Difference between revisions of "Tutorial"

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[[Lobo]]
 
[[Lobo]]
 
= Lobo =
 
 
Lobo is a Loop Modeling software that uses pre-calculated look-up tables (LUTs) thta represent loop fragments of various sizes to speed up calculation. Conformations are produced by recursively dividing the segment until the backbone coordinates can be derived analytically.
 
 
 
==How to create a lookup table==
 
The construction of the look-up tables (LUTs) is separated from modeling and has to be executed only once.
 
LoboLUT is a perl script used to create a lookup table of a specific length.
 
 
To create a lookup table for a fragment of an N lenght
 
 
N=2
 
        ./loboLUT -A 1 -B 1 -O aa2.lt --table <destination path>
 
N=3
 
        ./loboLUT -A aa2.lt -B 1 -O aa3.lt --table <destination path>
 
N=4
 
        ./loboLUT -A ../data/aa2.lt -B ../data/aa2.lt -O aa4.lt --table <destination path>
 
 
Is recomended to use as a destination path the data folder inside victor library
 
 
 
 
==How to create a lookup table for a fragment of length n==
 
LoboLUT_all is a perl script used to create all the lookup tables needed. For the modeling of a fragment of lenght N. The algorithm to create the tables, is based on some of the previous created tables. It always considers the half of the length and the half of it until arriving to the 2 or 3 length with are the based tables.
 
To create the Lookup tables for a fragment of 5 you could use the following line
 
./loboLUT_all -c 5
 
this will create the lookup table for 2, 3 and 5, that will be the needed ones. Remember that the Lobo algorithm divides in two the lenght of the fragment thats why the aa2.lt and aa3.lt should also be created.
 
 
Also you can create a lookup table of a specific lenght of
 
N=2
 
        ./loboLUT -A 1 -B 1 -O aa2.lt --table <destination path>
 
N=3
 
        ./loboLUT -A aa2.lt -B 1 -O aa3.lt --table <destination path>
 
N=4
 
        ./loboLUT -A ../data/aa2.lt -B ../data/aa2.lt -O aa4.lt --table <destination path>
 
 
Is recomended to use as a destination path the data folder inside victor library
 
 
 
==How to see the content of a lookup table==
 
the lookUp table is created an a not plain text file, this is why a diferent application is needed to see the content of the table or to plot their content to more complex programs to perform loop modeling. LoopTablePlot is a c++ program that is used to do this, remember that this table file is create by loboLUT_all / loboLUT .
 
To see the lookup table aa5.lt (created previously), in this example s option allows to define the size for the output
 
./LoopTablePlot -i ../data/aa5.lt  -o PLotoutput -s l
 
The output created in the  Plotoutput file contains the list of possible loop angles.
 
 
==How to model a single loop from a given protein==
 
CreateLoopTestset is a c++ program that allos you to model a single loop. It gives the user full flexibility concerning the setting of parameters for ranking and modeling. It finds the starting and ending positions in a PDB file or in many PDB files. Its output could be used to model the loop with LoopModelTest application .
 
To obtain the list of starting and ending points for the files 119L 16PK
 
./createLoopTestset -o listLoops -i ../samples/filelist
 
 
Content in filelist file
 
  ../samples/119L
 
  ../samples/16PK
 
 
the output will be printed and will be like
 
index1 (-s): 7 index2 (-e) 14
 
index1 (-s): 48 index2 (-e) 52
 
index1 (-s): 86 index2 (-e) 89
 
index1 (-s): 99 index2 (-e) 104
 
….........
 
where the -s is the starting position and the -e is the ending position
 
if many pdbs are evaluated, the application will show all the loops for the first pdb listed and then all the loops for the following ones.
 
 
==How to model a loop==
 
LoopModelTest is a c++ program that allows the creation of multiple possible loops and creates a pdb file for each of them .
 
This program needs as input the pdb and the start and end position to set the loop
 
To create the loop from a start position X to an end position Y of the chain A of an specific pdb file
 
./LoopModelTest -i ../samples/ZZZZ.pdb -c A -s X -e Y
 
Using the information obtained with the app CreateLoopTestset 
 
./LoopModelTest -i ../samples/119L.pdb -c A -s 7 -e 14
 
Remember to create the lookup table for a 7 length fragment using    ./loboLUT_all -c 7
 
 
The new pdbs files fill be created in the working path, and in the printed output will be shown the global RMS, end RMS, bond lenght, bond angle and torsion angle
 
 
Printed output
 
Results:      1.35    121    180
 
  0  global RMS=  0.416  ( 0.366) end-RMS=  0.234     1.17    126    175
 
  1  global RMS=  0.356  ( 0.295) end-RMS= 0.0822     1.38    121    -176
 
…....
 
 
==How to obtain a PDB`s torsion angles==
 
Loop2torsion is a c++ program that allows to obtain all the phi and psi angles of all the amino acids in a selected  PDB chain .
 
 
To obtain the angles a PDB file is needed as input and also the chain should be specified
 
 
    ./loop2torsion -i ../samples/2R8O.pdb -c A 
 
The printed output is the list of the angles and the Bfactor of 1.
 
  -72.1    157    1.0
 
    -165    142    1.0
 
    122    -172    1.0
 
    -126    98.1    1.0
 
  …....
 
 
 
 
==How to Clustering data==
 
Using the tor file created in Energy package, ClusterRama, a c++ program clusters the data contained in a Ramachandran distribution file
 
To obtain the clustered data using a cutoff value of 100 
 
    ./ClusterRama -i ../data/tor.par -o outRama -c 100.0
 
 
The output contains the number of the values found the angles values and the corresponding residue
 
12
 
-55.07    -44.61  GLY
 
  76.11    -172.4  GLY
 
-139.2      129  GLY
 
…...
 
 
==How to generate clustered lookup tables==
 
Based in the clustered data the LoopTableTest c++ program generates tables of protein entries for the Lobo algorithm .
 
    ./LoopTableTest -A 1 -B 1 -O output.lt -R outRama -S s
 
To create the Ramachandran input file that contains the clustered data use ClusterRama application.
 
The output created is not a plan text file, use the  LoopTablePlot application
 
The printed output, includes the corresponding angle values (see figure)
 
Min:
 
EP: -4.126 ED: -1.281 N: -0.9997 MP: -1.582 MD: -0.4919 MN: -0.9949
 
EP:  2.6 ED: -1.332 N:    -1 MP: 1.521 MD: 0.4671 MN: -0.8217
 
EP: -3.966 ED: -1.289 N: -0.9836 MP: -1.598 MD: -0.7378 MN: -0.5885
 
Max:
 
EP: 3.437 ED: 1.022 N: 0.6597 MP: 0.9131 MD: 0.5203 MN: 0.8068
 
EP: 4.856 ED: 0.1761 N: 0.6105 MP: 2.486 MD: 0.9987 MN: 0.6888
 
EP: 3.592 ED:  1.27 N: 0.9813 MP: 1.307 MD: 0.8342 MN: 0.7185
 
----------------------------
 
Entry    0 EP: -2.737 ED: -0.01248 N: -0.02252 MP: -0.8014 MD: 0.2146 MN: 0.6219
 
EP: 2.699 ED: -1.172 N: 0.5104 MP: 1.879 MD: 0.921 MN: -0.3856
 
EP: 1.984 ED: -0.6955 N: -0.8596 MP: 1.022 MD: 0.3252 MN: 0.6816
 
 
 
 
==How to generate lookup tables using Ramachandran`s clustered data==
 
Based on a lookup table already created with LoboLUT/loboLUT_all and defining a cutoff value. The ClusterLoopTable program allows you to create the new clustered lookuptable.
 
In this example, a cutoff of 10 is set, and it uses the lookup table for a length of 5.
 
    ./ClusterLoopTable -I ../data/aa5.lt -O ../data/aa5clustered.lt -C 10.0
 
The created output is not a plain text file, to see the content use the LoopTablePlot application
 
 
 
==How to analyze the backbone  geometry of a PDB==
 
BackboneAnalyzer is an application that allows to analyze a PDB file in terms of bond lengths and bond angles .
 
As input it uses the PDB file and the chain to evaluate
 
      ./backboneAnalyzer -i ../samples/2R8O.pdb -c A
 
 
The printed output includes the minimum, maximum, average bonds lengths and angles and the corresponding standard deviations.
 
-------------------------------------------------------
 
      Bond Lengths Bond Angles
 
Num N->CA CA->C' C'->N N->CA CA->C' C'->N
 
-------------------------------------------------------
 
Min: 1.4450  1.5019             1.3206 116.87             104.83 112.55
 
Max: 1.4804             1.5479             4.0701 158.03             118.34 158.56
 
-------------------------------------------------------
 
Avg: 1.4636 1.5272 1.3505 121.58 111.71 116.73
 
SD: 0.0054 0.0067 0.2074   2.45   2.16 1.98
 
  
 
= Energy =
 
= Energy =

Revision as of 09:56, 3 July 2014

Biopool

The Biopool class implementation follows the composite design pattern and for a complete description of the class hierarchy we reccomend to see the [Doxygen documentation]. Whitout going into implementation details a Protein object is just a container for vectors representing chains. Each vector has 2 elements: the Spacer and the Ligand Set. The Spacer is the container for AminoAcid objects whereas the LigandSet is a container for all other melecules and ions, including DNA/RNA chains. Ultimately all molecules, both in the Spacer and in the LigandSet are collections of Atom objects. The main feature in Biopool is that each AminoAcid object in the Spacer is connected to its neighbours by menas of one rotational vector plus one translational vector. This implementation make ease the modification of the protein structure and lot of functions were implemented to modify/perturbate/transformate the residue relative position in an efficent way. Rotation and Translation vectors:


The object representation look like that:

immagine:SchemeProteinclass.jpg


Victor includes different packages: Biopool, Lobo and Energy. Every package is identified by a direcotry, starting with a capital letter, in the main Victor path. Inside each package you will find the Source folder containing the classes code and the APPS directory including useful utilities. In the main Victor path you will find the bin directory containing most important porgrams simply copied from the APPS folders. In the main path you should also find the data folder containing symbolic links to data files used by singular packages.


Parsing a PDB file (PdbLoader)

Biopool uses the PdbLoader class to load PDB files. By default it loads all standard residues and hetero atoms excluding nucleotides and water molecules. When possible it also tries to place hydrogen atoms to every amino acid included in the spacer and determine the secondary structure with the DSSP algorithm. The simplest way to load a PDB into a Protein object is:

  1.   #include <PdbLoader.h>
  2.   #include <Protein.h>
  3.   #include <iostream>
  4.  
  5.   int main( int argc, char* argv[] ) {
  6.  
  7.      string inputFile = "MyPdbFile.pdb";
  8.      ifstream inFile( inputFile.c_str() );
  9.      PdbLoader pl(inFile);    // creates the PdbLoader object
  10.  
  11.      Protein prot;            
  12.      prot.load( pl );         // creates the Protein object
  13.   }

Modify the structure

Add hydrogen atoms

Get the secondary structure

There are 3 different ways in Victor to get the secondary structure. The first (innacurate) is just parsing the HELIX and SHEET fields in the PDB file. The second method is to infer the secondary structure from torsional angles. The last choice is to use an implementation of the DSSP algorithm, consider that you can find little (negligible) differences compared to the original algorithm but it is the most accurate way to calculate the secondary structure.


Lobo

Energy

How to obtain the solvation potential

pdb2solv is an application that creates a file containing all the frequencies of occurrence of residue a with burial r, that are needed to derived the solvation potentials for all the amino acids in the given PDB. A solvation potential for an amino acid residue a is defined as: =RTln(fa(r)/f(r)) where r is the degree of residue burial,fa (r) is the frequency of occurrence of residue a with burial r and f(r) is the frequency of occurrence of all residues with burial r.

The degree of burial for a residue is defined as the number of other Cβ atoms located within 10 Å(non polar)/ 7 Å (polar)of the residue’s Cβ atom.

As input a PDB is needed

The output will depend on the given options Output considering 30 maximum binds possible (by default test.out, use -o option to set a name)

Non polar option


total quantity of residues evaluated | AA type(3L) | frecuencies


Polar option


P | total quantity of residues evaluated | AA type(3L) | frecuencies | Polar frecuency |



To obtain the solv.par file used for pdb2energy, frst, etc applications you need to use the following line all the pdbs in the TOP500H database.

./pdb2solv -i ../samples/119L.pdb 


More reference "Victor/Frst function for model quality Estimation" GenTHREADER: an efficient and reliable protein fold recognition method for genomic sequences1 David T. Jones The TOP500H database was used to create the file (solv.par)

How to obtain the torsion angles from the PDB residues

The application pdb2tor obtains the set of angle for each residue. As input it uses a PDB file and the corresponding chain, or a file with the PDB ids which can include the chain, if a chain is not included the application uses the first found chain.

Structure of the pdb filelist Uses the first chain for each pdb PDBID PDBID PDBID

To use the corresponding chain for each pdb, need to use the --complete option PDBID(complete name of the corresponding file) chain PDBID chain PDBID chain if many chains from the same pdb are input, just repeat the PDBid and use a different chain

This application can be used also to generate the tor.par file used for TAP application. To generate it you need to use the following line with the TOP500H database. ./pdb2tor -i ../samples/filelist -A -r


OUTPUT FORMAT (default option)


AA Type(one letter format) | Number | pre-phi | pre-psi | phi | psi | omega | chi1 | chi2


!Total file analized: Number of files analized


OUTPUT FORMAT (using -r option)


Numbers of lines in the file


phi | psi | AA type | pre phi | pre psi | omega | #carbons | chi1 | chi2



How to obtain normalized energy from a PDB

The application pdb2torenergy calculates a pseudo-energy to evaluate the quality of a given protein structural model, as expressed in a single (real) number.This program allows you to obtain the normalized energy mentioned in TAP paper.

INPUT DEFAULT DATA tor.par , created by pdb2tor using TOP500H database

To calculate the normalized energy multiple PDBs and PDB chain(s) can be used

Output Depending of the options the energy can be calculated for all the chain residues or for each of them. Per residue, one energy for each of the residues in the pdb

./pdb2torenergy -i ../samples/119L.pdb --allchains -p 

Per pdb(one energy value)

./pdb2torenergy -i ../samples/119L.pdb --allchains 

For chain A in each model each model(many energy values as models in the pdb file)

./pdb2torenergy -i ../samples/1IHQ.pdb -c A 


How to obtain FRST value from a PDB

The application frst allows to calculates the frst value using solvation potential, torsion angles, rapfdf . To use this application some input files are needed. All this mentioned files can be generated using another energy/lobo applications or you can use the already generated ones saved in the victor2.0/data folder.

Default Input files tor.par, created by pdb2tor using TOP500H database solv.par created by pdb2solv using TOP500H database ram.par


Output The application prints the value of first for the given pdb if use the option -v it will print also the values of Rapdf energy ,Solvation energy ,Mainchain hydrogen bonds ,Torsion energy .

To calculate the average over a chain in a NMR ensemble

./frst -i ../samples/16PK.pdb  

To calculate the average over many pdb files

./frst -I ../samples/filelist

How to obtain TAP value from a PDB

The pdb2tap application allows to evaluate the quality of a model, using TAP method (). Used for the evaluation of the quality of protein models determined by X-ray crystalography. The method is based on a relative pseudo-energy calculated from the side chain torsion angle propensities and the backbone, both then are normalized against the global minimum and maximum for the protein sequence under consideration.

Methods Torsion angle potential (based on frst) Pseudo Energy i, maximum and minimum

TAP = (E-Emin)/(Emax-Emin) Known as normalized torsion angle propensity, gives a indication of the degree of nativeness of the protein model.

INICIAL DEFAULT DATA (can be created with pdb2tor) The file tor.par is used to calculate the TAP value, this file can be created with the pdb2tor application, and by default is created using the TOP500H database. tor.par: file containing all torsion angles availabe from TOP500H database. For more reference see: For the database TOP500H is the list of 500 proteins used for the Ramachandran-plot distributions, with File ID {PDB code + chainID (if not the full PDB file) + H (to signify H's added), structure factor deposition status, resolution, and protein name. 500High resolution xRay resolved to 1.8 A or more and less than 60%seq ident. 609NMR structures(9578 models)http://kinemage.biochem.duke.edu/databases/top500.php For method Fine-grained statistical torsion angle potentials are effective in discriminating native protein structures. PMID: 16712465 [PubMed - indexed for MEDLINE]

Output format A plain text file containing: Numbers of lines in the file


phi | psi | AA type | pre phi | pre psi | omega | #carbons | chi1 | chi2



Output interpretation Value close to 1 for a native structure Value close to 0 for a largely incompatible sequence.


Input data the aplication can be used with one or many PDBs and PDB chains. Single structure Xray using one chain

./pdb2tap -i ../samples/102M.pdb -c A   

as shown in http://www.biomedcentral.com/content/supplementary/1471-2105-8-155-s1.txt

Output: Prints the tap value Single structure Xray using all chains(all chains in pdb)

./pdb2tap -i ../samples/1A3W.pdb -P sal  --allchains as shown in 				

http://www.biomedcentral.com/content/supplementary/1471-2105-8-155-s1.txt

Output: Prints the tap value average value for all chains

Multiple models NMR using one chain

./pdb2tap -i ../samples/1IHQ.pdb -P sal -c A --nmr 

Output: Prints the tap value for the selected for each model, the average tap value for all models, standard Deviation, minimum and maximum tap value

Multiple models NMR using all chains(all chains in pdb)

./pdb2tap -i ../samples/1IHQ.pdb -P sal --allchains --nmr 

Output: Prints the tap value average value for all chains in each model, the average tap value for all models, standard Deviation, minimum and maximum tap value