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2020 Workshops

Introduction to PyMOL

PyMOL is a molecular visualization software used to visualize protein, DNA, and RNA in 3D. This software allows the user to view and analyze their system of interest and create high quality images and movies of their work.

This half-day workshop, designed for new and existing users, will be run by a team from Schrödinger, designers of the PyMOL software.

Who should attend
Computational biologists, software engineers, chemists and other Broad Institute employees and affiliates, interested in enhancing their ability to effectively use the PyMOL software. Space is limited to 30 attendees.

How to get PyMOL at the Broad?
It is recommended that you bring your laptop with PyMOL preinstalled and a three button mouse to this workshop. The Broad has a site license for the commercial version of PyMOL for Windows and Mac, to install it please bring your laptop to BITStop at 75A-6001. Alternatively, Mac users can install the PyMOL software themselves using the Self Service Tools by following the directions in this link.

February 11

From Missense Variants to Protein Sequence and Structure
With high-throughput next-generation sequencing platforms, it is now feasible to analyze the exome and genome of thousands, and soon millions, of people. Such growth of data comes with the daunting challenge of the segregation and interpretation of neutral and disease-associated amino acid altering missense variation, particularly for clinical variants observed in patients. Thus far, both functional and clinical interpretation of variation in disease-associated genes lags far behind data generation. In this workshop, we will describe how to use two Broad-hosted online resources, PER (Pathogenic variants Enriched Regions) and MISCAST (Missense variant to Protein Structure Analysis Suite), to analyze the impact of missense mutations on protein sequence and structure, and therefore, interpret the variant. MISCAST is a platform with which a user can explore missense variants (single amino acid substitutions) mapped on linear protein sequence and 3-dimensional protein structure. In addition, MISCAST provides amino-acid-based annotations of proteins' structural, physicochemical, and functional features, combined and aggregated from multiple open source databases. On the one hand, the user can explore the impact of amino acid substitution in the context of perturbation of protein features and functions. On the other hand, through the PER browser, the user can investigate a missense mutation position in the context of essential regions of protein sequences that are constrained from variation from the general population and enriched with pathogenic variants observed in patients. The course will be divided into three parts: 1) a short lecture on the problem and background, 2) how to use MISCAST and PER browser, and 3) hands-on tasks using the online tools.

January 24