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Table 8 Overview of the combination methods (242 Residues). The residue RMSD values are given for all of the 25 combinations consisting of AMBER (A), PARSE (P), MCCE (M), UHBD (U) and PROPKA (P). Figures marked in bold indicate an improvement while the asterisk indicates the best score.

From: Benchmarking pKa prediction

 

A + P

A +M

A + U

A + PR

P + M

ASP

1.556

1.245

1.174

0.837

1.161

GLU

1.301

1.012

0.816

0.676

1.026

HIS

1.331

0.631

0.827

1.000

0.727

LYS

1.281

0.763

0.742

0.646

0.793

TYR

1.899

1.512

1.238

1.028

1.502

 

P + U

P + PR

M + U

M + PR

U + PR

ASP

1.074

0.786

0.910

0.818

0.596

GLU

0.834

0.690

0.660

0.766

0.393

HIS

0.812

0.987

0.566

1.289

0.955

LYS

0.742

0.647

0.713

0.755

0.366

TYR

1.212

1.016

0.974

0.956

0.466

 

A + P + M

A + P + U

A + P + PR

A + M + U

A + M + PR

ASP

1.262

1.242

1.000

1.038

0.837

GLU

1.064

0.973

0.844

0.761

0.714

HIS

0.792

0.954

0.942

0.520

0.839

LYS

0.868

0.913

0.846

0.615

0.590

TYR

1.607

1.446

1.300

1.195

1.097

 

A + U + PR

P + M + U

P + M + PR

M + U + PR

A + P + M + U

ASP

0.773

0.972

0.795

0.681

1.101

GLU

0.539

0.770

0.720

0.529

0.870

HIS

0.771

0.523

0.840

0.897

0.646

LYS

0.518

0.634

0.610

0.597

0.718

TYR

0.869

1.188

1.098

0.782

1.345

 

A + P + M + PR

A + P + U + PR

A + M + U + PR

P + M + U + PR

A + P + M + U + PR

ASP

0.929

0.905

0.779

0.738

0.866

GLU

0.798

0.706

0.588

0.592

0.690

HIS

0.754

0.771

0.690

0.668

0.650

LYS

0.683

0.689

0.525

0.540

0.605

TYR

1.256

1.112

0.959

0.959

1.115