Nithin C

@nithin_aneesh
13 Followers
24 Following
28 Posts

- Engineer, Researcher, Epistemophilic, Pluviophile, Hodophile, Nemophilist.

- Bioinformatics/RNA Scientist, Molecure SA

- Assistant Professor (adiunkt), Laboratory of Computational Biology, CNBCh, University of Warsaw.

- Bioinformatics, RNA, RNA-protein complexes, protein-protein complexes, C++, STL and Linux.

- Doctor of Philosophy - PhD in Bioinformatics and Computational Biology from IIT Kharagpur.

- Former postdoc, Laboratory of Bioinformatics and Protein Engineering, IIMCB, Warsaw.

Nithin COct 13
Does molecular dynamics improve RNA models? This short video presents key findings from our latest paper. We asked when and why molecular dynamics helps (or fails to help) refine RNA structures. In this work, we share practical guidelines on how to use MD as a diagnostic tool, not a universal fixer.
Full paper: https://doi.org/10.1016/j.csbj.2025.10.003
#RNA #ComputationalBiology #Bioinformatics #RNAstructure #MolecularDynamics #CASP
Nithin CMay 30, 2025

🧬 New review out in Drug Discovery Today:

🔗 https://doi.org/10.1016/j.drudis.2025.104382

We take a critical look at how AI — especially AlphaFold(-Multimer/3) — has changed protein complex prediction.

End-to-end models work well for rigid complexes. Flexibility, disorder, and transient interfaces remain unsolved.

AI is shiny. Biology is complicated. We map what’s working, what isn’t, and what’s next.

#ComputationalBiology #Bioinformatics #DrugDiscovery #AlphaFold

Nithin CDec 2, 2024

"RNA-Puzzles Round V dives into blind predictions by 18 modeling groups for 23 #RNA structures. 🧬

From #aptamers to #riboswitches, it highlights progress and challenges in RNA #3D #modeling.

Proud to contribute to this incredible journey! A heartfelt thank you to the organizers, collaborators, and the amazing community advancing RNA #structural #biology.

Together, we’re pushing the boundaries of #RNA3D, #StructuralBiology, #Bioinformatics, and #ComputationalBiology.

https://doi.org/10.1038/s41592-024-02543-9

Nithin CJun 26, 2024
Our latest study published in NAR evaluates six RNA 3D structure prediction methods and includes an assessment of AlphaFold 3. Using a diverse set of RNA structures, we discovered varying strengths among the methods. Some excel in predicting global RNA folds, while others are better at local interactions.
Discover the potential for therapeutic breakthroughs: https://doi.org/10.1093/nar/gkae541
Comparative analysis of RNA 3D structure prediction methods: towards enhanced modeling of RNA–ligand interactions

Abstract. Accurate RNA structure models are crucial for designing small molecule ligands that modulate their functions. This study assesses six standalone

OUP Academic
Nithin CApr 25, 2023
Nithin CApr 25, 2023
"#Time goes faster the more #hollow it is. Lives with no meaning go straight past you, like #trains that don’t stop at your #station."

-- Carlos Ruiz Zafón, The Shadow of the Wind (The Cemetery of Forgotten Books, #1)

#pkp #Poland #Polska #countryside
#fields #beautiful #spring #life #travel #green #beautifuldestinations #randomclick #picturesque #piękna
Nithin CMar 3, 2023
Nithin CMar 3, 2023
The view point of #Wielki #Staw is at 1489 m above sea level in the #Karkonosze range. The Wielki Staw glacial lake is at 1225 m above sea level. The #lake is not accessible to tourists but the view from the top is breath taking. The Karkonosze National Park (Karkonoski Park Narodowy) is full with #picturesque #landscape, breathtaking views and #tranquil greenery.

#throwback
#mountains
#Poland
#Polska
#karkonowskiparknarodowy
#wielkistaw
#beautifuldestinations
#karkonoszenationalpark
Nithin CMar 3, 2023
Nithin CMar 2, 2023
"Although I deeply love #oceans, #deserts and other #wild #landscapes, it is only #mountains that beckon me with that sort of painful magnetic pull to walk deeper and deeper into their #beauty. They keep me continuously wanting to know more, feel more, see more." -- Victoria Erickson

#karkonosze
#karkonowskiparknarodowy
#Poland
#Polska
#green
#throwback
#beautifuldestinations
#tranquil
#nature
#clouds
#blue
Nithin CMar 3, 2023
Nithin CMar 2, 2023
The #spectacular view of #Morskie Okio #lake (at 1395 m above MSL) from the Czarny Staw pod Rysami" Lake (1,583 m above MSL) in the #Polish side of Mount #Rysy in the #Tatra #mountain range. The Tatra National Park has many mesmerizing views. #tatranationalpark #morskieoko #czarnystawpodrysami #Polska #Poland #tatrzanskiparknarodowy #throwback
Nithin CDec 12, 2022
It is very exciting and inspiring to be at the first CASP meeting with RNA modeling introduced as a category.
#CASP15 #RNA #Modeling #StructuralBiology #computationalbiology #bioinformatics
Nithin CMay 8, 2022

Our new publication in NAR:
MAPIYA contact map server for identification and visualization of molecular interactions in proteins and biological complexes

A detail description prepared by Karol Wroblewski is available at https://youtu.be/9JnTBgiGCy4

A special thanks to Prof. Sebastian Kmiecik, Dr. Mateusz Kurcinski, Aleksandra Badaczewska-Dawid, Karol Wroblewski.

MAPIYA is available at https://mapiya.lcbio.pl/ and online tutorials at https://mapiya.lcbio.pl/about

https://doi.org/10.1093/nar/gkac307

MAPIYA contact map web server for visualizing molecular interactions in proteins and their complexes

YouTube