EnvFold is a program for search of homology of sequence with DB PDB sequences.

The Fold program searches for the homologues of a processed sequence in the PDB with use of files specially prepared by envbc program, which contain the following fields for each position:
• Amino acid in three letter code
• Area Buried
• Fraction Polar
• Secondary structure assignment

Keys for program run string:
1. Name of a file containing the processed sequence in FASTA format with size of not more than 1000 nucleotides and with strings' length of not more than 80 positions. As such a file, the specially prepared file of alignments of the processed sequence with other ones that does not contain gaps in test sequence can be used (see example for SSPAL program).
2. Name of a file containing the secondary structure of the processed sequence (see description for SSPAL or PSSF output files).
3. Name of the output file containing the results of comparison in the following format:

   
   	T0234  165
       
   	1VL7A Sc_b= 34906.0 Sc_lg= 1393.7 l2= 135
   	1G79A Sc_b=  3770.0 Sc_lg=  139.5 l2= 199
   	1G76A Sc_b=  3755.0 Sc_lg=  138.9 l2= 199
   

   The first string contains the name and length of tested sequence, the following ones - names of PDB sequences, common and relevant homology scores, and lengths of PDB sequences.
4. Aligning mode: 'f' - Global, 'l' - Local.
5. Name of the output file containing the alignment of the processed sequence with most homologous PDB sequence.
6. Name of a file containing the PDB sequence.
7. The path to DB files. The last symbol - '/'.