├── CPMlib ├── pECgnBSA1.lib ├── pECgnBSA2.lib ├── pECgnBSA3.lib ├── pScgnBSA1.lib ├── pScgnBSA2.lib └── pScgnBSA3.lib ├── EDTSurf ├── CommonPara.h ├── EDTSurf.cpp ├── EDTSurf.license ├── Makefile ├── ParsePDB.cpp ├── ParsePDB.h ├── ProteinSurface.cpp ├── ProteinSurface.h └── patch.EDTSurf ├── EXAMPLE_CASE_STUDY ├── 1OYV.pdb ├── 1OYV.pdb.fasta ├── 1OYV.pdb.fasta.fasta ├── D1OYV-a102a-delpatch.ProQDock ├── D1OYV-a102a-delpatch.Rterms ├── D1OYV-a102a-delpatch.SVMfeatures ├── D1OYV-a102a-delpatch.SVMfeatures.pred5 ├── D1OYV-a102a-delpatch.pdb ├── D1OYV-a104c-delpatch.ProQDock ├── D1OYV-a104c-delpatch.Rterms ├── D1OYV-a104c-delpatch.SVMfeatures ├── D1OYV-a104c-delpatch.SVMfeatures.pred5 ├── D1OYV-a104c-delpatch.pdb ├── D1OYV-a106c-delpatch.ProQDock ├── D1OYV-a106c-delpatch.Rterms ├── D1OYV-a106c-delpatch.SVMfeatures ├── D1OYV-a106c-delpatch.SVMfeatures.pred5 ├── D1OYV-a106c-delpatch.pdb ├── D1OYV-a115c-delpatch.ProQDock ├── D1OYV-a115c-delpatch.Rterms ├── D1OYV-a115c-delpatch.SVMfeatures ├── D1OYV-a115c-delpatch.SVMfeatures.pred5 ├── D1OYV-a115c-delpatch.pdb ├── D1OYV-a41b-delpatch.ProQDock ├── D1OYV-a41b-delpatch.Rterms ├── D1OYV-a41b-delpatch.SVMfeatures ├── D1OYV-a41b-delpatch.SVMfeatures.pred5 ├── D1OYV-a41b-delpatch.pdb ├── D1OYV-a61c-delpatch.ProQDock ├── D1OYV-a61c-delpatch.Rterms ├── D1OYV-a61c-delpatch.SVMfeatures ├── D1OYV-a61c-delpatch.SVMfeatures.pred5 ├── D1OYV-a61c-delpatch.pdb ├── D1OYV-a61d-delpatch.ProQDock ├── D1OYV-a61d-delpatch.Rterms ├── D1OYV-a61d-delpatch.SVMfeatures ├── D1OYV-a61d-delpatch.SVMfeatures.pred5 ├── D1OYV-a61d-delpatch.pdb ├── D1OYV-a62c-delpatch.ProQDock ├── D1OYV-a62c-delpatch.Rterms ├── D1OYV-a62c-delpatch.SVMfeatures ├── D1OYV-a62c-delpatch.SVMfeatures.pred5 ├── D1OYV-a62c-delpatch.pdb ├── D1OYV-a81d-delpatch.ProQDock ├── D1OYV-a81d-delpatch.Rterms ├── D1OYV-a81d-delpatch.SVMfeatures ├── D1OYV-a81d-delpatch.SVMfeatures.pred5 ├── D1OYV-a81d-delpatch.pdb ├── D1OYV-a82d-delpatch.ProQDock ├── D1OYV-a82d-delpatch.Rterms ├── D1OYV-a82d-delpatch.SVMfeatures ├── D1OYV-a82d-delpatch.SVMfeatures.pred5 ├── D1OYV-a82d-delpatch.pdb └── D1OYV-models.status.results ├── EXEC ├── TmR.pl ├── accall.f ├── accall.pars ├── conv2.pl ├── cys2cyxs.pl ├── extAllTerms.bash ├── generateprm26.pl ├── metRrename.csh ├── metcoord.f ├── metsph.f ├── naccess.bash ├── pdb2fasta.pl ├── renameRT.csh └── scaleRterms.pl ├── HELP ├── features.description ├── input.compatibility └── proqdock.ascii ├── LIBR ├── Embur1.probdist ├── Embur2.probdist ├── Embur3.probdist ├── Smbur1.probdist ├── Smbur2.probdist ├── Smbur3.probdist ├── amber.crg ├── amber_dummy.siz ├── cb.Pgrid ├── cb.inc ├── cb.outc ├── cb.trsq ├── contpref.mat ├── dot.inp ├── librf.list ├── met.radii ├── pb.Pgrid ├── pb.inc ├── pb.outc ├── pb.trsq ├── pe.Pgrid ├── pe.inc ├── pe.outc ├── pe.trsq ├── resGbur.libr ├── scalingET.params ├── standard.data └── vdw.radii ├── MAINEXEC ├── CPMgScEC.pl ├── repack.script ├── run.rosettaE └── runProQ.bash ├── ProQDock.pdf ├── README.md ├── SVMmodels.CPscore ├── train1-MOAL-svm-5fold-c0-0-2-1024-0.0009765625-0.2-1.model ├── train2-MOAL-svm-5fold-c0-0-2-1024-0.0009765625-0.2-1.model ├── train3-MOAL-svm-5fold-c0-0-2-1024-0.0009765625-0.2-1.model ├── train4-MOAL-svm-5fold-c0-0-2-1024-0.0009765625-0.2-1.model └── train5-MOAL-svm-5fold-c0-0-2-1024-0.0009765625-0.2-1.model ├── SVMmodels ├── train1-CAPRInMOAL-svm-5fold.model ├── train2-CAPRInMOAL-svm-5fold.model ├── train3-CAPRInMOAL-svm-5fold.model ├── train4-CAPRInMOAL-svm-5fold.model └── train5-CAPRInMOAL-svm-5fold.model ├── TEMP ├── .SVMfeatures ├── 1u07.pdb.fasta ├── 1u07.pdb.fasta.acc ├── 1u07.pdb.fasta.acc.out ├── 1u07.pdb.fasta.chk ├── 1u07.pdb.fasta.fasta ├── 1u07.pdb.fasta.fasta.blastpgp ├── 1u07.pdb.fasta.mtx ├── 1u07.pdb.fasta.psi └── 1u07.pdb.fasta.ss2 ├── TESTPDB ├── 1m26.pdb ├── 1u07.ProQDock ├── 1u07.Rterms ├── 1u07.SVMfeatures.pred5 ├── 1u07.pdb ├── 2b4h.pdb ├── 2boj.pdb ├── 2djz.pdb ├── 2gey.pdb ├── 2xwl.pdb ├── 3q8t.pdb ├── 4alh.pdb ├── 5tim.pdb ├── blank.pdb 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