Table 2 The data sets where the initial structures and affinities were based on.

From: The maximal and current accuracy of rigorous protein-ligand binding free energy calculations

Data set name

Proteins in data set

No. compounds

FEP+ R-group set16

BACE1, CDK2, JNK1, Mcl1, p38, PTP1B, thrombin, TYK2

199

FEP+ charge-change55

CDK2, DLK, EGFR, EPHX2, IRAK4, ITK, JAK1, JNK1, PTP1B, TYK2

53

OPLS stress set27

BACE1, CHK1, Factor Xa

114

OPLS drug discovery27

A, B, C, D, E

93

Water displacement34

BRD4(1), CHK1, Hsp90, scytalone dehydratase, TAF1(2), thrombin, urokinase

76

FEP+ Fragments57

T4 lysozyme, LigA, Mcl1, MUP-1, JAK-2, hsp90, p38

79

FEP+ macrocycles31

BACE1, CHK1, CK2, MHT1, HSP90

34

FEP+ scaffold-hopping32

BACE1, β-tryptase, CHK1, ERα, Factor Xa,

17

Merck sets56

CDK8, cMet, Eg5, HIF-2α, PFKFB3, SHP-2, SYK, TNKS2

264

GPCRs74,75

A2A, OX2, P2Y1

98

Bayer macrocycles54

Ftase, BRD4

8

Janssen BACE136,76

BACE1

74

MCS docking77

HNE, Renin

49

Miscellaneous

CDK878, Galectin10,79, BTK80, HIV1 protease81, FAAH82

79

 

Total

1237

  1. The proteins and number of ligands are shown. The citations on the data set names show the study where the initial protein and ligand structures were taken from.
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