GC4 Affinity Prediction

Grand Challenge 4 - Affinity Prediction - CATS

Kendall's τ

Legend
△ - Structure Based; ◯ - Ligand Based; ▢ - Free Energy
Gray Fill - Manual Intervention
Orange Outline - Machine Learning

RMSE_c

Legend
△ - Structure Based; ◯ - Ligand Based; ▢ - Free Energy
Gray Fill - Manual Intervention
Orange Outline - Machine Learning

Pearson's r

Legend
△ - Structure Based; ◯ - Ligand Based; ▢ - Free Energy
Gray Fill - Manual Intervention
Orange Outline - Machine Learning

Spearman's ρ

Legend
△ - Structure Based; ◯ - Ligand Based; ▢ - Free Energy
Gray Fill - Manual Intervention
Orange Outline - Machine Learning

Receipt ID	Submitter Name	PI/Group Name	Number of Ligands	Kendall's τ	Kendall's τ Error	Spearman's ρ	Spearman's ρ Error	Pearson's r	Pearson's r Error	RMSE_c	RMSE_c Error	Method Name	Software	Method Type
d8n3z	Antonia Mey	Julien michel	39	0.09	0.12	0.07	0.17	0.09	0.16	1.16	0.13	alchemical free energies using biosimspace.	biosimspace (feature-freenrgy) https//github.com/michellab/biosimspace/tree/feature-freenrg sire (feature-mapping) https//github.com/michellab/sire/tree/feature-mapping ambertools (18) gromacs (2018) pymbar (3.0.3) freenrgworkflows (1.1) fesetup 1.2.1, sui version 0.8.3 rdkit 18.09.01 protein forcefield amber ff14sb ligand forcefield amber gaff2 water model tip3p	free_energy
53cvi	Junjie Zou	Carlos simmerling/Daniel Raleigh	39	0.61	0.09	0.78	0.11	0.8	0.1	0.5	0.08	am1-bcc/ti	maestro/schrödinger,pmemd.gti,antechamber protein forcefield amber ff14sb ligand forcefield gaff2 water model tip3p	free_energy
szgth	Chuan Tian	Carlos simmerling	39	0.61	0.09	0.78	0.11	0.8	0.1	0.5	0.08	am1-bcc/ti	maestro/schrödinger,pmemd.gti,antechamber protein forcefield amber ff14sb ligand forcefield gaff2 water model tip3p	free_energy
3gjm2	Junjie Zou	Carlos simmerling/Daniel Raleigh	39	0.62	0.09	0.8	0.11	0.82	0.1	0.49	0.08	am1-bcc/ti	maestro/schrödinger,pmemd.gti,antechamber protein forcefield amber ff14sb ligand forcefield gaff2 water model tip3p	free_energy
tkkqh	Chuan Tian	Carlos simmerling	39	0.62	0.09	0.8	0.11	0.82	0.1	0.49	0.08	am1-bcc/ti	maestro/schrödinger,pmemd.gti,antechamber protein forcefield amber ff14sb ligand forcefield gaff2 water model tip3p	free_energy
pwv5e	Anita Chen	Dr. jie zheng at zheng lab	39	0.16	0.11	0.25	0.16	0.23	0.16	0.8	0.11	glide free energy scoring	maestro molecular modeling interface version 11.5.011, mmshare version 4.1.011, release 2018-1, platform linux-x86_64; glide protein forcefield opls3 (default) ligand forcefield opls3 (default) water model gb/sa continuum solvation (default)	structure_based_scoring
dm2x6	Thomas Evangelidis	Pavel hobza	39	-0.13	0.11	-0.19	0.16	-0.17	0.14	13.72	1.55	sqm-cosmo_allwat	homoligalign, sqm/cosmo protein forcefield amber14sb ligand forcefield gaff2 water model tip3p	structure_based_scoring
ka4xp	Thomas Evangelidis	Pavel hobza	39	0.01	0.11	0.03	0.15	0.04	0.15	4.94	0.58	sqm-cosmo_nowat	homoligalign, sqm/cosmo protein forcefield amber14sb ligand forcefield gaff2 water model tip3p	structure_based_scoring
seq8s	Thomas Evangelidis	Pavel hobza	39	-0.01	0.11	-0.01	0.16	0	0.15	7.44	0.99	sqm-cosmo_selwat	homoligalign, sqm/cosmo protein forcefield amber14sb ligand forcefield gaff2 water model tip3p	structure_based_scoring
40ixd	Thomas Evangelidis	Pavel hobza	39	-0.15	0.1	-0.25	0.15	-0.2	0.14	13.25	1.44	sqm-cosmo2_allwat	homoligalign, sqm/cosmo2 protein forcefield amber14sb ligand forcefield gaff2 water model tip3p	structure_based_scoring
4rgx7	Thomas Evangelidis	Pavel hobza	39	-0.09	0.11	-0.15	0.16	-0.1	0.15	5.7	0.73	sqm-cosmo2_nowat	homoligalign, sqm/cosmo2 protein forcefield amber14sb ligand forcefield gaff2 water model tip3p	structure_based_scoring
3h4sv	Thomas Evangelidis	Pavel hobza	39	0.01	0.11	-0.02	0.16	0.03	0.15	7.22	1.01	sqm-cosmo2_selwat	homoligalign, sqm/cosmo2 protein forcefield amber14sb ligand forcefield gaff2 water model tip3p	structure_based_scoring
k4gpy	Thomas Evangelidis	Thomas evangelidis	39	0.3	0.11	0.45	0.15	0.53	0.13	0.54	0.08	deepscaffopt_onlyecfpl_nolossweights	deepscaffopt	ligand_based_scoring
i7kce	Thomas Evangelidis	Thomas evangelidis	39	0.3	0.11	0.44	0.15	0.53	0.14	0.53	0.08	deepscaffopt_onlyfcfpl_lossweights	deepscaffopt	ligand_based_scoring
ffnbb	Thomas Evangelidis	Thomas evangelidis	39	0.33	0.11	0.47	0.14	0.54	0.14	0.53	0.08	deepscaffopt_onlyfcfpl_nolossweights	deepscaffopt	ligand_based_scoring
i3b0v	Antonia Mey	Julien michel	39	0.15	0.12	0.22	0.17	0.25	0.17	1.05	0.14	free energies from docking	flare 2.0 revision 34140 fkcombu rdkit 2018.09.01	ligand_based_scoring
f86i0	Rodrigo Quiroga	Villarreal marcos	39	0.13	0.11	0.19	0.16	0.24	0.17	0.75	0.11	2vinardo-beta	rdkit / mgltools/ smina (modified)	structure_based_scoring
znpsx	Xianjin Xu	Xiaoqin zou	39	-0.01	0.12	-0.02	0.17	-0.16	0.17	0.66	0.09	cnnscore-cats	tensorflow	structure_based_scoring
pfsfn	Xianjin Xu	Xiaoqin zou	39	0.19	0.12	0.26	0.16	0.32	0.16	0.9	0.12	cnnscore-pl	tensorflow	structure_based_scoring
mheam	Duc Nguyen	Guo-wei wei	39	0.28	0.1	0.44	0.14	0.43	0.13	0.57	0.09	deep learning package	ag/dg/tdl-bp/schrodinger	structure_based_scoring
24b03	Duc Nguyen	Guo-wei wei	39	0.48	0.1	0.66	0.13	0.69	0.13	0.48	0.08	deep-learning-package-d	ag/dg/tdl-bp/schrodinger	structure_based_scoring
ar5p6	Kaifu/duc Gao/nguyen	Guo-wei wei	39	0.45	0.1	0.62	0.13	0.67	0.13	0.47	0.08	deep-learning-package-d	ag/dg/tdl-bp/schrodinger	structure_based_scoring
2d76f	Duc Nguyen	Guo-wei wei	39	0.27	0.11	0.38	0.16	0.46	0.15	0.56	0.08	deep-learning-package-dc	ag/dg/tdl-bp/schrodinger	structure_based_scoring
qian4	Kaifu/duc Gao/nguyen	Guo-wei wei	39	0.47	0.1	0.64	0.13	0.6	0.14	0.5	0.08	deep-learning-package-dc	ag/dg/tdl-bp/schrodinger	structure_based_scoring
jxb8i	Menglun/duc Wang/nguyen	Guo-wei wei	39	0.34	0.11	0.46	0.15	0.41	0.15	0.59	0.09	deep-learning-package-mlc	ag/dg/tdl-bp/schrodinger	structure_based_scoring
4pnwo	Menglun/duc Wang/nguyen	Guo-wei wei	39	0.17	0.11	0.28	0.16	0.36	0.16	0.59	0.08	deep-learning-package-mlcl	ag/dg/tdl-bp/schrodinger	structure_based_scoring
wbvqk	Antonia Mey	Julien michel	39	0.01	0.11	0	0.16	0.05	0.15	2	0.27	free energies from docking	flare 2.0 revision 34140 fkcombu rdkit 2018.09.01	structure_based_scoring
txa7r	Xianjin Xu	Xiaoqin zou	39	-0.02	0.12	-0.04	0.17	0.06	0.18	1.16	0.14	itscore2	itscore	structure_based_scoring
vjzfo	Alejandro Varela rial	Gianni de fabritiis	39	-0.07	0.11	-0.12	0.16	-0.19	0.15	0.89	0.12	skeledock kdeep	htmd1.13.8/rdkit2018.03.4/kdeep	structure_based_scoring

Receipt ID

Submitter Name

PI/Group Name

Number of Ligands

Kendall's τ

Kendall's τ Error

Spearman's ρ

Spearman's ρ Error

Pearson's r

Pearson's r Error

RMSE_c

RMSE_c Error

Method Name

Software

Method Type

d8n3z

Antonia Mey

Julien michel

0.09

0.12

0.07

0.17

0.09

0.16

1.16

0.13

alchemical free energies using biosimspace.

biosimspace (feature-freenrgy) https//github.com/michellab/biosimspace/tree/feature-freenrg sire (feature-mapping) https//github.com/michellab/sire/tree/feature-mapping ambertools (18) gromacs (2018) pymbar (3.0.3) freenrgworkflows (1.1) fesetup 1.2.1, sui version 0.8.3 rdkit 18.09.01 protein forcefield amber ff14sb ligand forcefield amber gaff2 water model tip3p

free_energy

53cvi

Junjie Zou

Carlos simmerling/Daniel Raleigh

0.61

0.09

0.78

0.11

0.8

0.1

0.5

0.08

am1-bcc/ti

maestro/schrödinger,pmemd.gti,antechamber protein forcefield amber ff14sb ligand forcefield gaff2 water model tip3p

free_energy

szgth

Chuan Tian

Carlos simmerling

0.61

0.09

0.78

0.11

0.8

0.1

0.5

0.08

am1-bcc/ti

maestro/schrödinger,pmemd.gti,antechamber protein forcefield amber ff14sb ligand forcefield gaff2 water model tip3p

free_energy

3gjm2

Junjie Zou

Carlos simmerling/Daniel Raleigh

0.62

0.09

0.8

0.11

0.82

0.1

0.49

0.08

am1-bcc/ti

maestro/schrödinger,pmemd.gti,antechamber protein forcefield amber ff14sb ligand forcefield gaff2 water model tip3p

free_energy

tkkqh

Chuan Tian

Carlos simmerling

0.62

0.09

0.8

0.11

0.82

0.1

0.49

0.08

am1-bcc/ti

maestro/schrödinger,pmemd.gti,antechamber protein forcefield amber ff14sb ligand forcefield gaff2 water model tip3p

free_energy

pwv5e

Anita Chen

Dr. jie zheng at zheng lab

0.16

0.11

0.25

0.16

0.23

0.16

0.8

0.11

glide free energy scoring

maestro molecular modeling interface version 11.5.011, mmshare version 4.1.011, release 2018-1, platform linux-x86_64; glide protein forcefield opls3 (default) ligand forcefield opls3 (default) water model gb/sa continuum solvation (default)

structure_based_scoring

dm2x6

Thomas Evangelidis

Pavel hobza

-0.13

0.11

-0.19

0.16

-0.17

0.14

13.72

1.55

sqm-cosmo_allwat

homoligalign, sqm/cosmo protein forcefield amber14sb ligand forcefield gaff2 water model tip3p

structure_based_scoring

ka4xp

Thomas Evangelidis

Pavel hobza

0.01

0.11

0.03

0.15

0.04

0.15

4.94

0.58

sqm-cosmo_nowat

homoligalign, sqm/cosmo protein forcefield amber14sb ligand forcefield gaff2 water model tip3p

structure_based_scoring

seq8s

Thomas Evangelidis

Pavel hobza

-0.01

0.11

-0.01

0.16

0.15

7.44

0.99

sqm-cosmo_selwat

homoligalign, sqm/cosmo protein forcefield amber14sb ligand forcefield gaff2 water model tip3p

structure_based_scoring

40ixd

Thomas Evangelidis

Pavel hobza

-0.15

0.1

-0.25

0.15

-0.2

0.14

13.25

1.44

sqm-cosmo2_allwat

homoligalign, sqm/cosmo2 protein forcefield amber14sb ligand forcefield gaff2 water model tip3p

structure_based_scoring

4rgx7

Thomas Evangelidis

Pavel hobza

-0.09

0.11

-0.15

0.16

-0.1

0.15

5.7

0.73

sqm-cosmo2_nowat

homoligalign, sqm/cosmo2 protein forcefield amber14sb ligand forcefield gaff2 water model tip3p

structure_based_scoring

3h4sv

Thomas Evangelidis

Pavel hobza

0.01

0.11

-0.02

0.16

0.03

0.15

7.22

1.01

sqm-cosmo2_selwat

homoligalign, sqm/cosmo2 protein forcefield amber14sb ligand forcefield gaff2 water model tip3p

structure_based_scoring

k4gpy

Thomas Evangelidis

Thomas evangelidis

0.3

0.11

0.45

0.15

0.53

0.13

0.54

0.08

deepscaffopt_onlyecfpl_nolossweights

deepscaffopt

ligand_based_scoring

i7kce

Thomas Evangelidis

Thomas evangelidis

0.3

0.11

0.44

0.15

0.53

0.14

0.53

0.08

deepscaffopt_onlyfcfpl_lossweights

deepscaffopt

ligand_based_scoring

ffnbb

Thomas Evangelidis

Thomas evangelidis

0.33

0.11

0.47

0.14

0.54

0.14

0.53

0.08

deepscaffopt_onlyfcfpl_nolossweights

deepscaffopt

ligand_based_scoring

i3b0v

Antonia Mey

Julien michel

0.15

0.12

0.22

0.17

0.25

0.17

1.05

0.14

free energies from docking

flare 2.0 revision 34140 fkcombu rdkit 2018.09.01

ligand_based_scoring

f86i0

Rodrigo Quiroga

Villarreal marcos

0.13

0.11

0.19

0.16

0.24

0.17

0.75

0.11

2vinardo-beta

rdkit / mgltools/ smina (modified)

structure_based_scoring

znpsx

Xianjin Xu

Xiaoqin zou

-0.01

0.12

-0.02

0.17

-0.16

0.17

0.66

0.09

cnnscore-cats

tensorflow

structure_based_scoring

pfsfn

Xianjin Xu

Xiaoqin zou

0.19

0.12

0.26

0.16

0.32

0.16

0.9

0.12

cnnscore-pl

tensorflow

structure_based_scoring

mheam

Duc Nguyen

Guo-wei wei

0.28

0.1

0.44

0.14

0.43

0.13

0.57

0.09

deep learning package

ag/dg/tdl-bp/schrodinger

structure_based_scoring

24b03

Duc Nguyen

Guo-wei wei

0.48

0.1

0.66

0.13

0.69

0.13

0.48

0.08

deep-learning-package-d

ag/dg/tdl-bp/schrodinger

structure_based_scoring

ar5p6

Kaifu/duc Gao/nguyen

Guo-wei wei

0.45

0.1

0.62

0.13

0.67

0.13

0.47

0.08

deep-learning-package-d

ag/dg/tdl-bp/schrodinger

structure_based_scoring

2d76f

Duc Nguyen

Guo-wei wei

0.27

0.11

0.38

0.16

0.46

0.15

0.56

0.08

deep-learning-package-dc

ag/dg/tdl-bp/schrodinger

structure_based_scoring

qian4

Kaifu/duc Gao/nguyen

Guo-wei wei

0.47

0.1

0.64

0.13

0.6

0.14

0.5

0.08

deep-learning-package-dc

ag/dg/tdl-bp/schrodinger

structure_based_scoring

jxb8i

Menglun/duc Wang/nguyen

Guo-wei wei

0.34

0.11

0.46

0.15

0.41

0.15

0.59

0.09

deep-learning-package-mlc

ag/dg/tdl-bp/schrodinger

structure_based_scoring

4pnwo

Menglun/duc Wang/nguyen

Guo-wei wei

0.17

0.11

0.28

0.16

0.36

0.16

0.59

0.08

deep-learning-package-mlcl

ag/dg/tdl-bp/schrodinger

structure_based_scoring

wbvqk

Antonia Mey

Julien michel

0.01

0.11

0.16

0.05

0.15

0.27

free energies from docking

flare 2.0 revision 34140 fkcombu rdkit 2018.09.01

structure_based_scoring

txa7r

Xianjin Xu

Xiaoqin zou

-0.02

0.12

-0.04

0.17

0.06

0.18

1.16

0.14

itscore2

itscore

structure_based_scoring

vjzfo

Alejandro Varela rial

Gianni de fabritiis

-0.07

0.11

-0.12

0.16

-0.19

0.15

0.89

0.12

skeledock kdeep

htmd1.13.8/rdkit2018.03.4/kdeep

structure_based_scoring

Grand Challenge 4 - Affinity Prediction - CATS

Kendall's τ

RMSEc

Pearson's r

Spearman's ρ

RMSE_c