G-LoSA Toolkit
Standalone Java Applications
| Feature | Name | Description |
| Basic classes (non-executable classes) |
Atom | defines an atom (atom name, residue name, residue sequence, coordinates, etc) |
| Molecule | defines a molecule (atoms, residues, selected residues, etc) | |
| StructureHandler | provides basic methods for structure reading, writing, manipulating, and analysis | |
| NWAlign |
provides methods for sequence alignment by Needleman-Wunsch algorithm (http://zhanglab.ccmb.med.umich.edu/NW-align) |
|
| PDB structure library preparation | BuildLigandBSStructureLibrary | builds structure library for ligand, ligand binding site (BS), and protein chain for a given set of PDB files |
| RemoveRedundantLigandBS | removes structurally redundant ligand BS based on sequence identity between protein chains and structure similarity between ligands. Homologous protein chains are identified using a Blast clustering result file (bc-X.out) available in the PDB (http://www.rcsb.org/pdb/statistics/clusterStatistics.do) and ligand similarity is calculated using a path-based FP2 fingerprint in Open Babel | |
| BuildProteinStructureLibrary | builds structure library for protein chains for a given set of PDB files | |
| RemoveRedundantProteins | removes structurally redundant protein chains based on sequence identity. Homologous protein chains are identified using a Blast clustering result file (bc-X.out) available in the PDB (http://www.rcsb.org/pdb/statistics/clusterStatistics.do) | |
| GenerateCFFiles | generates chemical feature (CF) files for a given set of ligand BS structures | |
| Protein surface structure generation | GetSurfaceResiduesUsingSurfaceRacer | extracts surface residues from a protein structure using SurfaceRacer program (http://pharmacy.mc.uky.edu/faculty/tsodikov/software.php) |
| GetSurfaceResiduesUsingVisGrid | extracts surface residues from a protein structure using VisGrid program (http://kiharalab.org/VisGrid/) | |
| G-LoSA search | GLoSASearch | performs G-LoSA against ligand BS library for a given query structure |
| RunPBSJobs | submits multiple G-LoSA search jobs | |
| CheckGLoSASearchResults | checks if multiple G-LoSA search jobs are successfully completed | |
| MergeGLoSASearchResults | merges multiple G-LoSA search results into a single file (score.txt) | |
| GetTopTemplates | sorts G-LoSA search result by GA-score and filter the results by a cutoff GA-score or the number of top templates | |
| FilterTemplatesBySeqIdentity | filters G-LoSA search result by sequence identity to query protein | |
| GetAlignedTemplates | generates ligand and ligand BS structures aligned onto query protein | |
| FilterTemplatesByPositionalOverlapTanimoto | filters G-LoSA search results by overlap ratio, which is a Tanimoto coefficient representing the positional overlap between template ligands | |
| Miscellaneous | AddPropertyResolution | adds X-ray resolution to G-LoSA search result |
| SplitList | splits a list into a set of sub-lists | |
| GeneratePyMolScript | generates a PyMol script file (view_struct.pml) to display the structures of query and templates | |
| GetAnnotations | generates a html file (annotation.html) to retrieve protein function information for templates |
| Click here to download G-LoSA Toolkit |
| >javac *.java (for compiling all java classes) |
| >java Application_Name [options] (for executing an application) |
| >java Application_Name or Application_Name --help (for help) |
Databases
| Feature | Name | Description |
| Non-redundant small molecule ligand/binding site structure library (as of July. 2018) |
nr-ligand-bs-70 | Filtered by 70% protein sequence identity. If two binding sites are homologous and their ligands are not identical, both binding sites were kept in the structure library. |