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    15 repositories

    • ProFlex

      Public
      MSU ProFlex (formerly called FIRST) predicts the rigid and flexible regions in a protein structure, given a Protein Data Bank (PDB) file including hydrogen atom…
      Fortran
      •
      GNU General Public License v2.0
      •4•10•1•1•Updated Apr 16, 2022Apr 16, 2022

    • Protein-Alignment-Tool

      Public
      BRAT shows key residue (e.g., ligand-binding) correspondences between sequence-divergent homologs aligned by structural superposition. BAT displays residues an…
      Python
      •
      GNU General Public License v3.0
      •1•2•0•0•Updated Mar 10, 2020Mar 10, 2020

    • SimSite3D

      Public
      The SimSite3D Software tools are designed to quickly search a database of three dimensional structures, in Protein Data Bank format, with protein-ligand binding…
      GLSL
      •
      GNU General Public License v2.0
      •2•11•0•0•Updated Oct 18, 2018Oct 18, 2018

    • WatCH

      Public
      WatCH is a tool for the calculation of conserved water sites in a series of related structures in Protein Data Bank files.
      C
      •
      Other
      •0•1•0•0•Updated Apr 23, 2018Apr 23, 2018

    • SSA

      Public
      SSA is a tool to assign the secondary structure of a peptide from its atomic coordinates in PDB format based on their superposition with sequences of ideal seco…
      C
      •
      Other
      •1•1•0•0•Updated Apr 23, 2018Apr 23, 2018

    • SpeciFlex

      Public
      A tool to generate contour for volumes sampled via MD trajectories as well as computing difference-volumes from two trajectory volumes
      C
      •
      GNU General Public License v2.0
      •1•0•0•0•Updated Apr 21, 2018Apr 21, 2018

    • screenlamp

      Public
      screenlamp is a Python toolkit for hypothesis-driven virtual screening. Raschka, Scott, et al., (2018) JCAMD
      Python
      •
      Apache License 2.0
      •10•1•0•0•Updated Mar 20, 2018Mar 20, 2018

    • Consolv

      Public
      A tool for predicting whether water molecules bound to the surface of a protein are likely to be conserved or displaced in other, independently-solved crystallo…
      solvationwater
      C
      •
      Other
      •0•4•0•0•Updated Mar 9, 2018Mar 9, 2018

    • Sequery

      Public
      Sequery is a tool to search the sequences of the protein structures in the Protein Data Bank (PDB) for a particular pattern of residues, which may include exact…
      AGS Script
      •2•2•0•0•Updated Mar 2, 2018Mar 2, 2018

    • SLIDE

      Public
      SLIDE is a computational screening and flexible docking tool designed to discover ligands with good steric and chemical complementarity to the known three-dimen…
      C
      •
      Other
      •0•4•0•0•Updated Mar 1, 2018Mar 1, 2018

    • Hbind

      Public
      Calculates hydrogen-bond interaction tables for protein-small molecule complexes, based on protein PDB and protonated ligand MOL2 structure input. Raschka, Wol…
      C
      •
      Apache License 2.0
      •15•4•0•0•Updated Feb 6, 2018Feb 6, 2018

    • protein-recognition-index

      Public
      Calculates the Protein Recognition Index (PRI), measuring the similarity between intermolecular H-bonding features in a given protein-ligand complex and the H-b…
      Python
      •
      Apache License 2.0
      •5•4•0•0•Updated Feb 6, 2018Feb 6, 2018

    • HbindViz

      Public
      Generates a script to visualize protein-ligand H-bonds from an Hbind interaction table (see separate Hbind module) for display by PyMOL. Raschka, Wolf et al. (…
      Python
      •
      Apache License 2.0
      •5•0•0•0•Updated Feb 6, 2018Feb 6, 2018

    • predicting-activity-by-machine-learning

      Public
      Machine learning protocols for identifying biological activity determinants in the structural and chemical features of a set of small molecules that have been a…
      Jupyter Notebook
      •
      Apache License 2.0
      •17•6•0•0•Updated Aug 30, 2017Aug 30, 2017

    • siteinterlock

      Public
      A toolkit for predicting the binding mode of small molecules interacting with proteins based on interfacial rigidification, as assessed by graph theoretic const…
      pythonbioinformaticsprotein-structureprotein-ligand-dockingcomputational-biologybiological-data-analysisvirtual-screening
      Python
      •
      GNU General Public License v3.0
      •8•10•0•0•Updated Nov 22, 2016Nov 22, 2016