Molecular Modelling

Protein/Ligand Analysis

• Docking
• Virtual Screening
• Analysis of Antonin Holy Library

Aimed at both the BIO and CHEM clusters, we offer expertise/help/advice on various aspects of (bio)molecular modeling. For biomolecules (proteins, nucleic acids, carbohydrates) of interest, analyses of their dynamics beyond experimental structural information from X-ray crystallography, NMR, or cryo-EM can be performed using molecular dynamics simulations (MD) using AMBER, GROMACS or NAMD. For organic compounds, conformational analyses, calculation of properties (energies, atomic charges, electrostatic potentials, spectra, pKa’s) and reaction mechanisms can be carried out using quantum chemical calculations in Gaussian or Turbomole. For biomolecular complexes, docking and scoring approaches give their structures and energies, respectively, and can be used in virtual screening pipelines, i.e. finding hits in virtual compound libraries for a given biomolecular target. For the lead-optimization stage, free-energy stimulation protocols can be used.

How to ask for Protein/Ligand Analysis support
Drop an e-mail to Martin Lepšík. General questions on the service should be directed to Hector Martinez-Seara.

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Image processing

Under the umbrella of the Computational Facility at IOCB, we recently opened an Image Analysis (IA) service. The goal of the facility is to help microscopy users analyze their images. With support from our mathematically-minded colleagues, we will:

• Help you to design and build successful image analysis pipelines and data flows using a variety of software - mostly open-source (ImageJ macro language, Python) for the time being.
• Serve as a “walk-in” advisory service to suggest the most appropriate software and image analysis solution for your specific problem.

How to ask for Protein/Ligand Analysis support
Drop an e-mail to Petro Khoroshyy with the description of the problem. General questions on the service should be directed to Hector Martinez-Seara.

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Training and courses

The computational facility of IOCB would like to propose the following courses and hand-on sessions for employees and students:

• Introduction to the Aurum cluster
• Python for bioinformatics
• Introduction into python
• Python libraries for data science: numpy, matplotlib, pandas
• Introduction to Machine learning: tensor flow, Keras, scikit-learn
• Molecular dynamics simulations
• Introduction to Gromacs
• Introduction to Amber
• Quantum mechanics calculations
• Introduction to Gaussian
• PyMOL
• Introduction
• Advanced usage and scripting
• ImageJ
• 2D image processing and analysis with ImageJ/Fiji for beginners

A description of the courses can be found on the IOCB owncloud. Invitations to courses are published periodically on the IOCB news-board. Questions and proposals shall be directed to Petro Khoroshyy.