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Table 2 Overview of the prediction accuracy of the Large Dataset (404 Residues) I. The table shows the RMSD values for each of the residues from the whole dataset and the dataset following removal of non-physical values and of all outliers outside of a range of 3, 5, 7 and 10 pH units. Figures marked in bold indicate significant results (P = 0.05).

From: Benchmarking pKa prediction

 

AMBER COMPLETE

TRUE

WITHIN10

WITHIN7

WITHIN5

WITHIN3

PARSE COMPLETE

TRUE

WITHIN10

WITHIN7

WITHIN5

WITHIN3

ARG

*

*

*

*

*

*

*

*

*

*

*

*

ASP

2.698

1.928

2.513

1.495

1.354

1.273

3.743

1.729

2.251

1.837

1.25

1.106

CYS

*

*

*

*

*

*

*

*

*

*

*

*

GLU

1.885

1.466

1.616

1.62

1.42

1.026

3.175

1.48

1.841

1.681

1.442

1.034

HIS

3.691

2.171

3.016

2.281

2.022

1.417

3.691

2.122

2.997

2.293

1.993

1.465

LYS

1.244

1.263

1.263

1.263

1.122

0.84

25.78

1.162

1.162

1.162

0.991

0.741

TYR

2.739

2.195

2.195

2.195

1.939

1.516

3.163

2.143

2.143

2.143

1.882

1.481

 

MCCE COMPLETE

TRUE

WITHIN10

WITHIN7

WITHIN5

WITHIN3

PROPKA COMPLETE

TRUE

WITHIN10

WITHIN7

WITHIN5

WITHIN3

ARG

*

*

*

*

*

*

*

*

*

*

*

*

ASP

2.024

1.774

2.032

1.79

1.534

1.242

1.301

1.041

1.313

1.301

0.934

0.806

CYS

*

*

*

*

*

*

*

*

*

*

*

*

GLU

1.642

1.255

1.335

1.296

1.259

0.97

1.011

0.851

0.994

0.997

0.849

0.611

HIS

4.503

1.736

2.598

2.104

1.522

1.718

1.865

1.586

1.819

1.631

1.530

1.551

LYS

1.137

1.125

1.125

1.125

1.005

1.129

0.417

0.412

0.412

0.412

2.600

0.423

TYR

5.426

2.643

2.634

2.643

1.668

1.593

2.225

1.551

1.551

1.551

1.001

1.049

  1. Outliers
  2. COMPLETE 0 removed
  3. TRUE 52 removed
  4. WITHIN 10 23 removed
  5. WITHIN 7 27 removed
  6. WITHIN 5 89 removed
  7. WITHIN 3 110 removed