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@psa-lab

PSA-Lab

Protein Structural Analysis & Design Laboratory at Michigan State University

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  1. screenlamp screenlamp Public

    Forked from rasbt/screenlamp

    screenlamp is a Python toolkit for hypothesis-driven virtual screening. Raschka, Scott, et al., (2018) JCAMD

    Python 1 2

  2. siteinterlock siteinterlock Public

    Forked from rasbt/siteinterlock

    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 no…

    Python 9 4

  3. protein-recognition-index protein-recognition-index Public

    Forked from rasbt/protein-recognition-index

    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 protei…

    Python 2 1

  4. Hbind Hbind Public

    Forked from rasbt/Hbind

    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 Mol…

    C 1 4

  5. HbindViz HbindViz Public

    Forked from rasbt/HbindViz

    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 2

  6. predicting-activity-by-machine-learning predicting-activity-by-machine-learning Public

    Forked from rasbt/predicting-activity-by-machine-learning

    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…

    Jupyter Notebook 6 8

Repositories

Showing 10 of 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 7 GPL-2.0 3 1 1 Updated Apr 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 2 GPL-3.0 1 0 0 Updated Mar 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 11 GPL-2.0 2 0 0 Updated Oct 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 1 0 0 0 Updated Apr 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 0 1 0 0 Updated Apr 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 0 GPL-2.0 1 0 0 Updated Apr 21, 2018
  • screenlamp Public Forked from rasbt/screenlamp

    screenlamp is a Python toolkit for hypothesis-driven virtual screening. Raschka, Scott, et al., (2018) JCAMD

    Python 1 Apache-2.0 11 0 0 Updated Mar 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

    C 4 0 0 0 Updated Mar 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, 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 4 0 0 0 Updated Mar 1, 2018
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