Using the latest computational technologies to understand the behaviour of pharmaceutical targets at an atomic level

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What I do

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Molecular simulations

to characterise protein systems and identify new strategies for therapeutics design

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Protein engineering

to design, model, and characterise new constructs with specific biophysical and therapeutic properties

Methods

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Molecular dynamics

To study the dynamic behaviour and interactions of biomolecules and provide insights into molecular mechanisms at an atomic level

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Enhanced sampling

To investigate biological phenomena unaccessible by plain molecular dynamics such as conformational changes and protein-ligand unbinding events

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Homology modelling

To create accurate models of proteins using tools like AlphaFold3 and investigate systems with no experimental structures available

Boost your project

Pharmaceutical companies, biotech firms, and chemical manufacturers can leverage molecular simulations for...

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Faster therapeutics discovery

Prospective molecular dynamics studies consider the structural flexibility of drug-target complexes, enhancing the understanding of key interactions and speeding up the optimization of drug candidates.

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Deeper molecular insights

Detailed insights into the structure, dynamics, and function of biomolecules, including receptor activation, help uncover underlying molecular mechanisms. This knowledge facilitates the development of more effective and targeted therapies.

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Biopharmaceuticals optimization

Understanding the conformational dynamics of proteins aids in optimizing their amino acid sequences, resulting in improved biophysical properties and enhanced efficacy in clinical settings, including vaccine development.

FAQs

Let's discuss the project first to understand your specific needs, define the project scope, and outline the deliverables. Here’s the process I follow:
  • Preliminary Consultation: We will discuss the details of your project to identify goals and requirements.
  • Project Scoping: Based on our discussion, we will define the project scope, deliverables, and necessary activities.
  • Time and Cost Estimation: We will provide a detailed project outline, including time estimates in human hours, a breakdown of tasks, and costs.

As an example of a short project, a comprehensive structural analysis of a series of protein targets, which includes both plain and enhanced sampling simulations, scripts preparation, deployment, progress and final reports preparation, required approximately 60 hours spanned on a 2 months period, for a total budget of 4500 euros gross (excluding computational costs).

Please note that each project is unique, and costs can vary based on complexity and specific requirements.

A standard project might take anywhere from 6 weeks to a few months from start to finish. I strive to provide realistic timelines during the initial consultation phase based on the specifics of the project. If you have tight deadlines, please let me know, and I will do my best to accommodate your needs.

Gromacs and Plumed to run molecular simulations. VMD, Pymol, ChimeraX for molecular visualization. AlphaFold for protein structure prediction. Local installation of available tools and in-house Python scripts for data analysis and visualization.

The confidentiality of your data is top priority. I understand the sensitive nature of your data and adhere to strict confidentiality (NDA) agreements. Your data will be treated as highly confidential and will be used exclusively for the purposes outlined in our consulting agreement. I do not share your data to any third parties without your explicit consent. I retain your data only for as long as necessary to fulfill the purposes of our engagement. Upon completion of the services, you have the option to request the deletion or return of your data.

Through regular follow-up meetings, detailed reports, and a project dashboard. I will provide periodic status updates via email. You will have access to a project dashboard to track milestones, timelines, and deliverables in real-time (GitHub or Monday). Additionally, I am available via Slack for instant communication and any quick updates or questions.

Of course. We formalize the collaboration with a NDA (Non-Disclosure Agreement) to ensure the confidentiality of your data and sensitive information, and a conventional contract outlining the project scope, timings, milestones, and deliverables.
If needed, I can provide a template for your review and customization to fit your specific needs.

Contact

For consulting inquiries or collaboration opportunities,
please contact me at:

  • dorothea.gobbo@gmail.com
  • +39 335 10 29 834
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