CREDO
A Package of Four Programs to Add Missing Loops and Domains
to High and Low Resolution Models of Proteins
The package includes programs CREDO, CHADD, GLOOPY and CHARGE.
The programs implement the reconstruction algorithms described by
Petoukhov, M.V., N.A.J. Eady, K.A. Brown, and D.I. Svergun,
Addition of missing loops and domains to protein models using X-ray solution scattering.
Biophys. J. 2002 83(6) 3113-3125.
The users are referred to this paper for details.
Last edited : Thursday, 22 July, 2004
Program CREDO is an extension of the original DR program GASBOR and can be used
when the location of the interface between the known and missing portions of the structure
is unknown. The structure of missing part is represented by ensemble of dummy residues
forming a chain-compatible model. The spatial positions of these residues aim at approximately
corresponding to those of the Ca atoms belonging to the searched part of protein structure.
Thus, this program is best suited for generating low-resolution models of missing domains
without using information about
primary and secondary structures. 
Program CHADD is designed to build chains of dummy residues attached to given point(s)
or residue(s) in the known portion of the structure. In contrast to the previous model,
it is explicitly required that the i-th DR is separated by 0.38 nm from the (i+1)-th.
This program is useful for adding missing loops or terminal portions in high-resolution models
but can also be used for missing domain restoration. The variable part forms a Ca chain
attached to the given point(s) in
the known structure.
Program GLOOPY is similar to the previous one but accounts also for the residue-specific
information containing in the primary structure of the model. This permits to employ further
restrains to generate native-like
folds configuration of the missing loop or domain.
Program CHARGE is aimed at restoring the conformation of the missing loops, especially
if information about the secondary structure of the fragment is available. The algorithm
implemented in the program determines the conformation of short fragments like the missing
loops as interconnected polypeptide chains accounting to secondary structure prediction.
Thus, if a specific portion of the loop is known to form an a–helix or b–sheet,
an idealized secondary structure
template of the appropriate length is inserted.
Note that symmetry
axis (if any) of the initial model should coincide with Z !
The use of the programs is similar to that of GASBOR.
Similarly to GASBOR, the programs read output files of an indirect transformation program GNOM.
Using GNOM one must use high angle portions of the scattering patterns and the programs are able
to fit the data up to the resolution of 5 angstroem,
i.e. momentum transfer s=4*pi sin(theta)/lambda = 1.2 [1/Angstrom].
Most of parameters have the same meaning as in GASBOR.
The number of residues in the whole structure should be equal to that in the protein.
The most important difference from GASBOR is that in all programs excluding CREDO
the ordial sequence of dummy (CHADD) or individual (GLOOPY, CHARGE) residues
in the model is corresponding to the primary sequence of the protein!
After starting the program in the default USER mode you will need to specify
(i) Log-file name <name>,
(ii) project description,
(iii) name of the GNOM output file,
(iv) pdb file containing CA atoms belonging to the known part of protein structure
(v) if known, point symmetry of the particle:
Default group is P1(no symmetry)
Point groups P2, P22, P3, P32, P4, P42, P5, P52, P6, P62
are supported
(vi) the number of residues in the one searched subunit
and enter default answers to all other questions.
Example: artificial fusion protein (187 residues total, 58 in unknown part).
Enter complex.out, mon1.pdb,
P1, 58. 
After starting the program in the default USER mode you will need to specify
(i) Log-file name <name>,
(ii) project description,
(iii) name of the GNOM output file,
(iv) pdb file containing CA atoms belonging to the known part of protein structure
(v) if known, point symmetry of the particle:
Default group is P1(no symmetry)
Point groups P2, P22, P3, P32, P4, P42, P5, P52, P6, P62
are supported
(vi) the number of residues in the one searched subunit/loop.
(vii) ordial numbers (n1 and n2)of residues in the known part to attach the loop
(n2 equals to zero denotes the connection to the terminal corresponding to n1)
and enter default answers to all other questions.
Example: artificial fusion protein (187 residues total, 58 in unknown part).
Enter complex.out; mon1.pdb;
P1; 58; 129; 0.
After starting the program in the default USER mode you will need to specify
(i) Log-file name <name>,
(ii) project description,
(iii) name of the GNOM output file,
(iv) pdb file containing CA atoms belonging to the known part of protein structure
(v) if known, point symmetry of the particle:
Default group is P1(no symmetry)
Point groups P2, P22, P3, P32, P4, P42, P5, P52, P6, P62
are supported
(vi) only if the loop attached to the terminal: the ordial number of corresponding residue
(vii) the number of residues in the one searched loop.
(viii) *.seq, containing one-letter primary sequence of the whole structure
and enter default answers to all other questions.
Example: lysozyme, (129 residues total, 16 residues (40-55) are missed).
Enter lyz.out; lyzcut.pdb; P1;
16; lyz.seq.
After starting the program in the default USER mode you will need to specify
(i) Log-file name <name>,
(ii) project description,
(iii) name of the GNOM output file,
(iv) pdb file containing CA atoms belonging to the known part of protein structure
(v) if known, point symmetry of the particle:
Default group is P1(no symmetry)
Point groups P2, P222, P3, P32, P4, P42, P5, P52, P6, P62
are supported
(vi) ordial number of residue to which tail to be attached
(vii) the number of residues in the one searched loop.
(viii) ordial numbers (n1 and n2) of residues belonging to secondary structure elements
(ix) file *.seq, containing one-letter primary sequence of the whole structure
and enter default answers to all other questions.
Example: lysozyme, (129 residues total, 15 residues at N-terminal are missed residues 5-15 conform a-helix).
Enter lyz.out; lyzcut2.pdb;
P1; 1; 15; 5; 15; lyz.seq.
After any program is finished, you will get the files
<name>.log : log file
<name>.fit : fit to the desmeared and smoothed by GNOM data
<name>.fir : fit to the raw experimental data
<name>.pdb : resulting model in PDB-like format that can be viewed
e.g. with RasMol in the 'spacefill' or ‘backbone’ mode
or with MASSHA (see Atsas package)
CA-atoms: positions of residues
H-atoms: positions of dummy bound waters