Table 1. Data sets and programs.

Entry	Year	Subject area index label	Description
1 [9]	2007	VS_ML_1	9 activity classes (AC) with increasing structural diversity
2 [9]	2007	VS_ML_2	~1.44 million ZINC compounds used for various virtual screening trials
3 [10]	2007	PROG_1	Molecular similarity histogram filtering
4 [11]	2007	SSR_1	4 SD files with 26 selectivity sets; compounds are annotated with selectivity values for different targets
5 [12]	2008	SSR_2	7 compound selectivity sets containing 267 biogenic amine GPCR antagonists
6 [13]	2008	SSR_3	18 selectivity sets for targets from 4 families
7 [14]	2008	VS_ML_3	25 sets of compounds of increasing complexity and size
8 [15]	2009	VS_ML_4	242 hERG inhibitors
9 [16]	2009	SSR_4	243 ionotropic glutamate ion channel antagonists
10 [17]	2009	PROG_2	Combinatorial analog graph (CAG) program with a sample set consisting of 51 thrombin inhibitors
11 [18]	2009	VS_ML_5	20 AC from the literature and 15 AC from the Molecular Drug Data Report
12 [19]	2010	VS_ML_6	8 AC
13 [20]	2010	PROG_3	Program to generate target selectivity patterns of scaffolds
14 [21]	2010	PROG_4	Multi-target CAGs (see also entry 10) with a sample set containing 33 kinase inhibitors
15 [22]	2010	PROG_5	SARANEA
16 [23]	2010	PROG_6	3D activity landscape program with a sample set containing 248 cathepsin S inhibitors
17 [24]	2010	SAR_1	2 sets of MMPs from BindingDB and ChEMBL
18 [25]	2010	PROG_7	Similarity-potency tree (SPT) program with a sample set containing 874 factor Xa inhibitors
19 [26]	2010	VS_ML_7	17 target-directed compound sets; each set contains a minimum of 10 distinct scaffolds and each scaffold represents 5 compounds
20 [27]	2011	SAR_VZ	10,489 malaria screening hits
21 [28]	2011	SAR_2	458 target-based sets with scaffolds and scaffold hierarchies
22 [29]	2011	SAR_VZ	4 sets of compounds active against 3 or 4 targets
23 [30]	2011	SAR_VZ	881 factor Xa inhibitors
24 [31]	2011	VS_ML_8	50 AC prioritized for similarity searching
25 [32]	2011	VS_ML_9	25 data sets from successful ligand-based virtual screening applications
26 [33]	2011	SAR_3	26 conserved scaffolds in activity profile sequences of length 4
27 [34]	2011	PROG_8	Scaffold distance function
28 [35]	2011	SAR_4	2 sets of compounds with multiple K i or IC 50 measurements against the same targets that differed within 1 order of magnitude
29 [36]	2012	SAR_VZ	4 AC
30 [37]	2012	SAR_5	5 sets of different types of activity cliffs
31 [38]	2012	VS_ML_10	50 AC for scaffold hopping analysis
32 [39]	2012	SAR_6	61 AC consisting of SAR transfer series with regular potency progression
33 [40]	2013	SAR_7	4 activity measurement type-dependent sets of scaffolds
34 [41]	2013	VS_ML_11	2 multi-target compound sets
35 [42]	2013	VS_ML_12	4 multi-target compound sets and 3 multi-mechanism sets
36 [43]	2013	SAR_8	2337 compound series matrices
37 [44]	2013	SAR_9	128 AC containing ≥100 compounds with K i values
38 [45]	2014	SAR_10	30,452 and 45,607 target-based MMS with K i and IC 50 values, respectively
39 [46]	2014	SAR_11	221 drug-unique scaffolds
40 [47]	2014	SAR_12	92,734 MMPs based upon retrosynthetic rules for 435 AC
41 [8]	2014	SAR_13	20,073 and 25,297 MMP-based activity cliffs with K i and IC 50 values, respectively
42 [8]	2014	SAR_14	4 activity measurement type-dependent sets of SAR transfer series with approximate or regular potency progression
43 [8]	2014	SAR_15	169,889 and 240,322 transformation size-restricted MMPs based upon retrosynthetic rules with K i and IC 50 values, respectively

Data entries are organized according to scientific subject areas: structure-activity relationship (SAR) and structure-selectivity relationship (SSR) analysis, SAR visualization (SAR_VZ), virtual screening via similarity searching or machine learning (VS_ML), and programs (PROG). References in the Entry column provide the original publication introducing the program and/or data set. Program entries are described in more detail in Table 2 of our original data article ¹. The new compound data sets 31–43 are discussed in the text. Programs and data sets reported herein have been separately deposited in ZENODO for access and download.