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/BS structure library
(as of Feb. 2016)
nr-ligand-bs-50-0.7 filtered by 50% protein sequence identity and 0.7 ligand structure similarity
nr-ligand-bs-70-0.7 filtered by 70% protein sequence identity and 0.7 ligand structure similarity
nr-ligand-bs-90-0.7 filtered by 90% protein sequence identity and 0.7 ligand structure similarity