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Computational workflow to mine the PDB for local structural replacements
This project forked from aborrel/lsrs
Computational workflow to mine the PDB for local structural replacements
### Dependencies ### ################### TM align -> path l.13 script RunOtherSoft.py // http://zhanglab.ccmb.med.umich.edu/TM-align/ ShaEP -> path l.14 script RunOtherSoft.py // http://users.abo.fi/mivainio/shaep/ - blastp Requirements (Ubuntu 12.04): - openbabel - EMBOSS - R > release 3.2.2 (2015-08-14) Python (2.7) modules: - os - copy - re - subprocess - numpy - biopython (Bio.blast) - shutil - urllib - math ### Scripts py descriptions ### ########################### - RunBlast.py: run Blast queries - analysis.py: automated statistical analysis and draw R plots - arrangeResult.py: manage folders containing LSR - buildData.py: extract files from the PDB - cleanResult.py: clean folder result, remove temp files - downloadFile.py: Import fasta file and pdb file using urlretrieve protocol - ionSearch.py: search and analysis metals in the binding site - managePDB.py: clean and decompress PDB extracted - neighborSearch.py: define binding site - parseEMBOSS.py: parsing EMBOSS output - parsePDB.py: parsing pdb file - parseShaep.py: parsing ShaEP output - parseTMalign.py: parsing TMalign ouput - pathManage.py: path manager - refClassification.py: build pdb classification - runOtherSoft.py: run external tools - smileAnalysis.py: assign SMILES categories - substructTools.py: build reference substructure - superimpose.py: superimpose ligand using Kabsh's algorithm - superposeStructure.py: superimpose protein - tool.py: tool box functions - writePDBfile.py: write pdb files - main.py: MAIN with parameters l.574 thresold_RX = 2.7: minimal structure resolution thresold_BS = 4.5: distance threshold to define the binding site from ligand thresold_blast = 1e-100: threshold blast thresold_superimposed_pi = 2.5: distance threshold to extract LSR from ligand thresold_IDseq = 100: threshold identity sequence for similar PDB thresold_shaep = 0.2: threshold of shaep overlap l_ligand_out = ["AMP", "ADP", "ATP", "TTP", "DCP", "DGT", "DTP", "DUP", "ACP", "AD9", "NAD", "AGS", "UDP", "POP", "APC", "CTP", "AOV", "ANP", "GDP", "GTP", "ANP"]: list of ligand not considered ### other scripts ### ################## -downloadPDB.sh: download PDB database # R scripts for plots - histogram.R - histograms.R - histogramsRMSD.R - barplotQuantity.R - piePlot.R ### Paths management ### ######################## BLAST in local using PDB sequences ftp://ftp.wwpdb.org/pub/pdb/derived_data/pdb_seqres.txt.gz # 1. create db for blast # ##################### # format ncbi format seqret pdb.fasta pdb_ncbi.fasta -osf ncbi # make db makeblastdb -in pdb_ncbi.fasta -out pdb -dbtype prot # 2. run query blast for test fasta ################################### blastp -query test.fasta -db pdb -out result.txt # 3. export path # ################## export BLASTDB=/home/user/blast/db/ export PATH=$PATH:/home/user/softwares/clustal
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