About Nithin

Welcome to my blog. This is where I share practical solutions and tutorials from my daily experience working with Linux, dual-boot systems, and open-source tools. Posts here cover topics such as setting up NVIDIA drivers under Secure Boot, fixing EFI boot order problems in multi-boot systems, installing Microsoft Office with Wine, and many other step-by-step guides. Everything I publish is based on real fixes that I tested on my own machines, so you can reproduce them reliably.

Alongside technical tutorials, I also share my thoughts and personal experiences here. These posts reflect the challenges I face while working with Linux and multi-boot systems, as well as insights from my academic and professional journey. Writing them helps me document solutions and lessons learned, and I hope they are useful or relatable to others dealing with similar situations.

I also enjoy writing about my travels. Those stories and photographs are shared separately at travel.nithinaneesh.in, where I keep a record of the places I have visited and the experiences I have had along the way.

I am Nithin Chandran, an Assistant Professor (Adiunkt) at the Laboratory of Computational Biology, Biological and Chemical Research Centre, Faculty of Chemistry, University of Warsaw. My research focuses on understanding and targeting RNA and RNA–protein complexes using computational approaches. I work at the interface of RNA biology, structural bioinformatics, and molecular simulation, with a particular focus on developing and applying tools for 3D structure prediction, modeling, and design.

I contribute to community-wide benchmarks such as CASP and RNA-Puzzles, where I help evaluate and advance RNA structure prediction methods. My work in RNA modeling spans tertiary structure prediction, fragment assembly, structure refinement, and conformational ensemble analysis. I also investigate RNA–ligand interactions through docking and simulation to identify small molecules and oligonucleotide fragments that selectively bind functional RNA motifs. In addition, I design and evaluate short peptides that interact with RNA or protein targets, using pipelines that integrate machine learning–based sequence design with structure-based modeling and molecular dynamics.

A significant part of my research involves large-scale molecular docking and simulation workflows to identify and rank candidate binders. I routinely employ flexible docking protocols for peptides and oligonucleotides, as well as blind and targeted docking for small molecules. These efforts are supported by high-performance computing environments and custom automation pipelines. I actively develop and maintain scripts for parsing, scoring, structure filtering, and visualization using C++, R, Python, and Bash.

I earned my PhD in Bioinformatics and Computational Biology at the Indian Institute of Technology Kharagpur. I also completed an M.Tech in Biotechnology and Biochemical Engineering at IIT Kharagpur. My B.Tech in Biotechnology and Biochemical Engineering was from Sree Chitra Thirunal College of Engineering, Thiruvananthapuram (affiliated to University of Kerala). Previosly, I worked as a postdoctoral researcher at the Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, and as a Bioinformatician in industry at Molecure SA.

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