🎓 Ph.D., RNA molecular biologist & bioinformatician

Key papers:

• Mechanism of splicing catalysis with Konarska @ IMOL, Poland
• mqapRNA: model quality assessment program for RNA 3D models with Bujnicki @IIMCB, Poland
• Rearrangements within the U6 snRNA core at the transition between the two catalytic steps of splicing with Konarska @IMOL, Poland, 2019
• RNA 3D Structure Prediction Using Multiple Sequence Alignment Information with Das and Bujnicki @ Stanford University, USA & IIMCB, Poland, 2019
• RNA-Puzzles toolkit: A computational resource of RNA 3D structure benchmark datasets, structure manipulation, and evaluation tools with the RNA-Puzzle Team @ IIMCB & IMOL, Poland, 2020 http://rna-tools.online

IIMCB = International Institute of Molecular and Cell Biology, Warsaw, Poland IMOL = International Institute of Molecular Mechanisms and Machines, Polish Academy of Sciences, Warsaw, Poland

🗺 mapper https://www.openstreetmap.org/user/mmagnus

🦥 More about me: http://mmagnus.github.io

Papers https://www.semanticscholar.org/author/Marcin-Magnus/38336150 https://scholar.google.pl/citations?user=O2gLO2EAAAAJ&hl=en

SPLICING:

• PyMOL4Spliceosome - structures of spliceosome processed to be easily viewed with PyMOL
• yeast-spotifier - a script to process yeast plate image into figures :-)

RNA

• mqapRNA/mqapRNAweb/mqapRNAdb - (open soon) consensus, machine-learning based model quality assessment program for RNA 3D models
• EvoClustRNA - RNA 3D structure prediction using multiple sequence alignment information docs @ http://EvoClustRNA.rtfd.io
• rna-tools - a toolbox to analyze sequences, structures and simulations of RNA (and more) docs @ http://rna-tools.rtfd.io
• PyMOL4RNA - set of scripts to be used in PyMOL (based on rna-tools)
• RNA-Puzzles-Standardized-Submissions - Curated structures submitted to the RNA-Puzzles experiment

Workflows

• rna-tools-webserver-engine - The light-weight, complete webserver engine used by me for servers: NPDock (RNA/DNA-protein docking method, http://genesilico.pl/NPDock/), SimRNAweb (RNA 3D structure prediction method, http://iimcb.genesilico.pl/SimRNAweb/), mqapRNA (RNA 3D quality control, http://iimcb.genesilico.pl/mqapRNA/), RNAMasonry (building RNA models from recurrent 3D motifs, http://genesilico.pl/rnamasonry).

FOR NERDS:

• 💥 geekbook - G33KB00K3 - fun to read & fun to write -- 🤓 eXtreme eXtendable note taking system for nerds/geeks (including scientists!) docs: http://geekbook.rtfd.io = beautiful html generator of your markdown-based notes
• pubmex - get a fancy paper title based on detected or given DOI or PMID
• emacs-env - I've been using Emacs for almost 15 years (since 2007) now. This's my config file :-) it might be useful for someone.
• emacs-pdb-mode - pdb-mode is an emacs-lisp minor mode for Emacs to perform a number of useful editing functions on Protein DataBank (PDB) formatted files. XEmacs and/or GNU Emacs are available for most computing platforms.
• OrgModeClocking2Calendar - one way synchronization of your clocking (time tracking) entries from OrgMode Emacs to Calendar (Mac only)
• garmin2orgmode - Send your Garmin activities to OrgMode
• garmin2calendar - Send your Garmin activities to Calendar
• Pocket-Plus-Calibre-Plugin - send Pocket-ed articles from the Internet to your Kindle (or others)
• PocketX-Calibre-Plugin experimental version of Pocket-Plus-Calibre-Plugin