Help - MaxSprout FAQ


What is MaxSprout?

MaxSprout generates protein backbone and side chain co-ordinates for a given C(alpha) trace input. The backbone is assembled from fragments taken from known structures. Side chain conformations are optimized in rotamer space using a rough potential energy function to avoid clashes.
To constructs backbones, a protein structure database is first scanned for fragments that locally fit the chain trace according to distance criteria. A best path algorithm then sifts through these segments and selects an optimal path with minimal mismatch at fragment joints.
Sidechains are added from a library of frequently occurring rotamers using a simple and fast Monte Carlo procedure with simulated annealing.
For details, see L. Holm, C. Sander J.Mol.Biol. 218, 183-194 (1991) and Proteins 14, 213-223 (1992).


What input/output formats does MaxSprout use?

Inputs

MaxSprout expects input coordinates to be in PDB format. Non-standard amino acid names can create problems. Atom records not containing CA atoms are ignored.

Outputs

MaxSprout output coordinates are also in PDB format. Here is an example from an output file (for PDB entry 1anp). The format of the atom coordinate lines conforms to the PDB format in the atom number, atom name, residue name, chain identifier, residue number, and x,y,z coordinate columns. The last column reports the side chain potential energy per residue.

HEADER    HYPOTENSIVE HORMONE                     06-APR-94   1ANP              
REMARK
REMARK
ATOM      1  N   SER     1       1.230 -12.678   2.187       -0.63
ATOM      2  CA  SER     1       1.237 -11.227   2.261       -0.63
ATOM      3  C   SER     1       1.215 -10.745   0.817       -0.63
ATOM      4  O   SER     1       1.187 -11.581  -0.081       -0.63
ATOM      5  CB  SER     1       2.569 -10.821   2.884       -0.63
ATOM      6  OG  SER     1       3.680 -11.195   2.098       -0.63
ATOM      7  N   LEU     2       1.323  -9.467   0.665       -2.25
ATOM      8  CA  LEU     2       1.322  -8.803  -0.628       -2.25
ATOM      9  C   LEU     2       2.451  -7.874  -0.810       -2.25
ATOM     10  O   LEU     2       2.585  -7.111   0.205       -2.25
ATOM     11  CB  LEU     2       0.058  -7.949  -0.652       -2.25
ATOM     12  CG  LEU     2      -1.270  -8.766  -0.566       -2.25
ATOM     13  CD1 LEU     2      -2.522  -7.909  -0.378       -2.25
ATOM     14  CD2 LEU     2      -1.536  -9.621  -1.808       -2.25
ATOM     15  N   ASP     3       3.180  -7.869  -1.935       -2.04
ATOM     16  CA  ASP     3       4.353  -6.787  -1.959       -2.04
ATOM     17  C   ASP     3       4.184  -5.857  -3.088       -2.04
ATOM     18  O   ASP     3       3.199  -5.986  -3.839       -2.04
ATOM     19  CB  ASP     3       5.662  -7.519  -2.241       -2.04
ATOM     20  CG  ASP     3       6.106  -8.408  -1.007       -2.04
ATOM     21  OD1 ASP     3       5.804  -8.037   0.191       -2.04
ATOM     22  OD2 ASP     3       6.776  -9.495  -1.194       -2.04
....
....
ATOM    204  OH  TYR    28       5.817  -3.910   6.025       -3.82

What is the reference list of structures used for backbone construction?

9ins 1lh1 1mbo 1nxb 2ovo 8pti 2ptn 1rei 1rhd 3sga 2sns 4tln 1ppt 4cac 2pab 351c 2act 3app 2aza 3b5c 1bp2 2c2c 5cpa 4cpv 1crn 3cyt 3dfr 1ecd 2fb4 1fdx 4fxn 1hip


What is the library for side chain rotamers?

Residue type Number of rotamers Number of rotatable bonds
ALA 1 0
PRO 1 0
GLY 0 0
CYS 3 1
SER 3 1
THR 3 1
VAL 3 1
ASN 4 2
ASP 3 2
HIS 6 2
ILE 5 2
LEU 6 2
PHE 3 2
TRP 7 2
TYR 3 2
GLN 10 3
GLU 10 3
MET 10 3
LYS 16 3
ARG 10 3

Is there a limit on the size of structures that I can submit to MaxSprout?

The input for MaxSprout is limited to a maximum of 2MB of data.