Dialogues in the MIDST

Virtual Workshop in the MIDST of Centrality and Community Detection in Dynamic Residue Networks

Sabanci University, Istanbul, Turkey

Friday, March 26, 2021


This workshop will provide a tutorial about the construction of dynamics residue networks (RNs) and further analyses on these RNs with a focus on centralities and communities. The theory session will begin with a focus on node betweenness centrality (BC) which highlights the information control of a certain amino acid in an RN, and we will continue with edge (link) BC (Atilgan, 2018). Then, we will use edge BC to detect close-knit residue groups that are called communities by employing Girvan-Newman algorithm (Girvan, 2002). The term dynamic stems from changing protein structure through a molecular dynamics (MD) simulation leading an altering composition of communities. With the information derived from BC and community composition, we will discuss ligand binding and/or mutation of a protein complex. For the hands-on session, a prior knowledge on programming is beneficial, but not necessary. The handling of MD simulation and network construction/analyses will be conducted by Python programming language, especially by using Prody, Networkx and Numpy packages. Molecular visualization will be done by VMD. A detailed instruction will be sent via email before the workshop date.