p2rank
P2Rank: Protein-ligand binding site prediction from protein structure based on machine learning.
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Download Latest Version (.zip)- SKILL.md
- develop-adopt-openj9.yml
- develop-zulu.yml
- mac_java11.yml
- mac_java15.yml
- ubuntu_java11.yml
- ubuntu_java15.yml
- ubuntu_java8.yml
- win_java11.yml
- win_java15.yml
- win_java8.yml
- develop.yml
- cofactors_dropin_safety.sh
- petra.groovy
- prank-default-model.groovy
- rdk-baseline.groovy
- rdk-conservation.groovy
- rdk-dev.groovy
- ions-rdk-c1.groovy
- ions-rdk-c2-mg.groovy
- ions-rdk-c2-zn.groovy
- ions-rdk-c2.groovy
- ions-rdk-c3-mg.groovy
- ions-rdk-c3-zn.groovy
- ions-rdk-c4-grid-mg.groovy
- ions-rdk-c4-grid-zn.groovy
- ions-rdk-c5-grid-mg.groovy
- ions-rdk-c5-grid-zn.groovy
- ions-rdk-c6-grid-mg.groovy
- ions-rdk-c6-grid-zn.groovy
- ions-rdk.groovy
- aa.groovy
- aa20.groovy
- aa_new.groovy
- aug1.groovy
- aug2.groovy
- new.groovy
- oct1.groovy
- pept.groovy
- pept1.groovy
- pept2.groovy
- pept3.groovy
- dev-rescore.groovy
- dev.groovy
- physics-rich-v2-decoys.groovy
- physics-rich-v2-train.groovy
- physics-rich-v2.groovy
- readme.md
- test-alphafold.groovy
- test-conservation.groovy
- test-default.groovy
- train-conservation.groovy
- train-default.groovy
- alphafold.groovy
- alphafold_conservation_hmm.groovy
- conservation_hmm.groovy
- default.groovy
- default_rescore.groovy
- dev.groovy
- example.groovy
- readme.md
- rescore_2024.groovy
- rescore_conservation.groovy
- dataset-file-format.md
- alphafold_conservation_hmm_ProbabilityScoreTransformer.json
- alphafold_conservation_hmm_ZscoreTpTransformer.json
- alphafold_ProbabilityScoreTransformer.json
- alphafold_ZscoreTpTransformer.json
- conservation_hmm_ProbabilityScoreTransformer.json
- conservation_hmm_ZscoreTpTransformer.json
- default_ProbabilityScoreTransformer.json
- default_ZscoreTpTransformer.json
- readme.md
- alphafold_conservation_hmm_ProbabilityScoreTransformer.json
- alphafold_conservation_hmm_ZscoreTpTransformer.json
- alphafold_ProbabilityScoreTransformer.json
- alphafold_ZscoreTpTransformer.json
- conservation_hmm_ProbabilityScoreTransformer.json
- conservation_hmm_ZscoreTpTransformer.json
- default_ProbabilityScoreTransformer.json
- default_ZscoreTpTransformer.json
- features.txt
- model.zst
- features.txt
- model.zst
- features.txt
- model.zst
- features.txt
- model.zst
- ProbabilityScoreTransformer.json
- ZscoreTpTransformer.json
- features.txt
- model.zst
- ProbabilityScoreTransformer.json
- ZscoreTpTransformer.json
- features.txt
- model.zst
- ProbabilityScoreTransformer.json
- ZscoreTpTransformer.json
- features.txt
- model.zst
- readme.md
- 1i7xA_to_1i7wA.cif.gz
- 1jvaA_to_1ef0B.cif.gz
- 2hfzA_to_2hcnA.cif.gz
- 3gf2A_to_2yr2B.cif.gz
- 4tozA_to_3o9pA.cif.gz
- 1ef0.cif.gz
- 1i7w.cif.gz
- 2hcn.cif.gz
- 2yr2.cif.gz
- 3o9p.cif.gz
- zn_apoholo.ds
- 1a26A.pdb
- 1a2kC.pdb
- 1a82a.pdb
- 1aaxa.pdb
- 1afkA.pdb
- 1atlA.pdb
- 1bqoB.pdb
- 1nlu.pdb
- 1nlua.pdb.bak
- 1t7qa.pdb
- 1tjw_A.pdb
- 2ck3b.pdb
- 1a82a.pdb
- 1aaxa.pdb
- 1nlu.pdb
- 1nlua.pdb.bak
- 1t7qa.pdb
- 2ck3b.pdb
- 1a82a_A_concavity.scores
- 1a82a_concavity.dx
- 1a82a_concavity.pml
- 1a82a_concavity_pocket.pdb
- 1a82a_concavity_residue.pdb
- 1aaxa_A_concavity.scores
- 1aaxa_concavity.dx
- 1aaxa_concavity.pml
- 1aaxa_concavity_pocket.pdb
- 1aaxa_concavity_residue.pdb
- 1nlua_A_concavity.scores
- 1nlua_concavity.dx
- 1nlua_concavity.pml
- 1nlua_concavity_pocket.pdb
- 1nlua_concavity_residue.pdb
- 1t7qa_A_concavity.scores
- 1t7qa_concavity.dx
- 1t7qa_concavity.pml
- 1t7qa_concavity_pocket.pdb
- 1t7qa_concavity_residue.pdb
- 2ck3b_B_concavity.scores
- 2ck3b_concavity.dx
- 2ck3b_concavity.pml
- 2ck3b_concavity_pocket.pdb
- 2ck3b_concavity_residue.pdb
- pocket0_atm.pdb
- pocket0_vert.pqr
- pocket10_atm.pdb
- pocket10_vert.pqr
- pocket11_atm.pdb
- pocket11_vert.pqr
- pocket12_atm.pdb
- pocket12_vert.pqr
- pocket13_atm.pdb
- pocket13_vert.pqr
- pocket1_atm.pdb
- pocket1_vert.pqr
- pocket2_atm.pdb
- pocket2_vert.pqr
- pocket3_atm.pdb
- pocket3_vert.pqr
- pocket4_atm.pdb
- pocket4_vert.pqr
- pocket5_atm.pdb
- pocket5_vert.pqr
- pocket6_atm.pdb
- pocket6_vert.pqr
- pocket7_atm.pdb
- pocket7_vert.pqr
- pocket8_atm.pdb
- pocket8_vert.pqr
- pocket9_atm.pdb
- pocket9_vert.pqr
- 1a82a.pml
- 1a82a.tcl
- 1a82a_out.pdb
- 1a82a_pockets.pqr
- 1a82a_PYMOL.sh
- 1a82a_VMD.sh
- pocket0_atm.pdb
- pocket0_vert.pqr
- pocket10_atm.pdb
- pocket10_vert.pqr
- pocket11_atm.pdb
- pocket11_vert.pqr
- pocket12_atm.pdb
- pocket12_vert.pqr
- pocket13_atm.pdb
- pocket13_vert.pqr
- pocket14_atm.pdb
- pocket14_vert.pqr
- pocket15_atm.pdb
- pocket15_vert.pqr
- pocket16_atm.pdb
- pocket16_vert.pqr
- pocket17_atm.pdb
- pocket17_vert.pqr
- pocket18_atm.pdb
- pocket18_vert.pqr
- pocket19_atm.pdb
- pocket19_vert.pqr
- pocket1_atm.pdb
- pocket1_vert.pqr
- pocket2_atm.pdb
- pocket2_vert.pqr
- pocket3_atm.pdb
- pocket3_vert.pqr
- pocket4_atm.pdb
- pocket4_vert.pqr
- pocket5_atm.pdb
- pocket5_vert.pqr
- pocket6_atm.pdb
- pocket6_vert.pqr
- pocket7_atm.pdb
- pocket7_vert.pqr
- pocket8_atm.pdb
- pocket8_vert.pqr
- pocket9_atm.pdb
- pocket9_vert.pqr
- 1aaxa.pml
- 1aaxa.tcl
- 1aaxa_out.pdb
- 1aaxa_pockets.pqr
- 1aaxa_PYMOL.sh
- 1aaxa_VMD.sh
- pocket0_atm.pdb
- pocket0_vert.pqr
- pocket10_atm.pdb
- pocket10_vert.pqr
- pocket1_atm.pdb
- pocket1_vert.pqr
- pocket2_atm.pdb
- pocket2_vert.pqr
- pocket3_atm.pdb
- pocket3_vert.pqr
- pocket4_atm.pdb
- pocket4_vert.pqr
- pocket5_atm.pdb
- pocket5_vert.pqr
- pocket6_atm.pdb
- pocket6_vert.pqr
- pocket7_atm.pdb
- pocket7_vert.pqr
- pocket8_atm.pdb
- pocket8_vert.pqr
- pocket9_atm.pdb
- pocket9_vert.pqr
- 1nlua.pml
- 1nlua.tcl
- 1nlua_out.pdb
- 1nlua_pockets.pqr
- 1nlua_PYMOL.sh
- 1nlua_VMD.sh
- pocket0_atm.pdb
- pocket0_vert.pqr
- pocket10_atm.pdb
- pocket10_vert.pqr
- pocket11_atm.pdb
- pocket11_vert.pqr
- pocket12_atm.pdb
- pocket12_vert.pqr
- pocket13_atm.pdb
- pocket13_vert.pqr
- pocket14_atm.pdb
- pocket14_vert.pqr
- pocket1_atm.pdb
- pocket1_vert.pqr
- pocket2_atm.pdb
- pocket2_vert.pqr
- pocket3_atm.pdb
- pocket3_vert.pqr
- pocket4_atm.pdb
- pocket4_vert.pqr
- pocket5_atm.pdb
- pocket5_vert.pqr
- pocket6_atm.pdb
- pocket6_vert.pqr
- pocket7_atm.pdb
- pocket7_vert.pqr
- pocket8_atm.pdb
- pocket8_vert.pqr
- pocket9_atm.pdb
- pocket9_vert.pqr
- 1t7qa.pml
- 1t7qa.tcl
- 1t7qa_out.pdb
- 1t7qa_pockets.pqr
- 1t7qa_PYMOL.sh
- 1t7qa_VMD.sh
- pocket0_atm.pdb
- pocket0_vert.pqr
- pocket10_atm.pdb
- pocket10_vert.pqr
- pocket11_atm.pdb
- pocket11_vert.pqr
- pocket12_atm.pdb
- pocket12_vert.pqr
- pocket1_atm.pdb
- pocket1_vert.pqr
- pocket2_atm.pdb
- pocket2_vert.pqr
- pocket3_atm.pdb
- pocket3_vert.pqr
- pocket4_atm.pdb
- pocket4_vert.pqr
- pocket5_atm.pdb
- pocket5_vert.pqr
- pocket6_atm.pdb
- pocket6_vert.pqr
- pocket7_atm.pdb
- pocket7_vert.pqr
- pocket8_atm.pdb
- pocket8_vert.pqr
- pocket9_atm.pdb
- pocket9_vert.pqr
- 2ck3b.pml
- 2ck3b.tcl
- 2ck3b_out.pdb
- 2ck3b_pockets.pqr
- 2ck3b_PYMOL.sh
- 2ck3b_VMD.sh
- pocket1_atm.pdb
- pocket1_vert.pqr
- pocket2_atm.pdb
- pocket2_vert.pqr
- pocket3_atm.pdb
- pocket3_vert.pqr
- pocket4_atm.pdb
- pocket4_vert.pqr
- pocket5_atm.pdb
- pocket5_vert.pqr
- pocket6_atm.pdb
- pocket6_vert.pqr
- pocket7_atm.pdb
- pocket7_vert.pqr
- pocket8_atm.pdb
- pocket8_vert.pqr
- 1a82a.pml
- 1a82a.tcl
- 1a82a_info.txt
- 1a82a_out.pdb
- 1a82a_pockets.pqr
- 1a82a_PYMOL.sh
- 1a82a_VMD.sh
- pocket10_atm.pdb
- pocket10_vert.pqr
- pocket11_atm.pdb
- pocket11_vert.pqr
- pocket12_atm.pdb
- pocket12_vert.pqr
- pocket13_atm.pdb
- pocket13_vert.pqr
- pocket1_atm.pdb
- pocket1_vert.pqr
- pocket2_atm.pdb
- pocket2_vert.pqr
- pocket3_atm.pdb
- pocket3_vert.pqr
- pocket4_atm.pdb
- pocket4_vert.pqr
- pocket5_atm.pdb
- pocket5_vert.pqr
- pocket6_atm.pdb
- pocket6_vert.pqr
- pocket7_atm.pdb
- pocket7_vert.pqr
- pocket8_atm.pdb
- pocket8_vert.pqr
- pocket9_atm.pdb
- pocket9_vert.pqr
- 1aaxa.pml
- 1aaxa.tcl
- 1aaxa_info.txt
- 1aaxa_out.pdb
- 1aaxa_pockets.pqr
- 1aaxa_PYMOL.sh
- 1aaxa_VMD.sh
- pocket10_atm.pdb
- pocket10_vert.pqr
- pocket1_atm.pdb
- pocket1_vert.pqr
- pocket2_atm.pdb
- pocket2_vert.pqr
- pocket3_atm.pdb
- pocket3_vert.pqr
- pocket4_atm.pdb
- pocket4_vert.pqr
- pocket5_atm.pdb
- pocket5_vert.pqr
- pocket6_atm.pdb
- pocket6_vert.pqr
- pocket7_atm.pdb
- pocket7_vert.pqr
- pocket8_atm.pdb
- pocket8_vert.pqr
- pocket9_atm.pdb
- pocket9_vert.pqr
- 1nlua.pml
- 1nlua.tcl
- 1nlua_info.txt
- 1nlua_out.pdb
- 1nlua_pockets.pqr
- 1nlua_PYMOL.sh
- 1nlua_VMD.sh
- pocket10_atm.pdb
- pocket10_vert.pqr
- pocket11_atm.pdb
- pocket11_vert.pqr
- pocket1_atm.pdb
- pocket1_vert.pqr
- pocket2_atm.pdb
- pocket2_vert.pqr
- pocket3_atm.pdb
- pocket3_vert.pqr
- pocket4_atm.pdb
- pocket4_vert.pqr
- pocket5_atm.pdb
- pocket5_vert.pqr
- pocket6_atm.pdb
- pocket6_vert.pqr
- pocket7_atm.pdb
- pocket7_vert.pqr
- pocket8_atm.pdb
- pocket8_vert.pqr
- pocket9_atm.pdb
- pocket9_vert.pqr
- 1t7qa.pml
- 1t7qa.tcl
- 1t7qa_info.txt
- 1t7qa_out.pdb
- 1t7qa_pockets.pqr
- 1t7qa_PYMOL.sh
- 1t7qa_VMD.sh
- pocket10_atm.pdb
- pocket10_vert.pqr
- pocket11_atm.pdb
- pocket11_vert.pqr
- pocket12_atm.pdb
- pocket12_vert.pqr
- pocket13_atm.pdb
- pocket13_vert.pqr
- pocket14_atm.pdb
- pocket14_vert.pqr
- pocket15_atm.pdb
- pocket15_vert.pqr
- pocket16_atm.pdb
- pocket16_vert.pqr
- pocket1_atm.pdb
- pocket1_vert.pqr
- pocket2_atm.pdb
- pocket2_vert.pqr
- pocket3_atm.pdb
- pocket3_vert.pqr
- pocket4_atm.pdb
- pocket4_vert.pqr
- pocket5_atm.pdb
- pocket5_vert.pqr
- pocket6_atm.pdb
- pocket6_vert.pqr
- pocket7_atm.pdb
- pocket7_vert.pqr
- pocket8_atm.pdb
- pocket8_vert.pqr
- pocket9_atm.pdb
- pocket9_vert.pqr
- 2ck3b.pml
- 2ck3b.tcl
- 2ck3b_info.txt
- 2ck3b_out.pdb
- 2ck3b_pockets.pqr
- 2ck3b_PYMOL.sh
- 2ck3b_VMD.sh
- pocket_1.json
- pocket_2.json
- pocket_3.json
- alphaspheres.pdb
- pockets.json
- summary.txt
- pocket_1.json
- pocket_2.json
- pocket_3.json
- pocket_4.json
- pocket_5.json
- pocket_6.json
- pocket_7.json
- pocket_8.json
- alphaspheres.pdb
- pockets.json
- summary.txt
- pocket_1.json
- pocket_2.json
- pocket_3.json
- pocket_4.json
- alphaspheres.pdb
- pockets.json
- summary.txt
- pocket_1.json
- pocket_2.json
- alphaspheres.pdb
- pockets.json
- summary.txt
- pocket_1.json
- pocket_2.json
- pocket_3.json
- alphaspheres.pdb
- pockets.json
- summary.txt
- readme.md
- A.pdb
- B.pdb
- C.pdb
- D.pdb
- E.pdb
- F.pdb
- protein.pdb
- 0_A_pkt.pdb
- 0_B_pkt.pdb
- 1_A_pkt.pdb
- without_clus_pkt.pdb
- protein.pdb
- 0_A_pkt.pdb
- 1_A_pkt.pdb
- 2_A_pkt.pdb
- without_clus_pkt.pdb
- protein.pdb
- 0_A_pkt.pdb
- 0_B_pkt.pdb
- 1_A_pkt.pdb
- without_clus_pkt.pdb
- protein.pdb
- protein.pdb
- 0_C_pkt.pdb
- without_clus_pkt.pdb
- protein.pdb
- 0_A_pkt.pdb
- 1_A_pkt.pdb
- 2_A_pkt.pdb
- 3_A_pkt.pdb
- without_clus_pkt.pdb
- 1a26A_predictions.txt
- 1a2kC_predictions.txt
- 1afkA_predictions.txt
- 1atlA_predictions.txt
- 1bqoB_predictions.txt
- grid0_score_0.8070.mol2
- pocket0_score_0.8070.mol2
- grid0_score_0.5351.mol2
- grid1_score_0.4442.mol2
- grid2_score_0.3573.mol2
- grid3_score_0.2369.mol2
- pocket0_score_0.5351.mol2
- pocket1_score_0.4442.mol2
- pocket2_score_0.3573.mol2
- pocket3_score_0.2369.mol2
- grid0_score_0.6907.mol2
- grid1_score_0.2879.mol2
- grid2_score_0.0650.mol2
- pocket0_score_0.6907.mol2
- pocket1_score_0.2879.mol2
- pocket2_score_0.0650.mol2
- grid0_score_0.7288.mol2
- grid1_score_0.0664.mol2
- grid2_score_0.3433.mol2
- pocket0_score_0.7288.mol2
- pocket1_score_0.0664.mol2
- pocket2_score_0.3433.mol2
- grid0_score_0.6535.mol2
- grid1_score_0.2790.mol2
- pocket0_score_0.6535.mol2
- pocket1_score_0.2790.mol2
- grid0_score_0.2778.mol2
- grid1_score_0.2404.mol2
- grid2_score_0.2156.mol2
- grid3_score_0.1252.mol2
- grid4_score_0.1299.mol2
- grid5_score_0.1728.mol2
- pocket0_score_0.2778.mol2
- pocket1_score_0.2404.mol2
- pocket2_score_0.2156.mol2
- pocket3_score_0.1252.mol2
- pocket4_score_0.1299.mol2
- pocket5_score_0.1728.mol2
- 184L.pdb
- 1AFL.pdb
- 1AHP.pdb
- 1CZS.pdb
- 1fbl.bcif
- 1fbl.cif
- 1fbl.cif.gz
- 1fbl.cif.zst
- 1fbl.pdb
- 1fbl.pdb.gz
- 1fbl.pdb.zst
- 1fbl_pymol.cif
- 1HI4.pdb
- 2W83.bcif.gz
- 2W83.cif
- 2W83.cif.gz
- 2W83.cif.zst
- 2W83.pdb
- 2W83.pdb.gz
- 2W83.pdb.zst
- basic.ds
- concavity.ds
- fpocket.ds
- fpocket3.ds
- pocketeer.ds
- puresnet.ds
- readme.md
- specified-chains-and-ligands.ds
- specified-chains.ds
- specified-ligands-2.ds
- specified-ligands.ds
- swinsite.ds
- test.ds
- LICENSE.txt
- prank
- prank.bat
- prank_burst
- balancing-01-ploop-1_DCA_4_0.png
- ions-prediction-method-development-log.md
- cofactors.md
- evaluation-metric-fixes-2.6.md
- jvm-performance-tuning.md
- DCA_4_0_cons.png
- DCA_4_0_default.png
- pocket_grid_chimerax.png
- pocket_grid_chimerax_2.png
- pocket_grid_chimerax_2_small.png
- pocket_grid_chimerax_small.png
- 1fbl.cif
- 1fbl.cif_points.pdb.gz
- 1fbl.cif_chimerax.cxc
- 1fbl.cif_pymol.pml
- 1fbl.cif_points.csv
- 1fbl.cif_predictions.csv
- 1fbl.cif_residues.csv
- params.txt
- analyze_p2rank_output.ipynb
- readme.md
- aa-mapping.md
- cofactors.md
- conservation.md
- docking.md
- export-pocket-descriptors.md
- export-pocket-grid.md
- export-points.md
- feature-setup.md
- hyperparameter-optimization-tutorial.md
- new-feature-evaluation-tutorial.md
- readme.md
- rescoring.md
- training-score-transformers.md
- training-tutorial.md
- user-guide.md
- utility-commands.md
- gradle-wrapper.jar
- gradle-wrapper.properties
- faster-molecular-surface-1.8.jar
- faster-molecular-surface-1.8.pom
- FasterForest-2.11.0.jar
- FasterForest-2.11.0.pom
- FasterForest-2.13.0.jar
- FasterForest-2.13.0.pom
- _remote.repositories
- biojava-structure-7.2.2-rdk.1.jar
- biojava-structure-7.2.2-rdk.1.pom
- _remote.repositories
- biojava-structure-7.2.4-rdk.1.jar
- biojava-structure-7.2.4-rdk.1.pom
- _remote.repositories
- biojava-structure-7.2.5-rdk.1.jar
- biojava-structure-7.2.5-rdk.1.pom
- FastRandomForest_0.99.jar
- FastRandomForest_0.99_src.jar
- readme.txt
- pockets_holo4k.csv
- pockets_holo4k.xlsx
- 2026-06-03-surface-strategies-holo4k.md
- 2026-06-05-predict-runtime-breakdown.md
- ALTERNATE_CHAIN_REDUCTION.md
- backlog.md
- ELECTROSTATICS_IMPLEMENTATION.md
- technical-debt.md
- commit.sh
- experiment.sh
- logc.sh
- push.sh
- update.sh
- p2rank_chimerax_visualization.png
- p2rank_chimerax_visualization_small.png
- p2rank_logo.svg
- p2rank_sas_points.png
- p2rank_sas_points_smaller.png
- info.txt
- table.txt
- aaindex1.txt
- notes.md
- atomic-hydrophobicity.csv
- info.txt
- 5sasa.invalids.csv
- 5sasa.valids.csv
- extract-atomtable.groovy
- extract.sh
- list.5sasa.invalids.csv
- list.5sasa.valids.csv
- list.raw.invalids.csv
- list.raw.valids.csv
- raw.invalids.csv
- raw.valids.csv
- aa-propensities.csv
- params.txt
- aa-propensities.csv
- params.txt
- aa_surf_seq_duplet_propensities.csv
- params.txt
- aa_surf_seq_duplet_propensities.csv
- params.txt
- aa_surf_seq_triplet_propensities.csv
- params.txt
- aa_surf_seq_triplet_propensities.csv
- params.txt
- aa_surf_seq_duplet_propensities.csv
- aa_surf_seq_triplet_propensities.csv
- aa-propensities.csv
- aa-shortcuts.csv
- bench-common.sh
- benchmark.sh
- eval_new_features.sh
- eval_session_features.sh
- kdtree-benchmark.sh
- pocket_grid_dataset_bench.sh
- pocket_grid_features_bench.sh
- predict_bench.sh
- predict_bench_jres.sh
- predict_bench_matrix.sh
- predict_breakdown.sh
- predict_profile_mt.sh
- README.md
- standard-benchmarks.sh
- surface_bench_jres.sh
- testsets.sh
- FOLLOWUP.md
- 1fbl.pdb
- 1fbl.pdb_points.pdb.gz
- 1fbl.pdb_chimerax.cxc
- 1fbl.pdb_pymol.pml
- 1fbl.pdb_predictions.csv
- 1fbl.pdb_residues.csv
- params.txt
- 1fbl.pdb
- 1fbl.pdb_points.pdb.gz
- 1fbl.pdb_chimerax.cxc
- 1fbl.pdb_pymol.pml
- 1fbl.pdb_predictions.csv
- 1fbl.pdb_residues.csv
- params.txt
- batch-profiling-and-scale-effects.md
- citations.md
- dca_bootstrap_ci.py
- development-notes.md
- extracted_schema_pockets.json
- local-env.sh
- CollectorFactory.groovy
- DataPreprocessor.groovy
- DoubleVector.groovy
- LigandabilityPointVectorCollector.groovy
- PointVectorCollector.groovy
- ResidueDerivedPointVectorCollector.groovy
- VectorCollector.groovy
- BinaryLabeling.groovy
- BinaryLabelings.groovy
- ColumnBasedResidueLabeler.groovy
- DoubleResidueLabeling.groovy
- LabeledPoint.java
- LabeledResidue.groovy
- LigandBasedPointLabeler.groovy
- LigandBasedResidueLabeler.groovy
- ModelBasedPointLabeler.groovy
- ModelBasedResidueLabeler.groovy
- PointLabeler.groovy
- ResidueBasedPointLabeler.groovy
- ResidueLabeler.groovy
- ResidueLabeling.groovy
- ResidueLabelings.groovy
- SprintLabelingLoader.groovy
- StaticResidueLabeler.groovy
- DelphiCubeLoader.groovy
- GaussianCube.groovy
- ConcavityLoader.groovy
- DeepSiteLoader.groovy
- FPocketLoader.groovy
- LiseLoader.groovy
- Loaders.java
- MetaPocket2Loader.groovy
- P2RankLoader.groovy
- PocketeerLoader.groovy
- PredictionLoader.groovy
- PUResNetLoader.groovy
- PUResNetPdbRepair.groovy
- Seq2PocketLoader.groovy
- SiteHoundLoader.groovy
- SwinSiteLoader.groovy
- AhojSiteInfo.groovy
- AhojUbsSiteParser.groovy
- ConservationLoader.groovy
- DatasetCachedLoader.groovy
- DatasetItemLoader.groovy
- ExplicitSitesIndex.groovy
- ExtendedResidueId.groovy
- LoaderParams.groovy
- AA.groovy
- AminoAcidMapper.groovy
- BindingSite.java
- CofactorHandler.groovy
- Dataset.groovy
- Ligand.groovy
- Ligands.groovy
- Pocket.groovy
- Prediction.groovy
- PredictionPair.groovy
- Protein.groovy
- Residue.groovy
- ResidueChain.groovy
- Residues.groovy
- ResidueSite.groovy
- SiteCenterMethod.groovy
- FastaExporter.groovy
- AtomicToSasFeatWrapper.groovy
- ResidueToAtomicFeatWrapper.groovy
- ResidueToSasFeatWrapper.groovy
- SasToAtomicFeatWrapper.groovy
- AbstractFeatureCalculator.groovy
- AtomFeatureCalculationContext.groovy
- AtomFeatureCalculator.groovy
- FeatureCalculator.groovy
- FeatureRegistry.groovy
- ProcessedItemContext.groovy
- ResidueFeatureCalculationContext.groovy
- ResidueFeatureCalculator.groovy
- SasFeatureCalculationContext.groovy
- SasFeatureCalculator.groovy
- GenericHeader.groovy
- GenericVector.java
- Asa2Feature.groovy
- AsaFeature.groovy
- AsaResiduesFeature.groovy
- ChemDefaults.groovy
- ChemFeature.groovy
- ChemVector.groovy
- ConservationProvider.groovy
- ConservationProviderException.groovy
- ConservationProviderFactory.groovy
- HmmServerConservationProvider.groovy
- ConservationCloudFeature.groovy
- ConservationCloudScaledFeature.groovy
- ConservationFeature.groovy
- ConservationScore.groovy
- ConservCloud2SF.groovy
- ConservCloudSF.groovy
- ConservRF.groovy
- ResidueNumberWrapper.groovy
- ZConservCloud2SF.groovy
- ZConservCloudSF.groovy
- ZConservRF.groovy
- ContactResidue1Feature.groovy
- ContactResidue1PositionFeature.groovy
- ContactResiduesPositionFeature.groovy
- ContactResiduesRF.groovy
- CsvFileFeature.groovy
- CsvFileFeatureValues.groovy
- AmberCharges.java
- CoulombKernel.java
- DelphiCubeAtomFeature.groovy
- DelphiCubeSasFeature.groovy
- ElectrostaticsSasFeature.groovy
- PartialChargeFeature.groovy
- PartialChargeTable.java
- AbstractMethylEnergyCloudSF.groovy
- LJEnergyCalculator.groovy
- MethylEnergyCloudSF.groovy
- MethylEnergyCloudX2FullSF.groovy
- MethylEnergyCloudX2SF.groovy
- MethylEnergyCloudXSF.groovy
- MethylEnergyFeature.groovy
- ProbePoints.groovy
- AtomRole.groovy
- EnergyCalculator.groovy
- EnergyCalculatorConfig.groovy
- ProbeParams.groovy
- ProbeType.groovy
- AbstractProbeEnergyFeature.groovy
- AbstractSingleProbeEnergyFeature.groovy
- AromaticRingProbeEnergyFeature.groovy
- AromaticRingSingleProbeEnergyFeature.groovy
- CationProbeEnergyFeature.groovy
- CationSingleProbeEnergyFeature.groovy
- HBAcceptorProbeEnergyFeature.groovy
- HBAcceptorSingleProbeEnergyFeature.groovy
- HBDonorProbeEnergyFeature.groovy
- HBDonorSingleProbeEnergyFeature.groovy
- NeutralApolarProbeEnergyFeature.groovy
- NeutralApolarSingleProbeEnergyFeature.groovy
- AbstractDirectProbeEnergyFeature.groovy
- AromaticRingDirectFeature.groovy
- CationDirectFeature.groovy
- HBAcceptorDirectFeature.groovy
- HBDonorDirectFeature.groovy
- NeutralApolarDirectFeature.groovy
- DistancePairHist.groovy
- PairHistogramFeature.groovy
- AnmEffectivenessRF.groovy
- AnmModel.groovy
- AnmMsfRF.groovy
- AnmSensorRF.groovy
- CgBetweennessRF.groovy
- CgClosenessRF.groovy
- CgDegreeRF.groovy
- ContactGraph.groovy
- AaPropensityFeature.groovy
- AtomTypePropensityFeature.groovy
- DupletsPropensityFeature.groovy
- TripletsPropensityFeature.groovy
- SecStructCloudSF.groovy
- SecStructRF.groovy
- SecStructSimpleCloudSF.groovy
- SecStructSimpleMotifRF.groovy
- SecStructSimpleRF.groovy
- SimpleSecStructType.java
- SsHistogram.groovy
- SsSimpleHistogram.groovy
- SsSimpleTriplet.groovy
- IsSidechainAtomFeature.groovy
- IsSidechainCloudFeature.groovy
- IsSidechainSasFeature.groovy
- ResidueMotif.java
- StructMotifFeature.groovy
- AAIndex1.groovy
- AAIndexAtomFeature.groovy
- AAIndexFeature.groovy
- AtomTableFeature.groovy
- PropertyTable.groovy
- PropertyTableKey.java
- ResidueTableFeature.groovy
- VolSiteAtomTable.java
- VolsiteFeature.java
- VolSitePharmacophore.java
- AtomicResidueFeature.groovy
- BfactorFeature.groovy
- HybridizationFeature.groovy
- IsExposedAtomFeature.groovy
- NearestExposedDistSasFeature.groovy
- ProteinMassFeature.groovy
- ProtrusionFeature.groovy
- ProtrusionHistogramFeature.groovy
- PyramidFeature.groovy
- SurfaceProtrusionFeature.groovy
- XyzDummyFeature.groovy
- WeightFun.groovy
- FeatureExtractor.groovy
- FeatureSetup.groovy
- FeatureVector.java
- PrankFeatureExtractor.groovy
- PrankFeatureVector.java
- ResidueTypeFeature.groovy
- AtomClusterer.groovy
- AtomGroupClusterer.groovy
- Clusterer.groovy
- SLinkClusterer.groovy
- SLinkClustererV2.java
- BinaryHeap.java
- IntervalHeap.java
- MaxHeap.java
- MinHeap.java
- Pair.java
- DistanceFunction.java
- info.txt
- KdNode.java
- KdTree3.java
- NearestNeighborIterator.java
- SquareEuclideanDistanceFunction.java
- AtomKdTreeV1.java
- KdTree.java
- AtomKdTreeV2.groovy
- KdTree3D.java
- AtomKdTree.java
- AtomsPointSampler.groovy
- GridGenerator.java
- GridPointSampler.groovy
- GridSample.java
- PointSampler.groovy
- RandomPointSampler.groovy
- SampledPoints.groovy
- SurfacePointSampler.groovy
- UniformGrid3D.java
- GeometricTransformation.groovy
- Rotation.groovy
- Rotations.java
- AlternateChainReducer.groovy
- AtomDeduplicator.java
- Atoms.java
- Box.java
- PatchedCdkNumericalSurface.groovy
- Point.java
- SecondaryStructureUtils.groovy
- Struct.groovy
- Surface.groovy
- SurfaceStrategy.groovy
- ClassifierStats.groovy
- Curve.groovy
- CurveMetrics.java
- Curves.groovy
- Histogram.groovy
- Metrics.groovy
- PredictedScores.java
- ClusteringStrategy.groovy
- SingleLinkageClustering.groovy
- ZScoreSingleLinkageClustering.groovy
- DCA.groovy
- DCC.groovy
- DPA.groovy
- DSA.groovy
- DSO.groovy
- DSWO.groovy
- PocketCriteria.groovy
- PocketCriterion.java
- IdentityRescorer.groovy
- InstancePredictor.java
- ModelBasedRescorer.groovy
- PLBIndexRescorer.groovy
- PocketRescorer.groovy
- PocketVolumeRescorer.groovy
- RandomRescorer.groovy
- PredictionSummary.groovy
- RescoringSummary.groovy
- PocketPredictor.groovy
- PointScoreCalculator.groovy
- PrankPocket.groovy
- ProbabilityScoreTransformer.groovy
- ScoreTransformer.groovy
- ZscoreTpTransformer.groovy
- DafaultPrankPredictor.groovy
- PrankFacade.java
- PrankPredictor.java
- ClassifierFactory.groovy
- ClassifierOption.groovy
- FeatureVectors.groovy
- FlattenComparison.groovy
- Model.groovy
- ModelCompatibility.groovy
- ModelConverter.groovy
- HExternalOptimizerBase.groovy
- HPyGpgoOptimizer.groovy
- HSpearmintOptimizer.groovy
- HObjectiveFunction.java
- HOptimizer.groovy
- HStep.groovy
- HVariable.groovy
- ConfigLoader.groovy
- IterativeParam.groovy
- ListParam.groovy
- ModelParam.groovy
- Parametrized.groovy
- Params.groovy
- RuntimeParam.groovy
- AnalyzeRoutine.groovy
- DataTable.groovy
- PrintRoutine.groovy
- TransformRoutine.groovy
- Benchmarks.groovy
- GridOptimizerRoutine.groovy
- HyperOptimizerRoutine.groovy
- ParamLooper.groovy
- FpocketAdHocHelper.groovy
- FpocketRunner.groovy
- AbstractScalarPocketDescriptor.java
- GridPointStats.java
- NumGridPointsDescriptor.java
- NumResiduesDescriptor.java
- NumSurfaceAtomsDescriptor.java
- PocketChargePolarityDescriptor.java
- PocketChargeStats.java
- PocketDescriptor.java
- PocketDescriptorRegistry.java
- PocketDipoleMagnitudeDescriptor.java
- PocketGridContext.java
- PocketNetChargeDescriptor.java
- PrincipalMomentsDescriptor.java
- RadiusOfGyrationDescriptor.java
- SphericityDescriptor.java
- VolumeDescriptor.java
- KdTreeAssigner.java
- PocketAssigner.java
- PocketAssignerRegistry.java
- VoxelHashAssigner.java
- ElectrostaticsGridPointDescriptor.java
- PocketGridPointContext.java
- PocketGridPointDescriptor.java
- PocketGridPointDescriptorRegistry.java
- VolsiteGridPointDescriptor.java
- VolsiteSmoothGridPointDescriptor.java
- ErodeDilateCloser.java
- FillKnobs.java
- LatticeMorphology.java
- MorphologicalCloser.java
- NoOpFiller.java
- PocketShapeFiller.java
- PocketShapeFillerRegistry.java
- PocketGrid.java
- PocketGridAnalysis.java
- PocketGridBuilder.java
- PocketGridConfig.java
- VdwRadiusTable.java
- DescriptorListValidator.java
- DescriptorSchemaHelper.java
- GetcleftOutputCalculator.groovy
- NamedRegistryHelper.java
- PocketDescriptorsExporter.groovy
- PocketDescriptorsRows.groovy
- PocketGridExporter.groovy
- PocketGridOutputs.groovy
- PocketGridRows.java
- PointExportData.groovy
- PointsExporter.groovy
- TableData.groovy
- TableExporter.groovy
- ExportPointsRoutine.groovy
- PredictPocketsRoutine.groovy
- PredictResiduesRoutine.groovy
- RescorePocketsRoutine.groovy
- EvalContext.groovy
- EvalResults.groovy
- Evaluation.groovy
- FeatureImportances.groovy
- MultiRunStats.groovy
- PredictResults.groovy
- ResultsBase.groovy
- CollectVectorsRoutine.groovy
- CrossValidation.groovy
- EvalPocketsRoutine.groovy
- EvalResiduesRoutine.groovy
- EvalRoutine.groovy
- Experiments.groovy
- ModelCache.groovy
- SeedLoop.groovy
- TrainEvalContext.groovy
- TrainEvalRoutine.groovy
- PreloadConservationRoutine.groovy
- Routine.groovy
- ChimeraXRenderer.groovy
- NewPymolRenderer.groovy
- PocketGridChimeraXRenderer.groovy
- PocketGridPdbSidecar.java
- PocketGridPymolRenderer.groovy
- PymolRenderer.groovy
- PredictionVisualizer.groovy
- RenderingModel.groovy
- CommandConfigCompatibility.groovy
- Commands.groovy
- Failable.groovy
- LogManager.groovy
- Main.groovy
- P2Rank.groovy
- PrankException.groovy
- TextBox.groovy
- CSV.groovy
- CsvRow.groovy
- RExecutor.groovy
- RPlotter.groovy
- CharMatchers.java
- FastSplitter.java
- FastTokenizer.java
- FastTokenizer2.java
- Tokenizer.java
- ATimer.java
- Bench.groovy
- BinCounter.groovy
- CdkUtils.groovy
- CmdLineArgs.groovy
- ColorUtils.groovy
- Console.groovy
- Cutils.groovy
- CutoffAtomsCallLog.java
- ErrorUtils.groovy
- Formatter.groovy
- Futils.groovy
- MathUtils.java
- Parallel.groovy
- PathUtils.groovy
- PdbUtils.groovy
- PerfUtils.java
- ProcessRunner.groovy
- StatSample.groovy
- StatSample2.java
- Sutils.groovy
- SysUtils.groovy
- ThreadUtils.groovy
- WekaUtils.groovy
- Writable.groovy
- pygpgo_template.py
- aa-mapping-pdbfixer.csv
- README.md
- hb-overrides.csv
- lj-params.csv
- role-rules.csv
- duplets.csv
- triplets.csv
- duplets.csv
- triplets.csv
- duplets.csv
- triplets.csv
- duplets.csv
- triplets.csv
- duplets.csv
- triplets.csv
- duplets.csv
- triplets.csv
- duplets.csv
- triplets.csv
- aa-propensity.csv
- atomtype-propensity.csv
- duplets.csv
- triplets.csv
- aa-propensity.csv
- atomtype-propensity.csv
- duplets.csv
- triplets.csv
- aa-propensity.csv
- atomtype-propensity.csv
- duplets.csv
- triplets.csv
- notes.md
- aa-5factors.csv
- aa-index-full.csv
- aa-propensities.csv
- atom-hybridization.csv
- atomic-properties.csv
- readme.md
- volsite-atomic-properties.csv
- build.properties
- help.txt
- log4j2.xml
- DelphiCubeLoaderTest.groovy
- ConcavityLoaderTest.groovy
- FPocketLoaderTest.groovy
- MissingPocketLoadersTest.groovy
- PocketeerLoaderTest.groovy
- PUResNetLoaderTest.groovy
- PUResNetPdbRepairTest.groovy
- Seq2PocketLoaderTest.groovy
- SwinSiteLoaderTest.groovy
- AhojUbsSiteParserTest.groovy
- ExplicitSitesIndexTest.groovy
- AminoAcidMapperTest.groovy
- ChainReductionTest.groovy
- CofactorHandlerTest.groovy
- CofactorIntegrationTest.groovy
- CofactorPipelineTest.groovy
- DatasetTest.groovy
- LigandFilteringTest.groovy
- LigandMatchingTest.groovy
- PocketFilterIntegrationTest.groovy
- PredictionFilterPocketsTest.groovy
- PredictionFinalizePocketsTest.groovy
- ProteinParsingTest.groovy
- SiteMetricsTest.groovy
- FastaExporterTest.groovy
- ConservationAlignmentTest.groovy
- ContactResiduesPositionFeatureTest.groovy
- CsvFileFeatureTest.groovy
- AmberChargesTest.groovy
- CoulombKernelTest.groovy
- PartialChargeTableTest.groovy
- MethylEnergyCloudEmptyCloudTest.groovy
- MethylEnergyCloudParamsRebuildTest.groovy
- MethylEnergyFeatureLazyInitTest.groovy
- AtomRoleTest.groovy
- ConcurrencyTest.groovy
- EnergyCalculatorTest.groovy
- ProbeEnergyFeaturesIT.groovy
- ProbeEnergyFeaturesTest.groovy
- DirectProbeEnergyFeaturesIT.groovy
- DistancePairHistTest.groovy
- AnmModelTest.groovy
- ContactGraphTest.groovy
- PhysicsFeaturesIT.groovy
- PropensityTablesDefaultTest.groovy
- AtomTableFeatureTest.groovy
- PropertyTableTest.groovy
- VolSiteAtomTableTest.groovy
- HybridizationFeatureTest.groovy
- FeatureVectorGoldenTest.groovy
- FasterNumericalSurfaceTest.groovy
- PatchedCdkNumericalSurfaceTest.groovy
- SLinkClustererTest.groovy
- KdTree3DTest.groovy
- KdTreeBenchmarkTest.groovy
- AtomKdTreeTest.groovy
- GridGeneratorBetweenTest.groovy
- UniformGrid3DTest.groovy
- AlternateChainReducerTest.groovy
- AtomDeduplicatorTest.groovy
- AtomsCountWithinSphereTest.groovy
- AtomsTest.groovy
- StructTest.groovy
- SurfaceStrategyTest.groovy
- CurveMetricsTest.java
- PredictedScoresTest.groovy
- WekaStatsHelper.groovy
- ZScoreClusteringStrategyTest.groovy
- PocketRescorerTest.groovy
- ClassifierStatsTest.groovy
- ScoreTransformerTest.groovy
- DafaultPrankPredictorTest.groovy
- PredictionOutputPinningTest.groovy
- FlattenGateTest.groovy
- ModelCompatibilityTest.groovy
- ModelConverterTest.groovy
- ConfigLoaderTest.groovy
- ParamsTypeCoercionTest.groovy
- CofactorAnalyzeTest.groovy
- DataTableCsvTest.groovy
- FpocketRunnerTest.java
- PocketDescriptorsTest.groovy
- PocketGridPointDescriptorRegistryTest.groovy
- PocketGridPointDescriptors.groovy
- VolsiteGridPointDescriptorTest.groovy
- VolsiteSmoothGridPointDescriptorTest.groovy
- ErodeDilateCloserTest.groovy
- MorphologicalCloserTest.groovy
- PocketGridBuilderTest.groovy
- PocketGridOverlapIntegrationTest.groovy
- PocketGridOverlapTest.groovy
- VdwRadiusTableTest.groovy
- ArrayTableData.groovy
- DescriptorListValidatorTest.groovy
- PocketDescriptorsRowsTest.groovy
- PocketGridRowsTest.groovy
- PointExportDataTest.groovy
- PointsExporterTest.groovy
- TableExporterTest.groovy
- ExportPointsRoutineTest.groovy
- RescoreSmokeTest.groovy
- EvaluationClosestPocketTest.groovy
- EvaluationSiteReachabilityTest.groovy
- EvaluationSuccessRateTest.groovy
- TrainEvalApoHoloTest.groovy
- TrainEvalRoutineTest.groovy
- PocketGridChimeraXRendererTest.groovy
- PocketGridPymolRendererTest.groovy
- RendererTestFixtures.groovy
- CommandConfigCompatibilityTest.groovy
- Log4jCapture.groovy
- DiscontinuedChainsTest.groovy
- FPocketTest.groovy
- StructureParsingTest.groovy
- 1a26A.pdb
- 1a26A_pocketfinder_pocket.pdb
- 1a26A_pocketfinder_residue.pdb
- 1bviC.pdb.csv
- 1bviC.pdb
- dataset.ds
- ahojubs_full.csv.gz
- ahojubs_reduced.csv
- readme.md
- delphi-2src.cube.gz
- pocket0_atm.pdb
- pocket0_atm.pdb.tmp
- pocket0_vert.pqr
- pocket10_atm.pdb
- pocket10_atm.pdb.tmp
- pocket10_vert.pqr
- pocket1_atm.pdb
- pocket1_atm.pdb.tmp
- pocket1_vert.pqr
- pocket2_atm.pdb
- pocket2_atm.pdb.tmp
- pocket2_vert.pqr
- pocket3_atm.pdb
- pocket3_atm.pdb.tmp
- pocket3_vert.pqr
- pocket4_atm.pdb
- pocket4_atm.pdb.tmp
- pocket4_vert.pqr
- pocket5_atm.pdb
- pocket5_atm.pdb.tmp
- pocket5_vert.pqr
- pocket6_atm.pdb
- pocket6_atm.pdb.tmp
- pocket6_vert.pqr
- pocket7_atm.pdb
- pocket7_atm.pdb.tmp
- pocket7_vert.pqr
- pocket8_atm.pdb
- pocket8_atm.pdb.tmp
- pocket8_vert.pqr
- pocket9_atm.pdb
- pocket9_atm.pdb.tmp
- pocket9_vert.pqr
- a.001.001.001_1mwba_unbound.pml
- a.001.001.001_1mwba_unbound.tcl
- a.001.001.001_1mwba_unbound_out.pdb
- a.001.001.001_1mwba_unbound_pockets.pqr
- a.001.001.001_1mwba_unbound_PYMOL.sh
- a.001.001.001_1mwba_unbound_VMD.sh
- a.001.001.pml
- pocket0_atm.pdb
- pocket0_atm.pdb.tmp
- pocket0_vert.pqr
- pocket1_atm.pdb
- pocket1_atm.pdb.tmp
- pocket1_vert.pqr
- a.004.005.004_1hw5b_unbound.pml
- a.004.005.004_1hw5b_unbound.tcl
- a.004.005.004_1hw5b_unbound_out.pdb
- a.004.005.004_1hw5b_unbound_pockets.pqr
- a.004.005.004_1hw5b_unbound_PYMOL.sh
- a.004.005.004_1hw5b_unbound_VMD.sh
- a.004.005.pml
- a.001.001.001_1mwba_unbound_out.pdb
- a.001.001.001_1s69a_ligand.pdb
- a.004.005.004_1hw5b_unbound_out.pdb
- pocket10_atm.cif
- pocket10_vert.pqr
- pocket11_atm.cif
- pocket11_vert.pqr
- pocket12_atm.cif
- pocket12_vert.pqr
- pocket13_atm.cif
- pocket13_vert.pqr
- pocket14_atm.cif
- pocket14_vert.pqr
- pocket15_atm.cif
- pocket15_vert.pqr
- pocket16_atm.cif
- pocket16_vert.pqr
- pocket17_atm.cif
- pocket17_vert.pqr
- pocket18_atm.cif
- pocket18_vert.pqr
- pocket19_atm.cif
- pocket19_vert.pqr
- pocket1_atm.cif
- pocket1_vert.pqr
- pocket2_atm.cif
- pocket2_vert.pqr
- pocket3_atm.cif
- pocket3_vert.pqr
- pocket4_atm.cif
- pocket4_vert.pqr
- pocket5_atm.cif
- pocket5_vert.pqr
- pocket6_atm.cif
- pocket6_vert.pqr
- pocket7_atm.cif
- pocket7_vert.pqr
- pocket8_atm.cif
- pocket8_vert.pqr
- pocket9_atm.cif
- pocket9_vert.pqr
- 1fbl_cif.pml
- 1fbl_cif.tcl
- 1fbl_cif_PYMOL.sh
- 1fbl_cif_VMD.sh
- 1fbl_info.txt
- 1fbl_out.cif
- 1fbl_pockets.pqr
- pocket10_atm.cif
- pocket10_vert.pqr
- pocket11_atm.cif
- pocket11_vert.pqr
- pocket12_atm.cif
- pocket12_vert.pqr
- pocket13_atm.cif
- pocket13_vert.pqr
- pocket14_atm.cif
- pocket14_vert.pqr
- pocket15_atm.cif
- pocket15_vert.pqr
- pocket16_atm.cif
- pocket16_vert.pqr
- pocket17_atm.cif
- pocket17_vert.pqr
- pocket18_atm.cif
- pocket18_vert.pqr
- pocket19_atm.cif
- pocket19_vert.pqr
- pocket1_atm.cif
- pocket1_vert.pqr
- pocket20_atm.cif
- pocket20_vert.pqr
- pocket21_atm.cif
- pocket21_vert.pqr
- pocket22_atm.cif
- pocket22_vert.pqr
- pocket23_atm.cif
- pocket23_vert.pqr
- pocket24_atm.cif
- pocket24_vert.pqr
- pocket25_atm.cif
- pocket25_vert.pqr
- pocket26_atm.cif
- pocket26_vert.pqr
- pocket27_atm.cif
- pocket27_vert.pqr
- pocket28_atm.cif
- pocket28_vert.pqr
- pocket29_atm.cif
- pocket29_vert.pqr
- pocket2_atm.cif
- pocket2_vert.pqr
- pocket30_atm.cif
- pocket30_vert.pqr
- pocket31_atm.cif
- pocket31_vert.pqr
- pocket32_atm.cif
- pocket32_vert.pqr
- pocket33_atm.cif
- pocket33_vert.pqr
- pocket34_atm.cif
- pocket34_vert.pqr
- pocket35_atm.cif
- pocket35_vert.pqr
- pocket36_atm.cif
- pocket36_vert.pqr
- pocket37_atm.cif
- pocket37_vert.pqr
- pocket38_atm.cif
- pocket38_vert.pqr
- pocket39_atm.cif
- pocket39_vert.pqr
- pocket3_atm.cif
- pocket3_vert.pqr
- pocket4_atm.cif
- pocket4_vert.pqr
- pocket5_atm.cif
- pocket5_vert.pqr
- pocket6_atm.cif
- pocket6_vert.pqr
- pocket7_atm.cif
- pocket7_vert.pqr
- pocket8_atm.cif
- pocket8_vert.pqr
- pocket9_atm.cif
- pocket9_vert.pqr
- 2W83_cif.pml
- 2W83_cif.tcl
- 2W83_cif_PYMOL.sh
- 2W83_cif_VMD.sh
- 2W83_info.txt
- 2W83_out.cif
- 2W83_pockets.pqr
- 1fbl.cif
- 2W83.cif
- pocket10_atm.pdb
- pocket10_vert.pqr
- pocket11_atm.pdb
- pocket11_vert.pqr
- pocket12_atm.pdb
- pocket12_vert.pqr
- pocket13_atm.pdb
- pocket13_vert.pqr
- pocket14_atm.pdb
- pocket14_vert.pqr
- pocket15_atm.pdb
- pocket15_vert.pqr
- pocket16_atm.pdb
- pocket16_vert.pqr
- pocket17_atm.pdb
- pocket17_vert.pqr
- pocket18_atm.pdb
- pocket18_vert.pqr
- pocket19_atm.pdb
- pocket19_vert.pqr
- pocket1_atm.pdb
- pocket1_vert.pqr
- pocket2_atm.pdb
- pocket2_vert.pqr
- pocket3_atm.pdb
- pocket3_vert.pqr
- pocket4_atm.pdb
- pocket4_vert.pqr
- pocket5_atm.pdb
- pocket5_vert.pqr
- pocket6_atm.pdb
- pocket6_vert.pqr
- pocket7_atm.pdb
- pocket7_vert.pqr
- pocket8_atm.pdb
- pocket8_vert.pqr
- pocket9_atm.pdb
- pocket9_vert.pqr
- 1fbl.pml
- 1fbl.tcl
- 1fbl_info.txt
- 1fbl_out.pdb
- 1fbl_pockets.pqr
- 1fbl_PYMOL.sh
- 1fbl_VMD.sh
- pocket10_atm.pdb
- pocket10_vert.pqr
- pocket11_atm.pdb
- pocket11_vert.pqr
- pocket12_atm.pdb
- pocket12_vert.pqr
- pocket13_atm.pdb
- pocket13_vert.pqr
- pocket14_atm.pdb
- pocket14_vert.pqr
- pocket15_atm.pdb
- pocket15_vert.pqr
- pocket16_atm.pdb
- pocket16_vert.pqr
- pocket17_atm.pdb
- pocket17_vert.pqr
- pocket18_atm.pdb
- pocket18_vert.pqr
- pocket19_atm.pdb
- pocket19_vert.pqr
- pocket1_atm.pdb
- pocket1_vert.pqr
- pocket20_atm.pdb
- pocket20_vert.pqr
- pocket21_atm.pdb
- pocket21_vert.pqr
- pocket22_atm.pdb
- pocket22_vert.pqr
- pocket23_atm.pdb
- pocket23_vert.pqr
- pocket24_atm.pdb
- pocket24_vert.pqr
- pocket25_atm.pdb
- pocket25_vert.pqr
- pocket26_atm.pdb
- pocket26_vert.pqr
- pocket27_atm.pdb
- pocket27_vert.pqr
- pocket28_atm.pdb
- pocket28_vert.pqr
- pocket29_atm.pdb
- pocket29_vert.pqr
- pocket2_atm.pdb
- pocket2_vert.pqr
- pocket30_atm.pdb
- pocket30_vert.pqr
- pocket31_atm.pdb
- pocket31_vert.pqr
- pocket32_atm.pdb
- pocket32_vert.pqr
- pocket33_atm.pdb
- pocket33_vert.pqr
- pocket34_atm.pdb
- pocket34_vert.pqr
- pocket35_atm.pdb
- pocket35_vert.pqr
- pocket36_atm.pdb
- pocket36_vert.pqr
- pocket37_atm.pdb
- pocket37_vert.pqr
- pocket38_atm.pdb
- pocket38_vert.pqr
- pocket39_atm.pdb
- pocket39_vert.pqr
- pocket3_atm.pdb
- pocket3_vert.pqr
- pocket4_atm.pdb
- pocket4_vert.pqr
- pocket5_atm.pdb
- pocket5_vert.pqr
- pocket6_atm.pdb
- pocket6_vert.pqr
- pocket7_atm.pdb
- pocket7_vert.pqr
- pocket8_atm.pdb
- pocket8_vert.pqr
- pocket9_atm.pdb
- pocket9_vert.pqr
- 2W83.pml
- 2W83.tcl
- 2W83_info.txt
- 2W83_out.pdb
- 2W83_pockets.pqr
- 2W83_PYMOL.sh
- 2W83_VMD.sh
- 1fbl.pdb
- 2W83.pdb
- pocket_1.json
- pocket_2.json
- pocket_3.json
- pocket_4.json
- pocket_5.json
- pocket_6.json
- alphaspheres.pdb
- pockets.json
- summary.txt
- pocket_1.json
- pocket_10.json
- pocket_11.json
- pocket_12.json
- pocket_13.json
- pocket_14.json
- pocket_15.json
- pocket_2.json
- pocket_3.json
- pocket_4.json
- pocket_5.json
- pocket_6.json
- pocket_7.json
- pocket_8.json
- pocket_9.json
- alphaspheres.pdb
- pockets.json
- summary.txt
- extracted_schema_pockets.json
- readme.md
- 1a26A_predictions.txt
- 1a26A_headeronly_predictions.txt
- 1a26A_unresolved_predictions.txt
- 1a26A_unsorted_predictions.txt
- readme.md
- grid0_score_0.7288.mol2
- grid1_score_0.0664.mol2
- grid2_score_0.3433.mol2
- grid0_score_0.2778.mol2
- grid1_score_0.2404.mol2
- grid2_score_0.2156.mol2
- grid3_score_0.1252.mol2
- grid4_score_0.1299.mol2
- grid5_score_0.1728.mol2
- pocket0_score_0.2778.mol2
- readme.md
- 1a2kC.pdb
- 1e5qA.pdb
- 1MDX.cif
- 1MDX.pdb
- 3CRK.cif
- 3CRK.pdb
- notes.md
- 1fbl.cif
- 1fbl_updated.cif
- 4gqq.cif
- 4gqq_updated.cif
- 4gqq_updated_2025.cif
- 8zz7.cif
- 1o6u.cif
- 1o6u.pdb
- 1uwy.cif
- 1uwy.pdb
- readme.md
- 11as.pdb
- 2nbr.pdb.gz
- 2src.pdb
- readme.txt
- invalid-params.groovy
- test-params.groovy
- testLProtein.groovy
- testMCC.groovy
- .gitattributes
- .gitignore
- breaking-changes.md
- build.gradle
- check-dependencies.sh
- CLAUDE.md
- gradle.properties
- gradlew
- gradlew.bat
- LICENSE.txt
- make-clean.sh
- make-distro.sh
- make.sh
- prank.sh
- README.md
- tests.sh
- unit-tests-parallel.sh
- unit-tests.sh
// repository documentation
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