Tomek Włodarski

Tomek Włodarski

Research Fellow

Department of Bioinformatics

Institute of Biochemistry and Biophysics Polish Academy of Sciences

About me

I am a computational biophysicist working as a research fellow in the Department of Bioinformatics at IBB PAS in Warsaw, Poland. My primary focus is on a project titled "Co-translational protein folding in the light of ribosome evolution" funded by the POLONEZ BIS grant from the National Science Centre. This project integrates bioinformatics, multi-scale molecular dynamics simulations and machine learning to unravel the complexities of ribosome heterogeneity, particularly around the exit tunnel, and its influence on the co-translational folding of proteins. During my postdoctorate stay at UCL in John Christodoulou's group and at the University of Cambridge in Michele Vendruscolo's group, I have worked on all-atom and coarse-grained molecular dynamics simulations of ribosomal nascent chain complexes with structural restraints derived from experimental data (mainly NMR and cryo-EM). Additionally, I have developed CryoENsemble - a computational method based on Bayesian inference to re-weight structural ensemble obtained from MD simulations to better capture heterogeneity in cryo-EM data. Using these tools, I have characterised in atomic detail the nascent chain structural ensembles, folding intermediate states and interactions between the ribosome and unfolded or folded nascent chains.

Download my resumé.

  • protein co-translational folding
  • molecular dynamics simulations
  • integrative structural biology
  • structural bioinformatics
  • protein design
  • machine learning
  • PhD in Bioinformatics and Biophysics, 2013

    University of Warsaw, Warsaw, Poland

  • MSc in Biophysics, 2008

    Jagiellonian University, Cracow, Poland


Python, Bash, AWK, Tcl, R, git, LaTeX

MD simulations codes



Polish(native), English(fluent), Russian(basic), German(basic)