POVME2

POVME2

POVME

POVME2 (POcket Volume MEasurer 2.0) scans a molecular-dynamics simulation and extracts druggable protein pockets with unique conformations. It is useful because ligand-binding pockets adopt many conformations in response to atomic forces. Characterizing these pocket geometries helps identify those that are particularly amenable to ligand binding. Computer-aided drug-discovery campaigns that incorporate these conformations often identify novel pharmacologically active molecules.



BINANA

BINANA

BINANA

BINANA (BINding ANAlyzer) analyzes the geometries of predicted ligand poses to identify molecular interactions that contribute to binding. It is useful because accurately characterizing these interactions allows medicinal chemists to assess whether a predicted ligand merits further study.



AutoGrow4

AutoGrow4

AutoGrow4

AutoGrow4 is an open-source program for semi-automated computer-aided drug discovery. It uses a genetic algorithm to evolve predicted ligands on demand and so is not limited to a virtual library of pre-enumerated compounds. AutoGrow4 is a useful tool for generating entirely novel drug-like molecules and for optimizing preexisting ligands.



Webina

Webina

Webina

Webina is a JavaScript/WebAssembly library that runs AutoDock Vina entirely in a web browser. The docking calculations take place on the user's own computer rather than a remote server. To encourage use, we have incorporated the Webina library into our own Webina web app. The app includes a convenient interface so users can easily setup their docking runs and analyze the results.



Protein-Structure Coloring Book (Halloween 2019)

Jennifer Walker, grad student in the Durrant Lab, put together a great protein coloring book for Halloween. The perfect way to share the excitement of structural biology with the little ones (or even grownups) in your life. 🙂

JenWalkerProteinColoringBookHalloween2019

ProteinVR

ProteinVR

ProteinVR

ProteinVR is a web-based application that allows users to view protein/ligand structures in virtual reality (VR) from their mobile, desktop, or VR-headset-based web browsers. Molecular structures are displayed within 3D environments that give useful biological context and allow users to situate themselves in 3D space.



Gypsum-DL: A New Program that Prepares Molecular Libraries for Virtual Screening

Happy to announce that the Durrant Lab recently released Gypsum-DL, a program that prepares molecular libraries for virtual screening.

Structure-based virtual screening requires carefully prepared 3D models of potential small-molecule ligands. Existing commercial programs for virtual-library preparation have restrictive and/or expensive licenses. In contrast, Gypsum-DL is open source. It accepts virtual compound libraries in SMILES or flat SDF formats as input. For each molecule in the library, it enumerates appropriate ionization, tautomeric, chiral, cis/trans isomeric, and ring-conformational forms. As output, it produces an SDF file with 3D coordinates assigned. A copy is available free of charge under the terms of the Apache License, Version 2.0: https://git.durrantlab.pitt.edu/jdurrant/gypsum_dl

Happy docking!

Gypsum-DL: an open-source program for preparing small-molecule libraries for structure-based virtual screening. Patrick J. Ropp, Jacob O. Spiegel, Jennifer L. Walker, Harrison Green, Guillermo A. Morales, Katherine A. Milliken, John J. Ringe & Jacob D. Durrant. Journal of Cheminformatics. Volume 11, Article number: 34 (2019)

PCAViz

PCAViz

PCAViz

PCAViz is an open-source Python/JavaScript toolkit for sharing and visualizing MD trajectories via a web browser. To encourage use, an easy-to-install PCAViz-powered WordPress plugin enables 'plug-and-play' trajectory visualization.



Gypsum-DL

Gypsum-DL

Gypsum-DL

Gypsum-DL is a free, open-source program that converts 1D and 2D small-molecule representations (SMILES strings or flat SDF files) into 3D models. It outputs models with alternate ionization, tautomeric, chiral, cis/trans isomeric, and ring-conformational states.



Dimorphite-DL

Dimorphite-DL

Dimorphite-DL

Dimorphite-DL adds hydrogen atoms to molecular representations, as appropriate for a user-specified pH range. It is a fast, accurate, accessible, and modular open-source program for enumerating small-molecule ionization states.