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Abstract

Selecting the appropriate macromolecular structure as the initial model is crucial for the success of a molecular dynamics (MD) simulation. The Protein Data Bank (PDB) is one of the largest repositories of experimentally determined biomolecular 3D structures, and often contains multiple structures for the same protein. There may also be fewer structures for some proteins making the selection of an initial model challenging.

PDBe and PDBe-KB provide a suite of tools and resources to assist users in searching for, finding, and evaluating the quality of their structure of interest. Familiarity with these tools and resources could help you set up a robust and relevant molecular system for your MD simulation.

This webinar will explore these tools and resources, highlighting several key features:

  1. PDBe and PBDe-KB resources: an integrated resource that aggregates functional annotations and structural data from the PDB and related databases. PDBe-KB provides a comprehensive overview of a protein, offering researchers detailed information about its structures, functions, and interactions, thus facilitating deeper insights into biomolecular mechanisms.
  2. PDBe’s 3D-Beacons Network: a collaborative, open-source resource that offers unified programmatic access to experimentally determined and predicted structure models. Participants will learn how to leverage the 3D-Beacons Network to effectively compare and select between experimental and predicted models, facilitating an informed choice of the starting model for their simulations.
  3. Validation report: an accessible report for each PDB entry which provides various metrics (clashscore, RMSZ, Ramachandran outliers, etc…) used to evaluate the structure quality. 
  4. Molecular Dynamics Data Bank (MDDB): a new resource designed to store and share MD simulations, enhancing their findability, accessibility, interoperability, and reusability.

In brief, you will learn where to find structures, search for them, evaluate them, and annotate them (as a bonus section).

Presenter

Sudakshina Ganguly completed her PhD. from Bose Institute, India, where she was interested in determining the structures and biophysical characterization of nucleic acid and ligand complexes. Thereafter, she did her postdoctoral studies at Clemson University, USA where her research focused on interactions of RNA with aminoglycoside antibiotics. Sudakshina joined the PDBe team in 2023 as a Scientific Database Curator where her work involves annotation and curation of preliminary PDB and EMDB submissions and extraction of relevant biological information. She is also a part of the PDBe training and outreach team where she is actively engaged in developing training material and outreach activities such as delivering workshops, webinars, etc. which  are aimed at researchers to leverage existing data in the PDB.

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LinkedIn: @Protein Data Bank in Europe (PDBe)