Pharmacophore screening using Pharmit in Boltzmann Maps

Boltzmann Maps is pleased to introduce an integration with Pharmit as an option for pharmacophore screening. Pharmit is a search tool for finding small molecule inhibitors that bind to a target of interest. The tool searches libraries for compounds with desired features in the right geometry. Boltzmann Maps integration allows the user to send a protein-ligand system from BMaps to Pharmit for search based on the compound’s features or other user-specified features. Pharmit’s nine built-in libraries include almost 250M compound entries, and the 1,059 publicly accessible user-contributed libraries contain another 45M entries.

Pharmit can be accessed via the Export button on the bottom right of the BMaps web app.

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Compound Energy Minimization with OpenMM

The Boltzmann Maps web app now employs GPU-accelerated OpenMM software for compound energy minimization in the context of a protein. The reported energies include van der Waals and electrostatic energies between compound and protein, as well as the change of a compound’s internal energies between the unbound and bound configurations (stress). These energy reports are a key metric for evaluating and comparing compounds and modifications. OpenMM integration allows Boltzmann Maps to provide this data with improved quality and speed.

OpenMM is an open-source toolkit for molecular simulation. It is highly flexible with its custom functions and has high performance, especially on recent GPUs. More information can be found at:

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New: Fragment maps for 10 SARS-CoV-2 proteins

Fragment maps for ten SARS-CoV-2 virus proteins are now available in the BMaps web app to accelerate the design of COVID-19 therapeutics. These structures include the main protein protease (NSP5), the Spike protein (S), the receptor binding domain (RDB) of the S protein, and several NS (non-structural) proteins NSP3, NSP9, NSP10, NSP15, NSP16. Available for each protein are druggability sites, water molecule maps, and a starting set of 117 chemical fragment binding maps.

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Fragment Maps for Coronavirus (6LU7) Available

Start designing your COVID-19 protease inhibitors using BMaps with an expanded set of 221 fragments. The example below started with a benzimidazole fragment, then grew to a benzene-CF3 via intermediate linkers. To get started with your own possibilities, view the BMaps prepared 6LU7 structure. And stay tuned for more coronavirus structures currently in BMaps fragment simulation (6LVN, 6VSB).

To learn more about the coronavirus, visit or

Image of an example coronavirus protease inhibitor, assembled from Boltzmann Maps simulated fragment maps.
CoV-2 Structures

Latest: More fragment grow results & “Rings-in-Drugs”

The latest BMaps update has support for a broader set of fragment linking options when growing with fragments, significantly expanding the opportunities for compound modifications. By accessing more fragments in new sub-pockets, the new linking features provide lots of new ideas for improvements to your compounds, ranked by fragment binding scores. In addition to simple bond linking, there is now:

  • methylene linking (–C– methane or single carbon);
  • ethane linking (–C–C– 2 carbons);
  • acetylene linking (–C≡C– 2 carbons connected by a triple bond).

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New: Fragment map summaries and more fragment libraries

The latest Boltzmann Maps enhancements make it easier to apply insights from fragment data to chemical design.

BMaps now includes visualization of fragment map summaries for each fragment map available for a given protein. Map summaries show the highest affinity (lowest chemical potential) pose of a fragment at each site on a protein where the fragment binds.  This information is useful in identifying promising scaffold fragments or new sub-pockets to exploit.

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Top VC-funded drug targets now available in BMaps

We are happy to announce that we have added fragment maps for over 70 unique proteins that are primary targets for ongoing, cutting edge research projects at top venture capitalist pharmaceutical companies. We looked into pharmaceutic/therapeutic companies from the most active pharmaceutical investors in recent years, such as OrbiMed Advisors, Novartis Venture Fund, RA Capital, etc.

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BMaps Web Application Now Supports Generating Boltzmann Water Maps

The BMaps web application now supports generating Boltzmann Water Maps on structures from the Protein Data Bank.

Maps of where water molecules bind to proteins are an important tool for drug designers to obtain insights about how bound waters may impact the binding affinity of their compounds. Water maps from simulations, unlike other methods, provide a reliable free energy ranking of affinity of waters, so weak versus strong binders can be distinguished.

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Boltzmann Maps Announces Release of BMaps Version 1.0

BMaps version 1.0 is now released at the website, launching the first Web-based fragment-based design application using Boltzmann Maps.

The BMaps Web application introduces fragment-based design based on Boltzmann fragment maps to a world-wide audience. A web application for in silico drug design, BMaps is a large software package that runs in your web browser, supported by AWS cloud-hosted data management and computational resources.

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