MODPROPEP File Formats¶
MODPROPEP suite of programs require several files formatted in specified manner. Following are the examples of files as required by various programs.
template.list¶
@chain A:PROTEIN_KINASE
@chain C:Peptide
@index=A
1APM.pdb AC
2PHK.pdb AC
1JBP.pdb AC
XXXX.pdb¶
Pair-Potential Matrix¶
# Narendra Kumar, PhD
# Institute of Cancer Sciences
# University of Glasgow
# UK
#
# mailto:narekum@gmail.com
#
# Pair potentials for protein folding: Choice of reference
# states and sensitivity of predicted native states
# to variations in the interaction schemes
#
# MARCOS R. BETANCOURT and D. THIRUMALAI
# https://dx.doi.org/10.1110/ps.8.2.361
#
# Table2
# Scoring Matrix for 20 * 20 pairs of amino acid - amino acid combinations
#
# Cys Phe Leu Trp Val Ile Met His Tyr Ala Gly Pro Asn Thr Ser Arg Gln Asp Lys Glu
# C F L W V I M H Y A G P N T S R Q D K E
C -1.34 -0.53 -0.50 -0.74 -0.51 -0.48 -0.49 -0.19 -0.16 -0.26 -0.09 -0.18 0.28 0.00 0.09 0.32 0.04 0.38 0.35 0.46
F 0.55 -0.82 -0.78 -0.78 -0.67 -0.65 -0.89 -0.19 -0.49 -0.33 0.11 -0.19 0.29 0.00 0.10 0.08 -0.04 0.48 0.11 0.34
L 0.57 0.04 -0.81 -0.70 -0.80 -0.79 -0.68 0.10 -0.44 -0.37 0.14 -0.08 0.36 0.00 0.26 0.09 0.08 0.62 0.16 0.37
W 0.30 -0.00 0.08 -0.74 -0.62 -0.65 -0.94 -0.46 -0.55 -0.40 -0.24 -0.73 -0.09 0.00 0.07 -0.41 -0.11 0.06 -0.28 -0.15
V 0.52 0.10 -0.04 0.11 -0.72 -0.68 -0.47 0.18 -0.27 -0.38 0.04 -0.08 0.39 0.00 0.25 0.17 0.17 0.66 0.16 0.41
I 0.49 0.06 -0.08 0.02 -0.02 -0.60 -0.60 0.19 -0.33 -0.35 0.21 0.05 0.55 0.00 0.35 0.18 0.14 0.54 0.21 0.38
M 0.46 -0.20 0.00 -0.29 0.17 -0.02 -0.56 -0.17 -0.51 -0.23 0.08 -0.16 0.32 0.00 0.32 0.17 -0.01 0.62 0.22 0.24
H 0.64 0.38 0.67 0.08 0.70 0.66 0.28 -0.33 -0.21 0.21 0.23 -0.05 0.10 0.00 0.15 0.04 0.22 -0.22 0.26 -0.11
Y 0.64 0.05 0.10 -0.04 0.22 0.10 -0.10 0.09 -0.27 -0.15 -0.04 -0.40 0.01 0.00 0.07 -0.37 -0.18 -0.07 -0.40 -0.16
A 0.51 0.18 0.14 0.07 0.08 0.05 0.15 0.48 0.08 -0.20 -0.03 0.07 0.24 0.00 0.15 0.27 0.21 0.30 0.20 0.43
G 0.68 0.62 0.65 0.23 0.50 0.61 0.46 0.50 0.20 0.17 -0.20 -0.01 0.10 0.00 0.10 0.14 0.20 0.17 0.12 0.48
P 0.53 0.25 0.36 -0.32 0.31 0.38 0.16 0.15 -0.23 0.20 0.12 -0.07 0.13 0.00 0.17 -0.02 -0.05 0.25 0.12 0.26
N 0.97 0.72 0.78 0.30 0.77 0.87 0.62 0.28 0.17 0.36 0.22 0.18 -0.04 0.00 0.14 0.02 -0.05 -0.12 -0.14 -0.01
T 0.67 0.41 0.41 0.37 0.36 0.30 0.28 0.17 0.14 0.10 0.10 0.04 0.02 0.00 0.00 0.00 0.00 0.00 0.00 0.00
S 0.70 0.44 0.60 0.37 0.54 0.58 0.53 0.25 0.14 0.18 0.13 0.14 0.09 -0.06 0.13 0.12 0.25 0.01 0.10 0.10
R 0.93 0.42 0.43 -0.11 0.46 0.41 0.39 0.14 -0.30 0.30 0.18 -0.05 -0.02 -0.06 -0.01 0.13 -0.12 -0.71 0.50 -0.75
Q 0.64 0.30 0.42 0.19 0.46 0.37 0.20 0.32 -0.11 0.24 0.23 -0.08 -0.10 -0.07 0.11 -0.25 0.14 0.12 -0.20 0.10
D 0.92 0.75 0.89 0.30 0.89 0.70 0.77 -0.19 -0.07 0.26 0.14 0.15 -0.24 -0.14 -0.19 -0.91 -0.08 0.27 -0.69 0.40
K 0.83 0.33 0.38 -0.10 0.33 0.32 0.31 0.23 -0.46 0.11 0.03 -0.03 -0.31 -0.19 -0.15 0.25 -0.46 -1.01 0.38 -0.87
E 0.90 0.53 0.55 -0.01 0.55 0.45 0.30 -0.17 -0.25 0.30 0.36 0.07 -0.21 -0.22 -0.19 -1.04 -0.20 0.04 -1.28 0.45