandan Mukherjee, Chandran Nithin, Yasaswi Divakaruni, Ranjit Prasad Bahadur

J Biomol Struct Dyn· March 2019

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QRNAS: software tool for refinement of nucleic acid structures.
Juliusz Stasiewicz, Sunandan Mukherjee, Chandran Nithin, Janusz M Bujnicki

BMC Struct Biol· March 2019

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Computational modeling of RNA 3D structure based on experimental data.
Almudena Ponce-Salvatierra, Astha, Katarzyna Merdas, Chandran Nithin, Pritha Ghosh

Biosci Rep· February 2019

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Bioinformatics Tools and Benchmarks for Computational Docking and 3D Structure Prediction of RNA-Protein Complexes.
Chandran Nithin, Pritha Ghosh, Janusz M Bujnicki

Genes (Basel)· August 2018

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Genome-wide identification of miRNAs and lncRNAs in Cajanus cajan.
Chandran Nithin, Amal Thomas, Jolly Basak, Ranjit Prasad Bahadur

BMC Genomics· November 2017

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A non-redundant protein-RNA docking benchmark version 2.0.
Chandran Nithin, Sunandan Mukherjee, Ranjit Prasad Bahadur

Proteins· February 2017

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Targeting Non-Coding RNAs in Plants with the CRISPR-Cas Technology is a Challenge yet Worth Accepting.
Jolly Basak, Chandran Nithin

Front Plant Sci· December 2015

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