BCL::EMFold™ Customer Help
Please return to this page any time you need assistance.
If you do not find the answers you need, please feel free to visit our Contact page and tell us about your issue.
We will post helpful answers to customer inquiries in this section on an ongoing basis in order to provide all of our customers with an effective and a productive experience while using the BCL::Jufo software.
Support for BCL::EMFold Software
Technical support is available throughout the license period.
For scientific or technical questions related to BCL::EMFold, please contact us.
If there is a major bug fix or significant improvements to the application, entities with current licenses will be notified via email and will be given access to the updated software.
Installation Procedures
BCL::EMFold
Copy the appropriate executable into the respective directory on your PC. No additional steps are required for installation. If there are major bug fixes or revisions, an email will be sent out to entities with current licenses so that the newest application can be installed.
Running BCL::EMFold
HOW TO RUN THE APPLICATION
Running BCL::EMFold consists of five main steps.
1.) Create the fasta sequence file for the protein to be studied. You will need the protein sequence in fasta format, and it should be stored in a <.fasta> file. An example is given below. For more information about fasta formats, please visit http://www.ncbi.nlm.nih.gov/blast/fasta.shtml.
2.) Create the pool file. This could be done by hand or using the CreatePool application in the BCL. An example is given below.
3.) Create the body restraint file. This is just like a pdb file containing helix coordinates wherever density rods are observed in the density map. An example is given below.
4.) Create the score file. Simply use the example that is given below.
5.) Run BCL::EMFold. At a command prompt, navigate to the location of your BCL::EMFold executable program. The syntax for running the application looks like the following:
bcl_emfold.exe Fold -nmodels 1 -fastas XXXXA.fasta -pool XXXX.pool -mc_number_iterations 2000 500 -mc_temperature_fraction 0.25 0.05 -prefix ./pdbs/ -body_restraint XXXX.cst_body 500 1.0 1.0 2.0 2.0 -1.0 true -random_seed -message_level Critical -score_weightset weights_assembly.score
BCL::EMFold needs a fasta sequence with the extension <.fasta>, a pool file <.pool>, a constraints file <.cst_body> and a score weightset file <.score> to exist in the same directory.
FLAGS
-nmodels 1
Number of models that a single run creates (1 in that case)
-fastas XXXXA.fasta
The fasta file containing the sequence of the protein.
-pool XXXX.pool
The pool file containing the secondary structure prediction of the protein.
-body_restraint XXXX.cst_body 500 1.0 1.0 2.0 2.0 -1.0 true
The file containing the restraints extracted from the density map, the weight for the occupancy score, and parameters describing the shape of the potential used in the occupancy score.
-score_weightset weights_assembly.score
The score file detailing which scores to use.
-mc_number_iterations 2000 500
The number of total steps (2000) as well as rejected steps in a row (500) before the Monte Carlo search is stopped.
INPUT AND OUTPUT.
BCL::EMFold requires four inputs, a) a fasta file, b) a pool file, c) a restraints file and d) a score file.
a) The fasta file uses one letter codes for protein sequence and looks
like the following:
>1UBI:A|PDBID|CHAIN|SEQUENCE MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG
b) The pool file specifies the predicted secondary structure elements and looks like the following:
bcl::assemble::SSEPool HELIX 1 1 TRP A 4 ALA A 19 16 HELIX 2 2 TRP A 4 LEU A 36 33 HELIX 3 3 LYS A 5 GLU A 18 14 HELIX 4 4 LYS A 5 SER A 33 29 HELIX 5 5 LYS A 7 THR A 22 16 HELIX 6 6 GLU A 20 SER A 33 14 HELIX 7 7 LEU A 21 LEU A 36 16 HELIX 8 8 LEU A 41 TRP A 51 11
c) The restraint file encodes the density rods as helices and looks like the following:
SEQRES 1 A 152 PRO PRO LYS TRP LYS VAL LYS LYS GLN LYS LEU ALA GLU SEQRES 2 A 152 LYS ALA ALA ARG GLU ALA GLU LEU THR ALA LYS LYS ALA SEQRES 3 A 152 GLN ALA ARG GLN ALA LEU SER ILE TYR LEU ASN LEU PRO SEQRES 4 A 152 THR LEU ASP GLU ALA VAL ASN THR LEU LYS PRO TRP TRP SEQRES 5 A 152 PRO GLY LEU PHE ASP GLY ASP THR PRO ARG LEU LEU ALA SEQRES 6 A 152 CYS GLY ILE ARG ASP VAL LEU LEU GLU ASP VAL ALA GLN SEQRES 7 A 152 ARG ASN ILE PRO LEU SER HIS LYS LYS LEU ARG ARG ALA SEQRES 8 A 152 MET LYS ALA ILE THR ARG SER GLU SER TYR LEU CYS ALA SEQRES 9 A 152 MET LYS ALA GLY ALA CYS ARG TYR ASP THR GLU GLY TYR SEQRES 10 A 152 VAL THR GLU HIS ILE SER GLN GLU GLU GLU VAL TYR ALA SEQRES 11 A 152 ALA GLU ARG LEU ASP LYS ILE ARG ARG GLN ASN ARG ILE SEQRES 12 A 152 LYS ALA GLU LEU GLN ALA VAL LEU ASP HELIX 1 1 PRO A 2 SER A 33 1 32 HELIX 5 5 GLY A 67 ARG A 79 1 13 HELIX 6 6 SER A 84 ARG A 97 1 14 HELIX 8 8 SER A 123 ASP A 152 1 30 ATOM 8 N PRO A 2 -34.913 10.141 21.737 1.00 45.99 N ATOM 9 CA PRO A 2 -34.039 10.544 20.632 1.00 46.41 C ATOM 10 C PRO A 2 -32.544 10.299 20.814 1.00 47.36 C ATOM 11 O PRO A 2 -32.078 9.922 21.893 1.00 48.61 O ATOM 12 CB PRO A 2 -34.341 12.030 20.469 1.00 45.93 C ATOM 13 CG PRO A 2 -35.724 12.173 21.015 1.00 46.71 C ATOM 14 CD PRO A 2 -35.693 11.293 22.226 1.00 46.13 C ATOM 15 N LYS A 3 -31.807 10.533 19.730 1.00 47.24 N ....
d) The score file specifies used scores and should look like the following:
bcl::storage::Table nr co rgyr aadist aasmooth aaneigh aavmd aanvec annsasa aaols loop ssepack_fr strand_fr sum rmsd rmsd100 weights 0 0 0 0 0 0 0 0 0 0 265 0 0 0 0 0
Column descriptions and score weights should be in one line respectively!
BCL::Jufo™ Customer Help
Please return to this page any time you need assistance.
If you do not find the answers you need, please feel free to visit our Contact page and tell us about your issue.
We will post helpful answers to customer inquiries in this section on an ongoing basis in order to provide all of our customers with an effective and a productive experience while using the BCL::Jufo software.
Support for BCL::Jufo Software
Technical support is available throughout the license period.
For scientific or technical questions related to BCL::Jufo, please contact us.
If there is a major bug fix or significant improvements to the application, entities with current licenses will be notified via email and will be given access to the updated software.
Installation Procedures
BCL::Jufo
Copy the appropriate BCL::Jufo executable into the respective directory on your PC. You will need to select the executable appropriate for the site-licensed PC operating system:
bcl_jufo_x86.exe [Linux 32-bit executable]
bcl_jufo_x86_64.exe [Linux 64-bit executable]
bcl_jufo_win32.exe [Windows 32-bit executable]
No additional steps are required for installation. If there are major bug fixes or revisions, an email will be sent out to entities with current licenses so that the newest application can be installed.
PsiBlast
In order to run BCL::Jufo, PsiBlast must be installed. Free downloads can be found at http://www.ncbi.nlm.nih.gov/BLAST/download.shtml. Please make sure to download the version for the correct platform and follow all instructions on the screen.
The Basic Local Alignment Search Tool (BLAST) finds regions of local similarity between sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches. BLAST can be used to infer functional and evolutionary relationships between sequences as well as help identify members of gene families. For more information please visit http://blast.ncbi.nlm.nih.gov/.
Running BCL::Jufo
GETTING INSTRUCTIONS OR HELP AT THE COMMAND LINE Helpful information concerning syntax and flags can be obtained by typing the following (simply substitute the file name of your executable):
For more general information about the product, type
HOW TO RUN THE APPLICATION
Running BCL::Jufo consists of three main steps.
1.) Create the fasta sequence file for the protein to be studied. You will need the protein sequence in fasta format for both BCL::Jufo and PsiBlast, and it should be stored in a <.fasta> file. An example is given below. For more information about fasta formats, please visit http://www.ncbi.nlm.nih.gov/blast/fasta.shtml.
2.) Create the PsiBlast position-specific scoring matrix. Run PsiBlast on the fasta sequence to produce a PsiBlast position-specific scoring matrix with extension .ascii. More information on running PsiBlast and adjusting various parameters can be found in the documentation which accompanied the download.
An example run of PsiBlast at the command line could look like the following, where $MyDataBase and $MyBlastProfile are the names of the database used and desired PsiBlast position-specific scoring matrix output file respectively:
3.) Run BCL::Jufo. At a command prompt, navigate to the location of your BCL::Jufo executable program. The syntax for running the application looks like the following:
BCL::Jufo needs a fasta sequence with the extension .fasta and a PsiBlast position-specific scoring matrix file with the extension .ascii to exist in the same directory.
FLAG
-pdbid <prefix>
The application finds fasta and Blast needed to run BCL::Jufo by adding .fasta and .ascii extensions to the <prefix> value provided. The <prefix> value is usually a four letter pdb code such as 1UBI but also can include path /home/user/sequences/1UBI.
-output <output_filename>
By default the output file is created with name <prefix> + .Jufo. The user can specify a different output name by providing it at <output_filename> such as sequence.Jufo or /home/user/sequences/1UBI.Jufo.
INPUT AND OUTPUT.
BCL::Jufo requires two inputs, a fasta file and a corresponding PsiBlast position-specific scoring matrix. The fasta file uses one letter codes for protein sequence and looks like the following:
The PsiBlast position-specific scoring matrix on the other hand looks like following: Last position-specific scoring matrix computed, weighted observed percentages rounded down, information per position, and relative weight of gapless real matches to pseudocounts
A R N D C Q E G H I L K M F P S T W Y V A R N D C Q E G H I L K M F P S T W Y V
1 M -4 -4 -5 -6 -4 -4 -5 -6 -5 4 2 -4 9 -3 -5 -4 -3 -4 -4 -1 0 0 0 0 0 0 0 0 0 24 13 0 63 0 0 0 0 0 0 0 1.72 1.27
2 Q -4 3 1 -1 -6 5 1 -5 -1 -2 -3 3 -1 -2 -4 -1 -2 2 -2 -5 0 15 6 3 0 32 6 0 1 3 2 20 1 1 0 4 2 3 1 0 0.74 1.36
Column 1: Amino acid position
Column 2: One letter code for amino acid type
Column 3: One letter code for the predicted secondary structure; U=Undefined/Loop, S=Strand, H=Helix
Column 4: Undefined/Loop probability (between 0 and 1) for this amino acid
Column 5: Helix probability (between 0 and 1) for this amino acid
Column 6: Strand probability (between 0 and 1) for this amino acid
