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psa-lab/WatCH

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Created over 6 years ago
Updated over 6 years ago

psa-lab/WatCH

psa-lab

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WatCH is a tool for the calculation of conserved water sites in a series of related structures in Protein Data Bank files.

SimSite3D

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.

ProFlex

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.

SLIDE

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.

Consolv

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

Sequery

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.

Protein-Alignment-Tool

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.