Downloads - Insilab

Downloads - insilab.org

General information about the database
Welcome to the downloads page of the insilab.org group. Here we store large collections of data used for in silico drug design. Feel free to download and explore the databases! Currently accessible databases include:

The DockReady Database

DockReady - a database of docking-ready ligands consists of manually curated collection of protein and other targets, interesting for docking experiments. The downloads are divided according to different species, as well as other criteria.

The whole database index is available here.
The file format is available here.
Database name Short description Count Download link
DockReady - Best All Whole DockReady database folder consisting of multiple different subsets. 91627 link
DockReady - Animals Animal-specific receptors 43654 link
DockReady - Human specific receptors Human-specific receptors 27600 link
DockReady - Cancer specific receptors Cancer-specific receptors 4170 link
DockReady - Kinase specific receptors Kinase-specific receptors 3782 link
DockReady - Bacteria Bacteria-specific receptors 34253 link
DockReady - Pathogenic Bacteria Bacteria-specific receptors 13803 link
DockReady - Virus specific receptors Virus-specific receptors 4518 link
DockReady - Plants and funghi Plants and funhgi 88 link

The GenProBiS database

GenProBiS database consists of large scale sequence variant-to-structure mappings.

Database name Short description Download link
GenProBiS - all (TSV) Whole database dump in TSV format. link
GenProBiS - all (JSON) Ligands folder - predicted and experimental protein-ligand interaction complexes link
Bresi folder - binding site to residue mappings link
Json folder - sequence variants, mapped to amino acid residues link

The ProBiS-ligands database

ProBiS-ligands database consists of large scale protein alignments.

Database name Short description Download link
ProBiS Ligands - all (bresi) All binding sites in JSON format link
ProBiS Ligands - all (centro) All centroids used for docking experiments link
ProBiS Ligands - all (evo) Evolutionary conservation for surfaces link
ProBiS Ligands - all (grid) Grids for docking experiments link
ProBiS Ligands - all (inte) Interaction surfaces link
ProBiS Ligands - all (json) All alignments link
ProBiS Ligands - all (ligands) All aligned ligands link
ProBiS Ligands - all (super) All superimpositions link
ProBiS Ligands - all (surf) All surface files link

The BoBER Database

BoBER database. This database includes bioisosteres as used in the BoBER webserver..

The whole database index is available here.
The file format is available here.
Database name Short description Download link
BoBER database folder Whole BoBER database. link

Complex networks database

Complex networks used in our studies.

Study name Short description Citation Download link
Insights from Ion Binding Site Network Analysis into Evolution and Functions of Proteins Many biological phenomena can be represented as complex networks. Using a protein binding site comparison approach, we generated a network of ion binding sites on the scale of all known protein structures from the Protein Data Bank. https://doi.org/10.1002/minf.201700144 Link to the network
Global organization of a binding site network gives insight into evolution and structure-function relationships of proteins The global organization of protein binding sites is analyzed by constructing a weighted network of binding sites based on their structural similarities and detecting communities of structurally similar binding sites based on the minimum description length principle. https://doi:10.1038/s41598-017-10412-z Link to the network