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:

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