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Table 1 Comparisons of 30 scoring functions on the CASF-2013 dataset

From: DLIGAND2: an improved knowledge-based energy function for protein–ligand interactions using the distance-scaled, finite, ideal-gas reference state

Function

PCC

RMSE

Description

Year

RF-Score-v2

0.803a

1.54

Machine learning

2014

ID-Score

0.753b

1.63

Descriptor-based and empirical

2013

ΔvinaRF20

0.686c

1.64

Machine learning

2016

AutoDockHybrid

0.64

n.a.

Force fields and machine learning

2016

X-ScoreHM

0.614

1.78

Empirical

2002

ΔSASA

0.606

1.79

Empirical

2014

ChemScore@SYBYL

0.592

1.82

Empirical

1998

ChemPLP@GOLD

0.579

1.84

Empirical

2009

DLIGAND2

0.572

1.85

Knowledge-based

This paper

SMoG2016

0.57d

1.68

Knowledge-based and empirical

2016

PLP1@DS

0.568

1.86

Empirical

2000

AutoDock Vina

0.563e

1.87

Knowledge-based and empirical

2010

G-Score@SYBYL

0.558

1.87

Energy-based

1997

ASP@GOLD

0.556

1.88

Statistical potential

2005

ASE@MOE

0.544

1.89

Empirical

n.a.

ChemScore@GOLD

0.536

1.90

Empirical

2003

DLIGAND

0.526

1.92

Knowledge-based

2005

D-Score@SYBYL

0.526

1.92

Energy-based

2001

Alpha-HB@MOE

0.511

1.94

Empirical

n.a.

LUDI3@DS

0.487

1.97

Empirical

1998

GoldScore@GOLD

0.483

1.97

Energy-based

1997

Affinity-dG@MOE

0.482

1.98

Empirical

n.a.

LigScore2@DS

0.456

2.02

Empirical

2005

GlideScore-SP

0.452

2.03

Energy-based

2006

SMoG2001

0.418

3.39

Knowledge-based

2001

Jain@DS

0.408

2.05

Empirical

2006

PMF@DS

0.364

2.11

Statistical potential

2006

GlideScore-XP

0.277

2.18

Energy-based

2004

London-dG@MOE

0.242

2.19

Empirical

n.a.

PMF@SYBYL

0.221

2.20

Statistical potential

1999

  1. The results for 23 scoring functions were collected from Li [5], the results for RF-score-v2, ID-score, ΔvinaRF20 and SMoG2016 (labeled as a, b, c, d) were collected from Ballester [57], Li [20], Wang [58] and Theau [31], separately, and the results for DLIGAND2, Autodock Vina, and DLIGAND were calculated with default options by ourselves
  2. n.a. not available