CREDO manual

Overview

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 C_α 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. Example

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 C_α chain attached to the given point(s) in the known structure. Example

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. Example

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. Example

Note that symmetry axis (if any) of the initial model should coincide with Z!

Examples

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!

CREDO

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. Output

CHADD

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. Output

GLOOPY

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. Output

CHARGE

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. Output

Output

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