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Frontiers Section Editor (Bioinformatics and Biophysics) for the Current Drug Targets ISSN: 1873-5592

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Section Editor (Bioinformatics in Drug Design and Discovery) for the Current Medicinal Chemistry ISSN: 1875-533X

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Member of the Editorial Board for the PeerJ ISSN: 2167-8359

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Member of the Editorial Board for the Current Bioinformatics ISSN: 2212-392X (Online) ISSN: 1574-8936 (Print)

 

Research

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Protein-Ligand Interacions

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Molecular Docking

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Bioinspired Computing

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Computational Systems Biology

 

Recent Publications

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Volkart PA et al. Cyclin-Dependent Kinase 2 in Cellular Senescence and Cancer. A Structural and Functional Review. Curr Drug Targets. 2018.

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de Ávila MB et al.. Structural Basis for Inhibition of Enoyl-[Acyl Carrier Protein] Reductase (InhA) from Mycobacterium tuberculosis. Curr Med Chem 2018.

Receptor-Ligand Systems Database

Here we have searchable datasets with biological systems to be used to develop targeted-scoring functions. We used the program SAnDReS (Xavier et al., 2016) to generate the datasets and the program AutoDockTools (Morris et al., 2009)  to create PDBQT files.  

Biological systems

Systems ZIP
AutoDock Dataset

 

1DWB,1ETR,1ETS,1ETT,1FKF,1HVJ,1HVR,1MBI,1RBP,1TLP,

1TMN,1ULB,2CPP,2ER6,2GBP,2IFB,2MCP,2XIS,2YPI,3CPA,

3PTB,4CNA,4DFR,4HMG,4HVP,4TLN,4TMN,5HVP,5TMN,6CPA

 

In this dataset we have 30 structures used to obtain the regression weights for the AutoDock 3 scoring function (Morris et al., 1998).

These structures might be employed as benchmark to test the predictive performance of new scoring functions. We generated PDBQT files using AutoDockTool4 (Morris et al., 2009).

Keywords

Automated docking; binding affinity; drug design; scoring function; AutoDock

References

Morris GM, Goodsell DS, Halliday RS, Huey R, Hart WE, Belew RK, Olson AJ. Automated Docking Using a Lamarckian Genetic Algorithm and an Empirical Binding Free Energy Funtion. J Comput Chem. 1998; 19(14):1639-1662.

Morris GM, Huey R, Lindstrom W, Sanner MF, Belew RK, Goodsell DS, Olson AJ. AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility. J Comput Chem. 2009; 30(16):2785-2791.

Beta Galactosidase with Inhibition Constant (Ki) Data

 

1JYX,1JZ7,1PX4,1UWT,1UWU,2CEQ,2CER,3DYO,3I3B,3I3D,

3MUZ,3MV0,3T08,3T09,3T0B,3T0D,3T2P,3T2Q,3VD4,3VD7,

3VD9,3VDB,3VDC,3WEZ

 

In this dataset we have 24 crystallographic structures of beta galactosidase (EC 3.2.1.23) with inhibition constant (Ki) data.

We used these structures to generate targeted-scoring functions for beta galactosidase. We generated PDBQT files using AutoDockTool4 (Morris et al., 2009).

Keywords

beta galactosidase; binding affinity; drug design; scoring function; inhibition constant

Reference

Morris GM, Huey R, Lindstrom W, Sanner MF, Belew RK, Goodsell DS, Olson AJ. AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility. J Comput Chem. 2009; 30(16):2785-2791.

Cyclin-Dependent Kinase with Half Maximal Inhibitory Concentration (IC50) Data

 

1DI8,1DM2,1E9H,1FVT,1FVV,1GII,1H00,1H07,1H0W,1H1Q,

1H1R,1JVP,1KE5,1KE6,1KE7,1KE8,1KE9,1OGU,1OI9,1OIQ,

1OIR,1OIT,1OIU,1OIY,1P2A,1PXI,1PXL,1PYE,1R78,1UNG,

1UNH,1URW,1V1K,1VYW,1VYZ,1W0X,1WCC,1Y8Y,1Y91,1YKR,

2A0C,2B52,2B53,2B54,2BHE,2BKZ,2BPM,2BTS,2C4G,2C5N,

2C5O,2C5Y,2C68,2C69,2C6I,2C6K,2C6L,2C6M,2DS1,2DUV,

2G9X,2I40,2IW6,2IW9,2R3F,2R3G,2R3H,2R3I,2R3J,2R3K,

2R3L,2R3M,2R3N,2R3O,2R3P,2R64,2UUE,2UZB,2UZD,2UZE,

2UZL,2UZN,2UZO,2VTA,2VTH,2VTI,2VTJ,2VTL,2VTM,2VTN,

2VTO,2VTP,2VTQ,2VTR,2VTS,2VTT,2VU3,2VV9,2W05,2W06,

2W17,2W1H,2WEV,2WIH,2WXV,3BHT,3BHU,3BHV,3BLR,3DDP,

3DDQ,3DOG,3EZR,3EZV,3FZ1,3IG7,3IGG,3LE6,3LFN,3LFS,

3LQ5,3NS9,3O0G,3PJ8,3PXZ,3PY0,3QQK,3QTR,3QTS,3QTU,

3QTW,3QTX,3QTZ,3QU0,3R8U,3R8V,3R8Z,3R9D,3R9H,3R9N,

3R9O,3RAH,3RAL,3RGF,3RJC,3RK5,3RK7,3RK9,3RKB,3RMF,

3RNI,3RPR,3RPV,3RPY,3RZB,3S00,3S0O,3S1H,3S2P,3TI1,

3TIY,3TIZ,3TN8,3ULI,3UNJ,3UNK,3WBL,4AU8,4AUA,4BGH,

4CFN,4CFW,4ERW,4EZ3,4GCJ,4LYN

 

In this dataset we have 176 crystallographic structures of cyclin-dependent kinase (CDK) (EC 2.7.11.22) with half maximal inhibitory concentration (IC50) data.

We used these structures to generate targeted-scoring functions for CDK. We generated PDBQT files using AutoDockTool4 (Morris et al., 2009).

Keywords

Cyclin-dependent kinase; CDK; cell cycle progression; binding affinity; drug design; scoring function; half maximal inhibitory concentration (IC50)

Reference

Morris GM, Huey R, Lindstrom W, Sanner MF, Belew RK, Goodsell DS, Olson AJ. AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility. J Comput Chem. 2009; 30(16):2785-2791.

Cyclin-Dependent Kinase 2 with Half Maximal Inhibitory Concentration (IC50) Data

 

1DI8,1DM2,1E9H,1FVT,1FVV,1GII,1H00,1H07,1H0W,1H1Q,

1H1R,1JVP,1KE5,1KE6,1KE7,1KE8,1KE9,1OGU,1OI9,1OIQ,

1OIR,1OIT,1OIU,1OIY,1P2A,1PXI,1PXL,1PYE,1R78,1URW,

1V1K,1VYW,1VYZ,1W0X,1WCC,1Y8Y,1Y91,1YKR,2A0C,2B52,

2B53,2B54,2BHE,2BKZ,2BPM,2BTS,2C4G,2C5N,2C5O,2C5Y,

2C68,2C69,2C6I,2C6K,2C6L,2C6M,2DS1,2DUV,2G9X,2I40,

2IW6,2IW9,2R3F,2R3G,2R3H,2R3I,2R3J,2R3K,2R3L,2R3M,

2R3N,2R3O,2R3P,2R64,2UUE,2UZB,2UZD,2UZE,2UZL,2UZN,

2UZO,2VTA,2VTH,2VTI,2VTJ,2VTL,2VTM,2VTN,2VTO,2VTP,

2VTQ,2VTR,2VTS,2VTT,2VU3,2VV9,2W05,2W06,2W17,2W1H,

2WEV,2WIH,2WXV,3BHT,3BHU,3BHV,3DDP,3DDQ,3DOG,3EZR,

3EZV,3FZ1,3IG7,3IGG,3LE6,3LFN,3LFS,3NS9,3PJ8,3PXZ,

3PY0,3QQK,3QTR,3QTS,3QTU,3QTW,3QTX,3QTZ,3QU0,3R8U,

3R8V,3R8Z,3R9D,3R9H,3R9N,3R9O,3RAH,3RAL,3RJC,3RK5,

3RK7,3RK9,3RKB,3RMF,3RNI,3RPR,3RPV,3RPY,3RZB,3S00,

3S0O,3S1H,3S2P,3TI1,3TIY,3TIZ,3ULI,3UNJ,3UNK,3WBL,

4BGH,4CFN,4CFW,4ERW,4EZ3,4GCJ,4LYN,

 

In this dataset we have 167 crystallographic structures of cyclin-dependent kinase 2 (CDK2) (EC 2.7.11.22) with half maximal inhibitory concentration (IC50) data.

We used these structures to generate targeted-scoring functions for CDK2. We generated PDBQT files using AutoDockTool4 (Morris et al., 2009).

Keywords

Cyclin-dependent kinase2; CDK2; cell cycle progression; binding affinity; drug design; scoring function; half maximal inhibitory concentration (IC50)

Reference

Morris GM, Huey R, Lindstrom W, Sanner MF, Belew RK, Goodsell DS, Olson AJ. AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility. J Comput Chem. 2009; 30(16):2785-2791.

Cyclin-Dependent Kinase (except CDK2) with Half Maximal Inhibitory Concentration (IC50) Data

 

1UNG,1UNH,3BLR,3LQ5,3O0G,3RGF,3TN8,4AU8,4AUA

 

In this dataset we have 9 crystallographic structures of cyclin-dependent kinase (CDK) (EC 2.7.11.22) with half maximal inhibitory concentration (IC50) data.

This dataset doesn't bring CDK2 structures.

We used these structures to generate targeted-scoring functions for non-CDK2 structure. We generated PDBQT files using AutoDockTool4 (Morris et al., 2009).

Keywords

Cyclin-dependent kinase2; CDK2; cell cycle progression; binding affinity; drug design; scoring function; half maximal inhibitory concentration (IC50)

Reference

Morris GM, Huey R, Lindstrom W, Sanner MF, Belew RK, Goodsell DS, Olson AJ. AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility. J Comput Chem. 2009; 30(16):2785-2791.

Cyclin-Dependent Kinase 2 (without cyclin) with Half Maximal Inhibitory Concentration (IC50) Data

 

1DI8,1DM2,1FVT,1GII,1H00,1H07,1H0W,1JVP,1KE5,1KE6,

1KE7,1KE8,1KE9,1OIQ,1OIR,1OIT,1P2A,1PXI,1PXL,1PYE,

1R78,1URW,1V1K,1VYZ,1W0X,1WCC,1Y8Y,1Y91,1YKR,2A0C,

2B52,2B53,2B54,2BHE,2BTS,2C5Y,2C68,2C69,2C6I,2C6K,

2C6L,2C6M,2DS1,2DUV,2R3F,2R3G,2R3H,2R3I,2R3J,2R3K,

2R3L,2R3M,2R3N,2R3O,2R3P,2R64,2UZN,2UZO,2VTA,2VTH,

2VTI,2VTJ,2VTL,2VTM,2VTN,2VTO,2VTP,2VTQ,2VTR,2VTS,

2VTT,2VU3,2VV9,2W05,2W06,2W17,2W1H,3EZR,3EZV,3FZ1,

3IG7,3IGG,3LE6,3LFN,3LFS,3NS9,3PJ8,3PXZ,3PY0,3QQK,

3QTR,3QTS,3QTU,3QTW,3QTX,3QTZ,3QU0,3R8U,3R8V,3R8Z,

3R9D,3R9H,3R9N,3R9O,3RAH,3RAL,3RJC,3RK5,3RK7,3RK9,

3RKB,3RMF,3RNI,3RPR,3RPV,3RPY,3RZB,3S00,3S0O,3S1H,

3S2P,3TI1,3TIY,3TIZ,3ULI,3UNJ,3UNK,3WBL,4BGH,4ERW,

4EZ3,4GCJ,4LYN

 

In this dataset we have 133 crystallographic structures of cyclin-dependent kinase 2 (CDK2) (without cyclin partner) (EC 2.7.11.22) with half maximal inhibitory concentration (IC50) data.

We used these structures to generate targeted-scoring functions for CDK2. We generated PDBQT files using AutoDockTool4 (Morris et al., 2009).

Keywords

Cyclin-dependent kinase2; CDK2; cell cycle progression; binding affinity; drug design; scoring function; half maximal inhibitory concentration (IC50)

Reference

Morris GM, Huey R, Lindstrom W, Sanner MF, Belew RK, Goodsell DS, Olson AJ. AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility. J Comput Chem. 2009; 30(16):2785-2791.

Cyclin-Dependent Kinase 2 (with cyclin) with Half Maximal Inhibitory Concentration (IC50) Data

 

1E9H,1FVV,1H1Q,1H1R,1OGU,1OI9,1OIU,1OIY,1VYW,2BKZ,

2BPM,2C4G,2C5N,2C5O,2G9X,2I40,2IW6,2IW9,2UUE,2UZB,

2UZD,2UZE,2UZL,2WEV,2WIH,2WXV,3BHT,3BHU,3BHV,3DDP,

3DDQ,3DOG,4CFN,4CFW

 

In this dataset we have 34 crystallographic structures of cyclin-dependent kinase 2 (CDK2) (with cyclin partner) (EC 2.7.11.22) with half maximal inhibitory concentration (IC50) data.

We used these structures to generate targeted-scoring functions for CDK2 in complex with cyclin. We generated PDBQT files using AutoDockTool4 (Morris et al., 2009).

Keywords

Cyclin-dependent kinase2; CDK2; Cyclin; cell cycle progression; binding affinity; drug design; scoring function; half maximal inhibitory concentration (IC50)

Reference

Morris GM, Huey R, Lindstrom W, Sanner MF, Belew RK, Goodsell DS, Olson AJ. AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility. J Comput Chem. 2009; 30(16):2785-2791.

Cyclin-Dependent Kinase 2 with Inhibition Constant (Ki) Data

 

1E1V,1E1X,1H1S,1JSV,1OGU,1PXM,1PXN,1PXO,1PXP,1PYE,

1V1K,2CLX,2EXM,2FVD,2XMY,2XNB,3DDQ,3LFN,3LFS,3MY5,

4ACM,4BCK,4BCM,4BCN,4BCO,4BCP,4BCQ,4EOP,4NJ3,5D1J

 

In this dataset we have 30 crystallographic structures of cyclin-dependent kinase 2 (CDK2) (EC 2.7.11.22) with inhibition constant (Ki) data.

We used these structures to generate targeted-scoring functions for CDK2. We generated PDBQT files using AutoDockTool4 (Morris et al., 2009).

Keywords

Cyclin-dependent kinase 2; CDK2; cell cycle progression; binding affinity; drug design; scoring function; inhibition constant (Ki)

Reference

Morris GM, Huey R, Lindstrom W, Sanner MF, Belew RK, Goodsell DS, Olson AJ. AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility. J Comput Chem. 2009; 30(16):2785-2791.

Cyclin-Dependent Kinase with Inhibition Constant (Ki) Data

 

1E1V,1E1X,1H1S,1JSV,1OGU,1PXM,1PXN,1PXO,1PXP,1PYE,

1V1K,2CLX,2EXM,2FVD,2XMY,2XNB,3BLR,3DDQ,3LFN,3LFS,

3MY5,4ACM,4BCK,4BCM,4BCN,4BCO,4BCP,4BCQ,4EOP,4NJ3,

5D1J

 

In this dataset we have 31 crystallographic structures of cyclin-dependent kinase (CDK) (EC 2.7.11.22) with inhibition constant (Ki) data.

We used these structures to generate targeted-scoring functions for CDK. We generated PDBQT files using AutoDockTool4 (Morris et al., 2009).

Keywords

Cyclin-dependent kinase; CDK; cell cycle progression; binding affinity; drug design; scoring function; inhibition constant (Ki)

Reference

Morris GM, Huey R, Lindstrom W, Sanner MF, Belew RK, Goodsell DS, Olson AJ. AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility. J Comput Chem. 2009; 30(16):2785-2791.

DHQD with Inhibition Constant (Ki) Data

 

1GU1,1H0S,1V1J,2BT4,2C4V,2C4W,2CJF,2XB8,2XD9,2XDA,

2Y71,2Y76,2Y77,3N8K,3N8N,3N86,3N87,4B6Q,4B6R,4B6S,

4CIW,4CIY

 

In this dataset we have 22 crystallographic structures of 3-dehydroquinate dehydratase (DHQD) (EC 4.2.1.10) with inhibition constant (Ki) data.

We used these structures to generate targeted-scoring functions for 3-dehydroquinate dehydratase. We generated PDBQT files using AutoDockTool4 (Morris et al., 2009).

Keywords

3-dehydroquinate dehydratase; DHQD; shikimate pathway; binding affinity; drug design; scoring function; inhibition constant (Ki)

Reference

Morris GM, Huey R, Lindstrom W, Sanner MF, Belew RK, Goodsell DS, Olson AJ. AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility. J Comput Chem. 2009; 30(16):2785-2791.

Enoyl Reductase with Inhibition Constant (Ki) Data

 

1NHG,1NHW,1NNU,1P45,1UH5,1V35,2B35,2B36,2B37,2NTJ,

2PR2,2X23,2Z6J,3AM3,3AM5,3LT0,3LT1,3LT2,3LT4,3NRC,

3ZU4,3ZU5,4CV3,4OHU,4OIM,4OXK,4OXY,4OYR

 

In this dataset we have 28 crystallographic structures of enoyl-[acyl-carrier-protein] reductase (EC 1.3.1.9) with inhibition constant (Ki) data.

We used these structures to generate targeted-scoring functions for enoyl-[acyl-carrier-protein] reductase. We generated PDBQT files using AutoDockTool4 (Morris et al., 2009).

Keywords

Enoyl-[acyl-carrier-protein] reductase; InhA; ENR, binding affinity; drug design; scoring function; inhibition constant (Ki)

Reference

Morris GM, Huey R, Lindstrom W, Sanner MF, Belew RK, Goodsell DS, Olson AJ. AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility. J Comput Chem. 2009; 30(16):2785-2791.

Estrogen Receptor Alpha with Half Maximal Inhibitory Concentration (IC50) Data

 

1A52,1ERE,1ERR,1G50,1GWR,1PCG,1QKT,1QKU,1X7R,1ZKY,

2AYR,2B1V,2BJ4,2FAI,2JF9,2JFA,2OCF,2POG,2Q70,2QA8,

2QE4,2QXS,2R6W,2R6Y,2YJA,3ERD,3ERT,3L03,3UUD,4PP6,

4PXM,4Q50

 

In this dataset we have 32 crystallographic structures of estrogen receptor alpha with half maximal inhibitory concentration (IC50) data.

We used these structures to generate targeted-scoring functions for estrogen receptor alpha. We generated PDBQT files using AutoDockTool4 (Morris et al., 2009).

Keywords

Estrogen receptor alpha; binding affinity; drug design; scoring function; half maximal inhibitory concentration (IC50)

Reference

Morris GM, Huey R, Lindstrom W, Sanner MF, Belew RK, Goodsell DS, Olson AJ. AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility. J Comput Chem. 2009; 30(16):2785-2791.

HIV1-Protease with DeltaG (ΔG) Data

 

1HXB,1K6C,1KZK,1MSM,1MSN,1SDT,1SDU,1SDV,1SGU,2AVO,

2AVS,2AVV,2BPX,2NMY,2NMZ,2NNK,2NNP,3CYX,3D1X,3D1Y,

3EKQ,3EL4,3K4V,3N3I,3NDT,3NDU,3OXC,3PWR,3S56,3TKG,

3TL9

 

In this dataset we have 31 crystallographic structures of HIV1-protease with DeltaG (ΔG) data.

We used these structures to generate targeted-scoring functions for estrogen receptor alpha. We generated PDBQT files using AutoDockTool4 (Morris et al., 2009).

Keywords

HIV1-protease; HIV; Aids; binding affinity; drug design; scoring function; Gibbs free energy

Reference

Morris GM, Huey R, Lindstrom W, Sanner MF, Belew RK, Goodsell DS, Olson AJ. AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility. J Comput Chem. 2009; 30(16):2785-2791.

HIV1-Protease with Inhibition Constant (Ki) Data

 

1A8G,1AJV,1AJX,1BWB,1D4H,1D4I,1D4J,1D4K,1D4L,1D4Y,

1EBW,1EBY,1EBZ,1EC0,1EC1,1EC2,1EC3,1G35,1HIH,1HPO,

1HVH,1HXW,1IIQ,1MTR,1ODW,1ODY,1PRO,1TCX,1VIK,1W5V,

1W5W,1W5X,1W5Y,1XL2,1XL5,1ZJ7,1ZSF,2AID,2AVM,2AVS,

2BPV,2BPY,2BQV,2CEJ,2CEM,2CEN,2HS1,2PYN,2RKG,2UPJ,

2UXZ,2UY0,2WKZ,3AID,3D1Y,3MXD,3MXE,3OXX,3QAA,3UPJ,

4CP7,4FE6,4HE9,4U8W,4UPJ,5UPJ,6UPJ,7UPJ

 

In this dataset we have 68 crystallographic structures of HIV1-protease with inhibition constant (Ki) data.

We used these structures to generate targeted-scoring functions for estrogen receptor alpha. We generated PDBQT files using AutoDockTool4 (Morris et al., 2009).

Keywords

HIV1-protease; HIV; Aids; binding affinity; drug design; scoring function; inhibition constant (Ki)

Reference

Morris GM, Huey R, Lindstrom W, Sanner MF, Belew RK, Goodsell DS, Olson AJ. AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility. J Comput Chem. 2009; 30(16):2785-2791.

High-Resolution Structures with DeltaG (ΔG) Data

 

1A9T,1AJ6,1GFW,1HXD,1KZK,1SG0,1T64,1US0,1YHS,1ZND,

1ZNG,1ZNH,1ZNK,2AVS,2BIK,2BYA,2C3I,2DM5,2FZD,2G1O,

2G1R,2G1S,2I4Q,2IKH,2IKO,2IKU,2IL2,2NMZ,2O3P,2O9A,

2PDK,2PZN,2Q6B,2QX8,2UXI,2UXP,2UXU,3AKM,3CCT,3CCW,

3CCZ,3K8Q,3M4H,4LCE,4QA0,4QOG,4RXD,5A14

 

In this dataset we have 48 high-resolution structures with DeltaG (ΔG) data.

We used these structures to create novel scoring functions. We generated PDBQT files using AutoDockTool4 (Morris et al., 2009).

Keywords

Drug design; scoring function; protein-ligand interactions; Gibbs free energy

Reference

Morris GM, Huey R, Lindstrom W, Sanner MF, Belew RK, Goodsell DS, Olson AJ. AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility. J Comput Chem. 2009; 30(16):2785-2791.

High-Resolution Structures with Inhibition Constant (Ki) Data

 

1BXO,1BXQ,1C1R,1C1T,1C5P,1C5Q,1C5S,1C5U,1E6Q,1E6S,

1F8D,1F8E,1GHZ,1GI1,1GI4,1GI6,1GYX,1GYY,1HYO,1K3Y,

1KZK,1ME3,1ME4,1MPL,1MQI,1O2P,1O2R,1O2W,1O33,1O35,

1O3D,1O3J,1O3L,1O8B,1PZP,1R5Y,1RMZ,1SQN,1T7R,1TBF,

1TF9,1U3W,1X1Z,1XOZ,1Y59,1Y5A,1ZQ5,1ZUA,2AH4,2ARM,

2AVS,2AW1,2BVR,2BVS,2BZZ,2C01,2C6Z,2CF8,2CN0,2CTC,

2F7O,2F7P,2HB3,2HDS,2HDU,2HS1,2HW2,2HXM,2HZY,2JEW,

2JKH,2NMZ,2NNG,2NNO,2QCF,2QD7,2QNN,2QNP,2QO8,2VEZ,

2W9H,2WEJ,2X9G,2X9N,2X9V,2Y5F,2Y5G,2Y5H,2YIV,2YR6,

2Z7K,2ZFF,3A2O,3ACX,3AYI,3B3C,3B3S,3B7E,3B9G,3BLB,

3C31,3CV2,3D4Z,3DD0,3DDF,3DJK,3DK1,3DX1,3DX2,3DX3,

3DX4,3DXH,3EJP,3EJQ,3EJR,3EPW,3EX6,3F17,3F5L,3FED,

3FF3,3FS6,3FX5,3G2Y,3G32,3G34,3G35,3GBA,3GC5,3HS4,

3HVH,3HVI,3HVK,3I6O,3IOF,3IOG,3IOI,3IUT,3K5X,3KKU,

3KL6,3L14,3LJG,3M0I,3M1K,3M2Y,3M8T,3MHW,3MI2,3MOE,

3NU3,3NXO,3NXX,3NYD,3O9I,3OCZ,3OE4,3OKV,3OYQ,3OZS,

3OZT,3P17,3P3C,3P58,3P5A,3PB7,3PB8,3PB9,3PC0,3PO6,

3PRS,3QAA,3QX5,3QYK,3RM0,3RM2,3RMO,3SI4,3SLZ,3ST5,

3SU0,3SU6,3SV2,3SV6,3T42,3T74,3T8F,3TJM,3TLL,3U98,

3V7X,3VBD,3VF5,3VH9,3WJX,3ZCL,4AZ6,4BF1,4BPS,4BS0,

4BT3,4BT5,4CAE,4CQ0,4CYN,4DDS,4DDY,4DE0,4DE1,4DE2,

4DE3,4DFG,4DJP,4DJQ,4DO4,4DRI,4DXH,4DZ7,4E49,4E4A,

4EZ8,4FCF,4FH2,4G95,4GE6,4GQL,4GQR,4GR3,4GR8,4H6Q,

4HE9,4HJS,4HZM,4I71,4I8H,4IGT,4JFI,4JFJ,4JFM,4JQA,

4JXH,4KB9,4KWO,4KWP,4KZ4,4KZ5,4KZ7,4KZB,4LBT,4LBU,

4LEQ,4LM3,4LM4,4NG5,4NUA,4NUC,4NUD,4NUE,4OHA,4P5E,

4Q4S,4Q7W,4Q8T,4Q8Y,4QOG,4R3N,4RUX,4RUY,4TW6,4TW7,

4TX0,4U8W,4UA4,4YW9,4YZU,4ZIP,5BYI,8A3H

 

In this dataset we have 278 high-resolution structures with inhibition constant (Ki) data.

We used these structures to create novel scoring functions. We generated PDBQT files using AutoDockTool4 (Morris et al., 2009).

Keywords

Drug design; scoring function; protein-ligand interactions; inhibition constant (Ki)

Reference

Morris GM, Huey R, Lindstrom W, Sanner MF, Belew RK, Goodsell DS, Olson AJ. AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility. J Comput Chem. 2009; 30(16):2785-2791.

High-Resolution Structures (Oxidoreductases) with Inhibition Constant (Ki) Data

 

1U3W,1ZQ5,1ZUA,2W9H,2X9G,2X9N,2X9V,2YIV,2YR6,3AYI,

3FS6,3M0I,3NXO,3NXX,3T42,4DXH,4G95,4H6Q,4JQA,4NG5,

4QOG,4R3N

 

In this dataset we have 22 high-resolution structures (Oxidoreductases)(EC 1. -. -.-) with inhibition constant (Ki) data.

We used these structures to create novel scoring functions specific for oxydoreductases. We generated PDBQT files using AutoDockTool4 (Morris et al., 2009).

Keywords

Drug design; oxidoreductases; scoring function; protein-ligand interactions; inhibition constant (Ki)

Reference

Morris GM, Huey R, Lindstrom W, Sanner MF, Belew RK, Goodsell DS, Olson AJ. AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility. J Comput Chem. 2009; 30(16):2785-2791.

High-Resolution Structures (Transferases) with Inhibition Constant (Ki) Data

 

1K3Y,1R5Y,2HW2,2VEZ,2Z7K,3ACX,3CV2,3D4Z,3GC5,3HVH,

3HVI,3HVK,3IOI,3OE4,3OZS,3OZT,3PB7,3PB8,3PB9,3TJM,

3TLL,3ZCL,4CAE,4CYN,4EZ8,4KWO,4KWP,4LBU,4LEQ,4NUA,

4Q4S,4Q8T

 

In this dataset we have 32 high-resolution structures (Transferases)(EC 2. -. -.-) with inhibition constant (Ki) data.

We used these structures to create novel scoring functions specific for oxydoreductases. We generated PDBQT files using AutoDockTool4 (Morris et al., 2009).

Keywords

Drug design; transferases; scoring function; protein-ligand interactions; inhibition constant (Ki)

Reference

Morris GM, Huey R, Lindstrom W, Sanner MF, Belew RK, Goodsell DS, Olson AJ. AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility. J Comput Chem. 2009; 30(16):2785-2791.

High-Resolution Structures (Hydrolases) with Inhibition Constant (Ki) Data

 

1BXO,1BXQ,1C1R,1C1T,1C5P,1C5Q,1C5S,1C5U,1E6Q,1E6S,

1F8D,1F8E,1GHZ,1GI1,1GI4,1GI6,1HYO,1KZK,1ME3,1ME4,

1MPL,1O2P,1O2R,1O2W,1O33,1O35,1O3D,1O3J,1O3L,1PZP,

1RMZ,1TBF,1TF9,1XOZ,1Y59,1Y5A,2AH4,2ARM,2AVS,2BVR,

2BVS,2BZZ,2C01,2C6Z,2CF8,2CN0,2CTC,2F7O,2F7P,2HB3,

2HDS,2HDU,2HS1,2HXM,2HZY,2JEW,2JKH,2NMZ,2QD7,2QNN,

2QNP,2Y5F,2Y5G,2Y5H,2ZFF,3A2O,3B3C,3B3S,3B7E,3B9G,

3BLB,3DDF,3DJK,3DK1,3DX1,3DX2,3DX3,3DX4,3DXH,3EJP,

3EJQ,3EJR,3EPW,3F17,3F5L,3FED,3FF3,3FX5,3G2Y,3G32,

3G34,3G35,3I6O,3IOF,3IOG,3IUT,3K5X,3KKU,3KL6,3LJG,

3MHW,3NYD,3P17,3P3C,3PRS,3QX5,3RM0,3RM2,3RMO,3SI4,

3ST5,3SU0,3SU6,3SV2,3T74,3T8F,3U98,3VH9,4AZ6,4BPS,

4BS0,4DDS,4DDY,4DE0,4DE1,4DE2,4DE3,4DFG,4DJP,4DJQ,

4DO4,4FCF,4FH2,4GE6,4GQL,4GQR,4GR3,4GR8,4HE9,4HZM,

4I71,4I8H,4KB9,4KZ4,4KZ5,4KZ7,4KZB,4LBT,4LM3,4LM4,

4P5E,4U8W,4YZU,4ZIP,8A3H

 

In this dataset we have 155 high-resolution structures (Hydrolases)(EC 3. -. -.-) with inhibition constant (Ki) data.

We used these structures to create novel scoring functions specific for oxydoreductases. We generated PDBQT files using AutoDockTool4 (Morris et al., 2009).

Keywords

Drug design; hydrolases; scoring function; protein-ligand interactions; inhibition constant (Ki)

Reference

Morris GM, Huey R, Lindstrom W, Sanner MF, Belew RK, Goodsell DS, Olson AJ. AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility. J Comput Chem. 2009; 30(16):2785-2791.

High-Resolution Structures (Lyases) with Inhibition Constant (Ki) Data

 

1X1Z,2AW1,2NNG,2NNO,2QCF,2QO8,2WEJ,3DD0,3HS4,3L14,

3M1K,3M2Y,3MI2,3MOE,3NU3,3OKV,3OYQ,3P58,3P5A,3PC0,

3PO6,3QYK,3V7X,3VBD,3WJX,4BF1,4BT3,4BT5,4CQ0,4DZ7,

4E49,4E4A,4Q7W,4Q8Y,4RUX,4RUY,4YW9,5BYI

 

In this dataset we have 38 high-resolution structures (Lyases)(EC 4. -. -.-) with inhibition constant (Ki) data.

We used these structures to create novel scoring functions specific for oxydoreductases. We generated PDBQT files using AutoDockTool4 (Morris et al., 2009).

Keywords

Drug design; lyases; scoring function; protein-ligand interactions; inhibition constant (Ki)

Reference

Morris GM, Huey R, Lindstrom W, Sanner MF, Belew RK, Goodsell DS, Olson AJ. AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility. J Comput Chem. 2009; 30(16):2785-2791.

High-Resolution Structures (Isomerases) with Inhibition Constant (Ki) Data

 

1GYX,1GYY,1O8B,4DRI,4JFI,4JFJ,4JFM,4TW6,4TW7,4TX0

 

In this dataset we have 10 high-resolution structures (Isomerases)(EC 5. -. -.-) with inhibition constant (Ki) data.

We used these structures to create novel scoring functions specific for oxydoreductases. We generated PDBQT files using AutoDockTool4 (Morris et al., 2009).

Keywords

Drug design; isomerases; scoring function; protein-ligand interactions; inhibition constant (Ki)

Reference

Morris GM, Huey R, Lindstrom W, Sanner MF, Belew RK, Goodsell DS, Olson AJ. AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility. J Comput Chem. 2009; 30(16):2785-2791.

Kinase with DeltaG (ΔG) Data

 

1A07,1A1B,1A1C,1A1E,1F1W,1FMK,1KC2,1KSW,1NZL,1NZV,

1P13,1SHA,1SHB,1SHD,1SPS,1XWS,1YHS,1YI6,2BIK,2BIL,

2C3I,2H8H,2O3P,3DQW,4LMU,5A14

 

In this dataset we have 26 structures of kinase with DeltaG (ΔG) data.

We used these structures to create novel scoring functions. We generated PDBQT files using AutoDockTool4 (Morris et al., 2009).

Keywords

Drug design; kinase; scoring function; protein-ligand interactions; Gibbs free energy

Reference

Morris GM, Huey R, Lindstrom W, Sanner MF, Belew RK, Goodsell DS, Olson AJ. AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility. J Comput Chem. 2009; 30(16):2785-2791.

Purine Nucleoside Phosphorylase with Inhibition Constant (Ki) Data

 

1A69,1B8N,1B8O,1C3X,1G2O,1K9S,1PF7,1PR1,1PR5,1PWY,

1RT9,1V41,1V48,1VFN,2A0W,2A0X,2A0Y,2I4T,2OC4,2OC9,

2ON6,2P4S,2Q7O,3BGS,3FUC,3K8O,3K8Q,3PHB,4EAR,4EB8,

5ETJ

 

In this dataset we have 31 structures of purine nucleoside phosphorylase with inhibition constant (Ki) data.

We used these structures to create novel scoring functions. We generated PDBQT files using AutoDockTool4 (Morris et al., 2009).

Keywords

Purine nucleoside phosphorylase; PNP; drug design; scoring function; protein-ligand interactions; inhibition constant (Ki)

Reference

Morris GM, Huey R, Lindstrom W, Sanner MF, Belew RK, Goodsell DS, Olson AJ. AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility. J Comput Chem. 2009; 30(16):2785-2791.

Shikimate Pathway Enzymes with Inhibition Constant (Ki) Data

 

4UMA,4UMC,4BQS,1V1J,2C4V,2XB8,2XB9,3N76,3N7A,3N86,

3N87,3N8K,3N8N,4B6O,4B6P,4B6S,4CIW,4CIY,4UMB,1GU1,

1H0R,2BT4,2C4W,4B6R

 

In this dataset we have 24 structures of shikimate pathway enzymes with inhibition constant (Ki) data.

We used these structures to create novel scoring functions. We generated PDBQT files using AutoDockTool4 (Morris et al., 2009).

Keywords

Shikimate pathway; drug design; scoring function; protein-ligand interactions; inhibition constant (Ki)

Reference

Morris GM, Huey R, Lindstrom W, Sanner MF, Belew RK, Goodsell DS, Olson AJ. AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility. J Comput Chem. 2009; 30(16):2785-2791.

U-Plasminogen Activator with Inhibition Constant (Ki) Data

 

1C5X,1C5Y,1EJN,1F5K,1F5L,1F92,1GI7,1GI8,1GI9,1GJ7,

1GJ8,1GJ9,1GJA,1GJC,1GJD,1O3P,1O5A,1O5C,1OWD,1OWH,

1OWK,1SC8,1SQA,1SQO,1SQT,1VJ9,1VJA,1W0Z,1W10,1W11,

1W12,1W13,1W14,2O8W,2R2W,2VNT,3KGP,3KHV,3KID,3MHW,

4FU7,4FU8,4FU9,4FUD,4FUE,4FUF,4FUG,4FUH,4FUJ,4H42

 

In this dataset we have 50 structures of U-plasminogen activator with inhibition constant (Ki) data.

We used these structures to create novel scoring functions. We generated PDBQT files using AutoDockTool4 (Morris et al., 2009).

Keywords

U-plasminogen activator; drug design; scoring function; protein-ligand interactions; inhibition constant (Ki)

Reference

Morris GM, Huey R, Lindstrom W, Sanner MF, Belew RK, Goodsell DS, Olson AJ. AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility. J Comput Chem. 2009; 30(16):2785-2791.

References

Morris GM, Huey R, Lindstrom W, Sanner MF, Belew RK, Goodsell DS et al (2009) AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility. J Comput Chem 30:2785–2791.   PubMed   

Xavier MM, Heck GS, de Avila MB, Levin NM, Pintro VO, Carvalho NL, Azevedo WF Jr. SAnDReS a Computational Tool for Statistical Analysis of Docking Results and Development of Scoring Functions. Comb. Chem. High Throughput Screen. 2016; 19(10): 80112.   PubMed    PDF    GitHub