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    • AutoGrow4
      This forum is archived and so is closed to new questions. Please post new issues on the appropriate github issues page. Thanks! 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.
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    • 10 months, 2 weeks ago

      Jacob Durrant

    • BINANA
      This forum is archived and so is closed to new questions. Please post new issues on the appropriate github issues page. Thanks! 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.
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    • 10 months, 3 weeks ago

      Jacob Durrant

    • BlendMol
      This forum is archived and so is closed to new questions. Please post new issues on the appropriate github issues page. Thanks! BlendMol is a Blender plugin that can easily import VMD 'Visualization State' and PyMOL 'Session' files. BlendMol empowers scientific researchers and artists by marrying molecular visualization and industry-standard rendering techniques. The plugin works seamlessly with popular analysis programs (i.e., VMD/PyMOL). Users can import into Blender the very molecular representations they set up in VMD/PyMOL.
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    • 1 year, 10 months ago

      Riccardo

    • DeepFrag
      This forum is archived and so is closed to new questions. Please post new issues on the appropriate github issues page. Thanks! DeepFrag is a deep convolutional neural network that guides ligand optimization by extending a ligand with a molecular fragment, such that the resulting extension is also highly complementary to the receptor.
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    • 1 year, 9 months ago

      Jacob Durrant

    • Dimorphite-DL
      This forum is archived and so is closed to new questions. Please post new issues on the appropriate github issues page. Thanks! 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.
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    • 10 months, 3 weeks ago

      Matt Tudor

    • FPocketWeb
      This forum is archived and so is closed to new questions. Please post new issues on the appropriate github issues page. Thanks! FpocketWeb is a browser app for identifying pockets on protein surfaces where small-molecule ligands (e.g., drugs) might bind. It runs the fpocket executable entirely in a web browser. The pocket-finding calculations occur on the user’s computer rather than a remote server.
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    • 10 months, 3 weeks ago

      Jacob Durrant

    • Gypsum-DL
      This forum is archived and so is closed to new questions. Please post new issues on the appropriate github issues page. Thanks! 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.
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    • 10 months, 3 weeks ago

      Jacob Durrant

    • LigGrep
      This forum is archived and so is closed to new questions. Please post new issues on the appropriate github issues page. Thanks! LigGrep is a free, open-source program for identifying docked poses that participate in user-specified receptor/ligand interactions. As input, LigGrep accepts a protein receptor file (PDB, PDBQT), a directory containing many docked-compound files (PDB, PDBQT, SDF), and a list of user-specified filters (JSON). It evaluates each docked pose and outputs the names of the compounds with poses that pass all filters.
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    • 10 months, 3 weeks ago

      Jacob Durrant

    • PCAViz
      This forum is archived and so is closed to new questions. Please post new issues on the appropriate github issues page. Thanks! PCAViz is an open-source Python/JavaScript toolkit for sharing and visualizing MD trajectories via a web browser.
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    • POVME2
      This forum is archived and so is closed to new questions. Please post new issues on the appropriate github issues page. Thanks! 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.
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    • 10 months, 3 weeks ago

      Jacob Durrant

    • Prot2Prot
      This forum is archived and so is closed to new questions. Please post new issues on the appropriate github issues page. Thanks! Prot2Prot is a deep-learning model trained to imitate a Blender-rendered image given a much simpler representation ('sketch') of a protein surface. Prot2Prot outputs an image that is often indistinguishable from a Blender/BlendMol-based visualization in a fraction of the time, allowing image 'rendering' even in a web browser.
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    • ProteinVR
      This forum is archived and so is closed to new questions. Please post new issues on the appropriate github issues page. Thanks! 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.
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    • 10 months, 3 weeks ago

      Pedro Murcia

    • Pyrite
      This forum is archived and so is closed to new questions. Please post new issues on the appropriate github issues page. Thanks! Pyrite is a Blender plugin that imports the atomic motions captured by molecular dynamics simulations. Using Pyrite, these motions can be rendered using Blender's state-of-the-art computer-graphics algorithms. All 3D protein representations (e.g., surface, ribbon, VDW spheres) are supported. Aside from advancing scientific and collaborative objectives, Pyrite renderings will also appeal to students and non-specialists.
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    • 10 months, 3 weeks ago

      Denise Poire

    • Scoria
      This forum is archived and so is closed to new questions. Please post new issues on the appropriate github issues page. Thanks! Scoria is a Python package for manipulating three dimensional molecular data. Unlike similar packages, Scoria is written in pure Python and so requires no dependencies or installation. One can incorporate the Scoria source code directly into their own programs. But Scoria is not designed to compete with other similar packages. Rather, it complements them. Our package leverages others (e.g., NumPy, SciPy, MDAnalysis), if present, to speed and extend its own functionality.
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    • SubPEx
      This forum is archived and so is closed to new questions. Please post new issues on the appropriate github issues page. Thanks! SubPEx (Sub-Pocket Explorer) is a tool to enhance ensemble (multiple-receptor/relaxed-complex) virtual screening. It uses weighted ensemble path sampling and molecular dynamics simulations to accelerate binding-pocket sampling.
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    • Webina
      This forum is archived and so is closed to new questions. Please post new issues on the appropriate github issues page. Thanks! 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.
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    • 10 months, 2 weeks ago

      Jacob Durrant

    • wisp
      This forum is archived and so is closed to new questions. Please post new issues on the appropriate github issues page. Thanks! WISP is a trajectory analysis tool that calculates and visualizes allosteric pathways.
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