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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 atoms.
      Fortran
      •
      GNU General Public License v2.0
      •4•9•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 and their numeric properties (from the B-value column) of PDB structures, given their structural superposition.
      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 sites to determine which binding sites in the database have steric and chemical similarities to the query binding site.
      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 secondary structure
      C
      •
      Other
      •1•0•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
      •11•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 crystallographic structures of the same protein
      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 matches and acceptable substitutions based on a user-specified amino acid substitution matrix and/or a numerical threshold.
      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-dimensional structure of a protein's binding site.
      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, Wolf, et al. (2018) J. Computer-Aided Molec. Design
      C
      •
      Apache License 2.0
      •15•1•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-bond trends observed in diverse protein-ligand complexes. Raschka, Wolf et al. (2018) JCAMD
      Python
      •
      Apache License 2.0
      •5•2•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. (2018) J. Computer-Aided Molec. Design
      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 assayed. Useful for structure-activity relationship analysis of compounds identified by Screenlamp and other screening approaches. See Raschka et al. (2018) (ISBN 1-4939-7755-5)
      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 constraint counting on the covalent and noncovalent bond network. Raschka et al. (2016) Proteins: Structure, Function, and Bioinformatics
      pythonbioinformaticsprotein-structureprotein-ligand-dockingcomputational-biologybiological-data-analysisvirtual-screening
      Python
      •
      GNU General Public License v3.0
      •8•9•0•0•Updated Nov 22, 2016Nov 22, 2016