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Version 2.0
September 2004
 
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EVAcon: prediction formats


All servers are now evaluated in the contact prediction category: comparative modelling, ab initio, threading, meta and contact specialists



Two possible prediction formats are allowed and shown below. Each format has its own records used for all submissions. The REMARK record is optional in both types.

1.- Residue-Residue contact prediction.

PFRMAT RR
TARGET Txxxx
AUTHOR Author's name
REMARK Predictor remarks
METHOD Description of methods used
METHOD Description of methods used
METHOD Description of methods used
SEQRES FLSDVLVAISLEDMYFDSL  	    	# <- SEQRES:
SEQRES VLVAISLEDM			# <- entire target sequence (up to 50 residues per line) 
MODEL 1
CONTC	1  9 F I 0 8 0.70		# explanation of the data in CONTC lines:
CONTC	3 10 S L 0 8 0.70		# 1.- CONTC indicates that this line contains a predicted pair
CONTC	3 12 S E 0 8 0.60		# 2.- sequence position of the first residue in the pair
CONTC	3 14 S M 0 8 0.60		# 3.- sequence position of the second residue in the pair
CONTC	2 15 L Y 0 8 0.50		# 4.- name in one-letter code of the first residue in the pair
CONTC	2 17 L D 0 8 0.50		# 5.- name in one-letter code of the second residue in the pair
CONTC	5 19 V L 0 8 0.50		# 6.- 0 8: the range of Cb-Cb distance predicted for the residue pair
CONTC	6  8 L A 0 8 0.40		# 7.- probability of contact between the Cb atoms of the residues of the pair
CONTC	3  7 S V 0 8 0.40
CONTC	3  8 S A 0 8 0.30	
CONTC	3 15 S Y 0 8 0.30	** IMPORTANT: the list of contacts must appear sorted by the probability value
CONTC	4  6 D L 0 8 0.20	
CONTC	7 14 V M 0 8 0.20	** IMPORTANT: the first residue in the pair must be the one with the lower sequence number
CONTC	9 14 I M 0 8 0.10
END


2.- Atomic coordinates (Tertiary Structure).
The primary format used for comparative modelling, threading, meta and ab initio submission categories.

PFRMAT TS
TARGET Txxxx
AUTHOR Author's name
REMARK Predictor remarks
METHOD Description of methods used
METHOD Description of methods used
METHOD Description of methods used
MODEL 1
ATOM     17  N   VAL A   3       6.308 -12.396  -0.278  1.00  1.70
ATOM     18  CA  VAL A   3       5.190 -12.030  -1.187  1.00  1.70
ATOM     19  C   VAL A   3       3.954 -12.870  -0.844  1.00  1.70
ATOM     20  O   VAL A   3       2.834 -12.471  -1.090  1.00  1.70
ATOM     21  CB  VAL A   3       5.608 -12.274  -2.641  1.00  1.70
ATOM     22  CG1 VAL A   3       5.542 -13.771  -2.959  1.00  1.70
ATOM     23  CG2 VAL A   3       4.664 -11.514  -3.573  1.00  1.70
ATOM     24  N   GLU A   4       4.146 -14.029  -0.272  1.00  1.70
ATOM     25  CA  GLU A   4       2.976 -14.882   0.086  1.00  1.60
ATOM     26  C   GLU A   4       2.153 -14.190   1.175  1.00  1.50
ATOM     27  O   GLU A   4       0.942 -14.141   1.109  1.00  1.40
ATOM     28  CB  GLU A   4       3.465 -16.238   0.597  1.00  1.30
ATOM     29  CG  GLU A   4       2.336 -17.264   0.479  1.00  1.20
ATOM     30  CD  GLU A   4       2.929 -18.671   0.391  1.00  1.10
ATOM     31  OE1 GLU A   4       4.056 -18.846   0.823  1.00  1.00
ATOM     32  OE2 GLU A   4       2.246 -19.551  -0.108  1.00  0.90
END


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