# Perl-RDB 
# PROFboth
# 
# Copyright          : Burkhard Rost, CUBIC NYC / LION Heidelberg
# Email              : rost@columbia.edu
# WWW                : http://cubic.bioc.columbia.edu
# Version            : 2000.02
# 
# --------------------------------------------------------------------------------
# About your protein :
# 
# VALUE    PROT_ID   : query
# VALUE    PROT_NCHN : 1
# VALUE    PROT_NRES : 36
# VALUE    PROT_NALI : 15
# VALUE    PROT_NFAR : 13
# VALUE    PROT_NFAR50-5: 2
# VALUE    PROT_NFAR40-5: 2
# VALUE    PROT_NFAR30-5: 2
# VALUE    PROT_NFAR5-5: 0
# 
# --------------------------------------------------------------------------------
# About the alignment:
# 
# VALUE    ALI_ORIG  : 1ppt.hssp
# 
# --------------------------------------------------------------------------------
# About PROF specifics:
# 
# VALUE    PROF_FPAR : acc=/usr/share/profphd/prof/net/PROFboth_best.par
# VALUE    PROF_NNET : acc=6
# 
# --------------------------------------------------------------------------------
# Notation used      :
# 
# ------------------------------------------------------------------------
# NOTATION HEADER    : PROTEIN
# NOTATION PROT_ID   : identifier of protein [w]
# NOTATION PROT_NRES : number of residues [d]
# NOTATION PROT_NCHN : number of chains (if PDB protein) [d]
# NOTATION PROT_NALI : number of proteins aligned in family [d]
# NOTATION PROT_NFAR : number of distant relatives [d]
# 
# ------------------------------------------------------------------------
# NOTATION HEADER    : ALIGNMENT
# NOTATION HEADER    : ALIGNMENT: input file
# 
# ------------------------------------------------------------------------
# NOTATION HEADER    : INTERNAL
# NOTATION PROF_FPAR : name of parameter file, used [w]
# NOTATION PROF_NNET : number of networks used for prediction [d]
# 
# 
# ------------------------------------------------------------------------
# NOTATION BODY      : PROTEIN
# NOTATION NO        : counting residues [d]
# NOTATION AA        : amino acid one letter code [A-Z!a-z]
# NOTATION CHN       : protein chain [A-Z!a-z]
# 
# ------------------------------------------------------------------------
# NOTATION BODY      : PROF
# 
# ------------------------------------------------------------------------
# NOTATION BODY      : PROFsec
# NOTATION OHEL      : observed secondary structure: H=helix, E=extended (sheet), blank=other (loop)
# NOTATION PHEL      : PROF predicted secondary structure: H=helix, E=extended (sheet), blank=other (loop) PROF = PROF: Profile network prediction HeiDelberg
# NOTATION RI_S      : reliability index for PROFsec prediction (0=lo 9=high) Note: for the brief presentation strong predictions marked by '*'
# NOTATION pH        : 'probability' for assigning helix (1=high, 0=low)
# NOTATION pE        : 'probability' for assigning strand (1=high, 0=low)
# NOTATION pL        : 'probability' for assigning neither helix, nor strand (1=high, 0=low)
# NOTATION OtH       : actual neural network output from PROFsec for helix unit
# NOTATION OtE       : actual neural network output from PROFsec for strand unit
# NOTATION OtL       : actual neural network output from PROFsec for 'no-regular' unit
# 
# ------------------------------------------------------------------------
# NOTATION BODY      : PROFacc
# NOTATION OACC      : observed solvent accessibility (acc) in square Angstroem (taken from DSSP: W Kabsch and C Sander, Biopolymers, 22, 2577-2637, 1983)
# NOTATION PACC      : PROF predicted solvent accessibility (acc) in square Angstroem
# NOTATION OREL      : observed relative solvent accessibility (acc) in 10 states: a value of n (=0-9) corresponds to a relative acc. of between n*n % and (n+1)*(n+1) % (e.g. for n=5: 16-25%).
# NOTATION PREL      : PROF predicted relative solvent accessibility (acc) in 10 states: a value of n (=0-9) corresponds to a relative acc. of between n*n % and (n+1)*(n+1) % (e.g. for n=5: 16-25%).
# NOTATION RI_A      : reliability index for PROFacc prediction (0=low to 9=high) Note: for the brief presentation strong predictions marked by '*'
# NOTATION Obe       : observerd relative solvent accessibility (acc) in 2 states: b = 0-16%, e = 16-100%.
# NOTATION Pbe       : PROF predicted  relative solvent accessibility (acc) in 2 states: b = 0-16%, e = 16-100%.
# NOTATION Obie      : observerd relative solvent accessibility (acc) in 3 states: b = 0-9%, i = 9-36%, e = 36-100%.
# NOTATION Pbie      : PROF predicted relative solvent accessibility (acc) in 3 states: b = 0-9%, i = 9-36%, e = 36-100%.
# NOTATION Ot4       : actual neural network output from PROFsec for unit 0 coding for a relative solvent accessibility of 4*4 - 5*5 percent (16-25%). Note: OtN, with N=0-9 give the same information for the other output units!
# 
# --------------------------------------------------------------------------------
# 
No	AA	OHEL	PHEL	RI_S	OACC	PACC	OREL	PREL	RI_A	pH	pE	pL	Obe	Pbe	Obie	Pbie	OtH	OtE	OtL	Ot0	Ot1	Ot2	Ot3	Ot4	Ot5	Ot6	Ot7	Ot8	Ot9
1	G	L	L	9	0	75	0	90	5	0	0	9	b	e	b	e	0	2	96	3	3	4	6	8	11	14	17	28	33
2	P	L	L	8	0	97	0	72	2	0	0	8	b	e	b	e	3	7	89	4	5	7	11	14	17	19	20	25	25
3	S	L	L	7	0	117	0	90	2	0	0	8	b	e	b	e	4	9	87	3	4	5	9	13	17	22	25	29	30
4	Q	L	L	7	0	83	0	42	3	0	1	8	b	e	b	e	3	11	87	2	3	6	12	18	24	29	27	24	19
5	P	L	L	7	0	97	0	72	1	0	0	8	b	e	b	e	4	8	87	6	8	10	14	16	18	20	20	24	24
6	T	L	L	7	0	127	0	90	4	0	1	8	b	e	b	e	3	13	86	1	2	5	8	11	14	19	23	31	34
7	Y	L	L	7	0	44	0	20	2	0	1	8	b	e	b	i	2	16	87	4	8	14	20	23	22	20	16	14	12
8	P	L	L	7	0	122	0	90	2	0	1	8	b	e	b	e	4	10	86	4	5	7	11	13	16	18	20	24	25
9	G	L	L	7	0	75	0	90	2	0	0	8	b	e	b	e	4	9	87	6	7	10	13	15	16	17	18	24	26
10	D	L	L	7	0	146	0	90	3	0	1	8	b	e	b	e	5	11	84	2	3	5	9	13	16	20	23	29	31
11	D	L	L	8	0	146	0	90	4	0	0	9	b	e	b	e	2	7	91	1	2	3	6	10	15	21	27	34	37
12	A	L	L	8	0	12	0	12	3	0	0	9	b	b	b	i	2	7	92	18	22	26	28	23	17	10	6	5	5
13	P	L	L	9	0	57	0	42	5	0	0	9	b	e	b	e	4	2	94	3	4	7	13	20	28	31	25	14	6
14	V	L	H	7	0	42	0	30	2	8	0	1	b	e	b	i	89	1	10	9	10	12	17	20	22	22	19	15	11
15	E	L	H	8	0	108	0	56	7	9	0	0	b	e	b	e	92	0	5	1	2	3	6	9	15	25	33	32	29
16	D	L	H	8	0	68	0	42	3	9	0	0	b	e	b	e	92	1	6	8	9	12	16	20	24	26	22	15	10
17	L	L	H	8	0	0	0	0	3	9	0	0	b	b	b	b	93	0	4	32	29	24	21	18	13	9	5	2	1
18	I	L	H	8	0	50	0	30	2	9	0	0	b	e	b	i	92	0	5	13	13	14	18	20	22	22	18	12	8
19	R	L	H	8	0	138	0	56	6	9	0	0	b	e	b	e	91	1	5	0	1	3	6	12	22	32	33	23	13
20	F	L	H	8	0	0	0	0	0	9	0	0	b	b	b	b	93	1	4	24	23	22	22	20	16	12	7	4	2
21	Y	L	H	9	0	0	0	0	0	9	0	0	b	b	b	b	95	0	4	23	22	23	23	21	16	12	8	5	3
22	D	L	H	9	0	91	0	56	5	9	0	0	b	e	b	e	94	0	4	3	4	5	8	12	19	27	29	24	19
23	N	L	H	8	0	47	0	30	3	9	0	0	b	e	b	i	93	0	5	9	10	12	17	21	25	25	21	14	9
24	L	L	H	8	0	0	0	0	7	9	0	0	b	b	b	b	93	0	5	38	31	19	14	11	8	5	3	2	1
25	Q	L	H	8	0	59	0	30	5	9	0	0	b	e	b	i	93	0	5	6	8	12	19	25	29	28	21	12	6
26	Q	L	H	7	0	83	0	42	4	8	0	0	b	e	b	e	88	1	9	5	5	7	10	15	22	27	26	18	12
27	Y	L	H	8	0	0	0	0	0	9	0	0	b	b	b	b	90	1	7	26	25	24	23	20	15	10	6	3	1
28	L	L	H	7	0	0	0	0	2	8	0	0	b	b	b	b	86	5	7	29	26	23	21	18	15	11	8	5	4
29	N	L	H	7	0	87	0	56	4	8	0	1	b	e	b	e	84	5	10	5	6	7	10	14	20	28	30	23	17
30	V	L	H	6	0	42	0	30	2	7	0	1	b	e	b	i	78	9	14	14	15	17	21	23	24	22	18	12	9
31	V	L	H	3	0	0	0	0	3	5	1	2	b	b	b	b	60	11	30	30	26	21	20	18	14	11	8	7	6
32	T	L	H	0	0	59	0	42	1	4	1	4	b	e	b	e	45	12	40	13	13	13	16	19	21	22	21	19	16
33	R	L	L	2	0	138	0	56	2	3	1	5	b	e	b	e	32	13	52	5	6	8	12	16	20	23	24	23	21
34	H	L	L	2	0	77	0	42	0	2	2	4	b	e	b	e	26	26	51	7	8	11	15	19	21	23	23	22	20
35	R	L	L	3	0	104	0	42	2	1	2	5	b	e	b	e	18	25	63	4	5	8	13	18	22	25	23	20	17
36	Y	L	L	8	0	199	0	90	3	0	0	9	b	e	b	e	2	5	92	5	6	8	11	14	14	15	15	22	26
