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Supporting Information High-Throughput Virtual Screening

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Supporting Information High-Throughput Virtual Screening Supporting Information High-Throughput Virtual Screening of Proteins using GRID Molecular Interaction Fields Simone Sciabola, Robert V. Stanton, James E. Mills, Maria M. Flocco, Massimo Baroni, Gabriele Cruciani, Francesca Perruccio and Jonathan S. Mason Contents Table S1 S2-S21 Figure S1 S22 * To whom correspondence should be addressed: Simone Sciabola, Pfizer Research Technology Center, Cambridge, 02139 MA, USA Phone: +1-617-551-3327; Fax: +1-617-551-3117; E-mail: [email protected] S1 Table S1. Description of the 990 proteins used as decoy for the Protein Virtual Screening analysis. PDB ID Protein family Molecule Res. (Å) 1n24 ISOMERASE (+)-BORNYL DIPHOSPHATE SYNTHASE 2.3 1g4h HYDROLASE 1,3,4,6-TETRACHLORO-1,4-CYCLOHEXADIENE HYDROLASE 1.8 1cel HYDROLASE(O-GLYCOSYL) 1,4-BETA-D-GLUCAN CELLOBIOHYDROLASE I 1.8 1vyf TRANSPORT PROTEIN 14 KDA FATTY ACID BINDING PROTEIN 1.85 1o9f PROTEIN-BINDING 14-3-3-LIKE PROTEIN C 2.7 1t1s OXIDOREDUCTASE 1-DEOXY-D-XYLULOSE 5-PHOSPHATE REDUCTOISOMERASE 2.4 1t1r OXIDOREDUCTASE 1-DEOXY-D-XYLULOSE 5-PHOSPHATE REDUCTOISOMERASE 2.3 1q0q OXIDOREDUCTASE 1-DEOXY-D-XYLULOSE 5-PHOSPHATE REDUCTOISOMERASE 1.9 1jcy LYASE 2-DEHYDRO-3-DEOXYPHOSPHOOCTONATE ALDOLASE 1.9 1fww LYASE 2-DEHYDRO-3-DEOXYPHOSPHOOCTONATE ALDOLASE 1.85 1uk7 HYDROLASE 2-HYDROXY-6-OXO-7-METHYLOCTA-2,4-DIENOATE 1.7 1v11 OXIDOREDUCTASE 2-OXOISOVALERATE DEHYDROGENASE ALPHA SUBUNIT 1.95 1x7w OXIDOREDUCTASE 2-OXOISOVALERATE DEHYDROGENASE ALPHA SUBUNIT 1.73 1d0l TRANSFERASE 35KD SOLUBLE LYTIC TRANSGLYCOSYLASE 1.97 2bt4 LYASE 3-DEHYDROQUINATE DEHYDRATASE 1.7 2c4w LYASE 3-DEHYDROQUINATE DEHYDRATASE 1.55 1nr5 LYASE 3-DEHYDROQUINATE SYNTHASE 2.1 2gfx TRANSFERASE 3-OXOACYL-[ACYL-CARRIER-PROTEIN] SYNTHASE 2 2.59 1okz TRANSFERASE 3-PHOSPHOINOSITIDE DEPENDENT PROTEIN KINASE 1 2.51 1q36 TRANSFERASE 3-PHOSPHOSHIKIMATE 1-CARBOXYVINYLTRANSFERASE 1.6 2vf3 TRANSFERASE 4-DIPHOSPHOCYTIDYL-2C-METHYL-D-ERYTHRITOL KINASE 2.2 1rr8 ISOMERASE/DNA DNA 2.6 1rrj ISOMERASE/DNA DNA 2.3 1jwl TRANSCRIPTION/DNA DNA 4 1jft TRANSCRIPTION/DNA DNA 2.5 1t8e TRANSFERASE/ELECTRON TRANSPORT/DNA DNA 2.54 1ryr TRANSFERASE/DNA DNA 2.28 1skm TRANSFERASE/DNA DNA 2.2 1k27 TRANSFERASE 5'-DEOXY-5'-METHYLTHIOADENOSINE PHOSPHORYLASE 1.95 1hxa LYASE 5-EPI-ARISTOLOCHENE SYNTHASE 2.32 1rqr TRANSFERASE 5'-FLUORO-5'-DEOXYADENOSINE SYNTHASE 2.67 2c5b TRANSFERASE 5'-FLUORO-5'-DEOXYADENOSINE SYNTHASE 2.4 2c2w TRANSFERASE 5'-FLUORO-5'-DEOXYADENOSINE SYNTHASE 2 1q8a TRANSFERASE 5-METHYLTETRAHYDROFOLATE S-HOMOCYSTEINE 1.7 1u22 TRANSFERASE 5-METHYLTETRAHYDROPTEROYLTRIGLUTAMATE-- 2.65 2qtg HYDROLASE 5'-METHYLTHIOADENOSINE NUCLEOSIDASE 1.84 1jdt TRANSFERASE 5'-METHYLTHIOADENOSINE PHOSPHORYLASE 2 2c97 TRANSFERASE 6,7-DIMETHYL-8-RIBITYLLUMAZINE SYNTHASE 2 1pgq OXIDOREDUCTASE (CHOH(D)-NADP+(A)) 6-PHOSPHOGLUCONATE DEHYDROGENASE 3.17 1mlz TRANSFERASE 7,8-DIAMINO-PELARGONIC ACID AMINOTRANSFERASE 2.15 2g6w TRANSFERASE 8-AMINO-7-OXONONANOATE SYNTHASE 2.14 1gkd HYDROLASE 92 KDA TYPE IV COLLAGENASE 2.1 1t9c TRANSFERASE ACETOLACTATE SYNTHASE, MITOCHONDRIAL 2.34 1t9b TRANSFERASE ACETOLACTATE SYNTHASE, MITOCHONDRIAL 2.2 1gqs HYDROLASE ACETYLCHOLINESTERASE 3 2jey HYDROLASE ACETYLCHOLINESTERASE 2.7 S2 1j07 HYDROLASE ACETYLCHOLINESTERASE 2.35 1jjb HYDROLASE ACETYLCHOLINESTERASE 2.3 1n5r HYDROLASE ACETYLCHOLINESTERASE 2.25 2vu2 TRANSFERASE ACETYL-COA ACETYLTRANSFERASE 2.65 2vu1 TRANSFERASE ACETYL-COA ACETYLTRANSFERASE 1.51 1pg3 LIGASE ACETYL-COA SYNTHETASE 2.3 3b6c TRANSCRIPTION ACTII PROTEIN 2.3 1n5s OXIDOREDUCTASE ACTVA-ORF6 MONOOXYGENASE 1.7 2hu8 HYDROLASE ACYLAMINO-ACID-RELEASING ENZYME 2.4 2a8h HYDROLASE ADAM 17 2.3 2fv9 HYDROLASE ADAM 17 2.02 2ddf HYDROLASE ADAM 17 1.7 1r55 HYDROLASE ADAM 33 1.58 2jih HYDROLASE ADAMTS-1 2.1 2ada HYDROLASE ADENOSINE DEAMINASE 2.4 2i6a TRANSFERASE ADENOSINE KINASE 2.2 3dhy HYDROLASE ADENOSYLHOMOCYSTEINASE 2 1s07 TRANSFERASE ADENOSYLMETHIONINE-8-AMINO-7-OXONONANOATE 2.42 1u0h LYASE ADENYLATE CYCLASE, TYPE V 2.9 1tl7 LYASE ADENYLATE CYCLASE, TYPE V 2.8 1cjk LYASE/LYASE/SIGNALING PROTEIN ADENYLATE CYCLASE, TYPE V 3 1cib LIGASE ADENYLOSUCCINATE SYNTHETASE 2.3 1p9b LIGASE ADENYLOSUCCINATE SYNTHETASE 2 1ab8 LYASE ADENYLYL CYCLASE 2.2 1v8t HYDROLASE ADP-RIBOSE PYROPHOSPHATASE 2.6 1s9d PROTEIN TRANSPORT/EXCHANGE FACTOR ADP-RIBOSYLATION FACTOR 1 1.8 1niv LECTIN AGGLUTININ 3 1jlx LECTIN AGGLUTININ 2.2 1msa LECTIN (AGGLUTININ) AGGLUTININ 2.29 1ugy SUGAR BINDING PROTEIN AGGLUTININ ALPHA CHAIN 2.4 1m9n TRANSFERASE, HYDROLASE AICAR TRANSFORMYLASE-IMP CYCLOHYDROLASE 1.93 1xql ISOMERASE ALANINE RACEMASE 1.8 1ee2 OXIDOREDUCTASE ALCOHOL DEHYDROGENASE 1.54 1s2c OXIDOREDUCTASE ALDO-KETO REDUCTASE FAMILY 1 MEMBER C3 1.8 1ah0 OXIDOREDUCTASE ALDOSE REDUCTASE 2.3 1eko OXIDOREDUCTASE ALDOSE REDUCTASE 2.2 1t40 OXIDOREDUCTASE ALDOSE REDUCTASE 1.8 1az1 OXIDOREDUCTASE ALDOSE REDUCTASE 1.8 2nvd OXIDOREDUCTASE ALDOSE REDUCTASE 1.55 1x97 OXIDOREDUCTASE ALDOSE REDUCTASE 1.4 1kap ZINC METALLOPROTEASE ALKALINE PROTEASE 1.64 1kn1 ELECTRON TRANSPORT ALLOPHYCOCYANIN 2.2 2bxu HYDROLASE ALPHA THROMBIN 2.8 2bvs HYDROLASE ALPHA THROMBIN 1.4 1bhx SERINE PROTEASE ALPHA THROMBIN 2.3 1kyu ENDOCYTOSIS/EXOCYTOSIS ALPHA-ADAPTIN C 1.8 1otj OXIDOREDUCTASE ALPHA-KETOGLUTARATE-DEPENDENT TAURINE 1.9 1nkh TRANSFERASE ACTIVATOR/TRANSFERASE ALPHA-LACTALBUMIN 2 1qw8 HYDROLASE ALPHA-L-ARABINOFURANOSIDASE 1.8 3d50 HYDROLASE ALPHA-MANNOSIDASE 2 1.79 S3 3ddg HYDROLASE ALPHA-MANNOSIDASE 2 1.74 3d52 HYDROLASE ALPHA-MANNOSIDASE 2 1.6 2f1b HYDROLASE ALPHA-MANNOSIDASE II 1.45 2f1a HYDROLASE ALPHA-MANNOSIDASE II 1.45 2f18 HYDROLASE ALPHA-MANNOSIDASE II 1.3 2f7p HYDROLASE ALPHA-MANNOSIDASE II 1.28 1ktc HYDROLASE ALPHA-N-ACETYLGALACTOSAMINIDASE 2.4 1d3t BLOOD CLOTTING ALPHA-THROMBIN 3 1bmn COMPLEX (SERINE PROTEASE/INHIBITOR) ALPHA-THROMBIN 2.8 1bmm COMPLEX (SERINE PROTEASE/INHIBITOR) ALPHA-THROMBIN 2.6 1lhd COMPLEX (SERINE PROTEASE/INHIBITOR) ALPHA-THROMBIN 2.35 1hdt COMPLEX (SERINE PROTEINASE/INHIBITOR) ALPHA-THROMBIN 2.6 1doj HYDROLASE/HYDROLASE INHIBITOR ALPHA-THROMBIN 1.7 1afe COMPLEX (SERINE PROTEASE/INHIBITOR) ALPHA-THROMBIN (SMALL SUBUNIT) 2 1ae8 COMPLEX (SERINE PROTEASE/INHIBITOR) ALPHA-THROMBIN (SMALL SUBUNIT) 2 1hlt COMPLEX(SERINE PROTEINASE/INHIBITOR) ALPHA-THROMBIN (SMALL SUBUNIT) 3 1abj HYDROLASE(SERINE PROTEINASE) ALPHA-THROMBIN (SMALL SUBUNIT) 2.4 1iht HYDROLASE(SERINE PROTEINASE) ALPHA-THROMBIN (SMALL SUBUNIT) 2.1 1ihs HYDROLASE(SERINE PROTEINASE) ALPHA-THROMBIN (SMALL SUBUNIT) 2 1nrr SERINE PROTEINASE/RECEPTOR ALPHA-THROMBIN (SMALL SUBUNIT) 2.4 1oip TRANSPORT ALPHA-TOCOPHEROL TRANSFER PROTEIN 1.95 1f2p HYDROLASE AMINOPEPTIDASE 1.8 1o69 STRUCTURAL GENOMICS, UNKNOWN FUNCTION AMINOTRANSFERASE 1.84 1jgi TRANSFERASE AMYLOSUCRASE 2 1gs4 ANDROGEN RECEPTOR ANDROGEN RECEPTOR 1.95 1j37 HYDROLASE ANGIOTENSIN CONVERTING ENZYME 2.4 1r4l HYDROLASE ANGIOTENSIN I CONVERTING ENZYME 2 3 1um5 IMMUNE SYSTEM ANTIBODY 21H3 L CHAIN 1.6 1a4k IMMUNOGLOBULIN ANTIBODY FAB 2.4 2z92 IMMUNE SYSTEM ANTI-CIGUATOXIN ANTIBODY 10C9 FAB HEAVY CHAIN 2.3 1vpo IMMUNE SYSTEM ANTI-TESTOSTERONE (LIGHT CHAIN) 2.15 1lk6 BLOOD CLOTTING ANTITHROMBIN-III 2.8 2nva LYASE ARGININE DECARBOXYLASE, A207R PROTEIN 1.8 1ls6 TRANSFERASE ARYL SULFOTRANSFERASE 1.9 1w6f TRANSFERASE ARYLAMINE N-ACETYLTRANSFERASE 2.1 1bkg AMINOTRANSFERASE ASPARTATE AMINOTRANSFERASE 2.6 1asd AMINOTRANSFERASE ASPARTATE AMINOTRANSFERASE 2.2 1ajs AMINOTRANSFERASE ASPARTATE AMINOTRANSFERASE 1.6 1toj TRANSFERASE ASPARTATE AMINOTRANSFERASE 1.9 2aat TRANSFERASE(AMINOTRANSFERASE) ASPARTATE AMINOTRANSFERASE 2.8 1aib TRANSFERASE(AMINOTRANSFERASE) ASPARTATE AMINOTRANSFERASE 2.8 1ams TRANSFERASE(AMINOTRANSFERASE) ASPARTATE AMINOTRANSFERASE 2.7 1art TRANSFERASE(AMINOTRANSFERASE) ASPARTATE AMINOTRANSFERASE 1.8 1tu0 HYDROLASE/HYDROLASE REGULATOR ASPARTATE CARBAMOYLTRANSFERASE CATALYTIC CHAIN 2.55 1r0c TRANSFERASE ASPARTATE CARBAMOYLTRANSFERASE CATALYTIC CHAIN 2.37 1at1 TRANSFERASE (CARBAMOYL-P,ASPARTATE) ASPARTATE CARBAMOYLTRANSFERASE, CATALYTIC CHAIN 2.8 1pqp OXIDOREDUCTASE ASPARTATE-SEMIALDEHYDE DEHYDROGENASE 2.06 1g51 LIGASE ASPARTYL-TRNA SYNTHETASE 2.4 1v47 TRANSFERASE ATP SULFURYLASE 2.49 1lel UNKNOWN FUNCTION AVIDIN 2.9 S4 2fhl SUGAR BINDING PROTEIN AVIDIN-RELATED PROTEIN 4/5 1.05 1a6v IMMUNOGLOBULIN B1-8 FV (LIGHT CHAIN) 1.8 2iq6 HYDROLASE BACTERIAL LEUCYL AMINOPEPTIDASE 2 2vsl LIGASE BACULOVIRAL IAP REPEAT-CONTAINING PROTEIN 4 2.1 1xb1 APOPTOSIS BACULOVIRAL IAP REPEAT-CONTAINING PROTEIN 8 2.7 1xb0 APOPTOSIS BACULOVIRAL IAP REPEAT-CONTAINING PROTEIN 8 2.2 1q6z LYASE BENZOYLFORMATE DECARBOXYLASE 1 1fgx TRANSFERASE BETA 1,4 GALACTOSYLTRANSFERASE 2.4 2vt4 RECEPTOR BETA1 ADRENERGIC RECEPTOR 2.7 3d4s MEMBRANE PROTEIN BETA-2 ADRENERGIC RECEPTOR/T4-LYSOZYME CHIMERA 2.8 1fiw HYDROLASE BETA-ACROSIN HEAVY CHAIN 2.1 1r43 HYDROLASE BETA-ALANINE SYNTHASE 2.8 1lq2 HYDROLASE BETA-D-GLUCAN GLUCOHYDROLASE ISOENZYME EXO1 2.7 1jyv HYDROLASE BETA-GALACTOSIDASE 1.75 1jyw HYDROLASE BETA-GALACTOSIDASE 1.55 1e1f GLYCOSIDE HYDROLASE BETA-GLUCOSIDASE 2.6 1e4n GLYCOSIDE HYDROLASE BETA-GLUCOSIDASE 2.1 2cer HYDROLASE BETA-GLUCOSIDASE A 2.29 1np0 HYDROLASE BETA-HEXOSAMINIDASE BETA CHAIN 2.5 1iem HYDROLASE BETA-LACTAMASE 2.3 1kds HYDROLASE BETA-LACTAMASE 2.15 1kvm HYDROLASE BETA-LACTAMASE 2.06 2pu2 HYDROLASE BETA-LACTAMASE 1.86 1ymx HYDROLASE BETA-LACTAMASE CTX-M-9 1.7 1hlk HYDROLASE BETA-LACTAMASE, TYPE II 2.5 1gx8 LIPOCALIN BETA-LACTOGLOBULIN 2.4 2vo5 HYDROLASE BETA-MANNOSIDASE 2.3 1m01 HYDROLASE BETA-N-ACETYLHEXOSAMINIDASE 2.1 1o03 ISOMERASE BETA-PHOSPHOGLUCOMUTASE 1.4 1o3e HYDROLASE BETA-TRYPSIN 1.64 1o2k HYDROLASE BETA-TRYPSIN 1.63 1o3o HYDROLASE BETA-TRYPSIN 1.55 1o34 HYDROLASE BETA-TRYPSIN 1.5 1o2v HYDROLASE BETA-TRYPSIN 1.5 1o2u HYDROLASE
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