Difference between revisions of "Energy"

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Remember that before trying any of the following applications the environment variables should be set
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export VICTOR_ROOT=/<your_folder>/victor2.0/ 
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export PATH=$PATH:/<your_folder>/victor2.0/bin/
  
 
==How to obtain the solvation potential==
 
==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.  
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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:  
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A '''solvation potential''' for an amino acid residue a is defined as:  
=RTln(fa(r)/f(r))  
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Solvation potential=R*T*ln(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  
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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.  
 
and f(r) is the frequency of occurrence of all residues with burial r.  
  
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As input a PDB is needed  
 
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  
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The output will depend on the given options, considering 30 maximum binds possible (by default test.out, use -o option to set a name)  
---------------------------------------------------------------------------------------------------------------
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total quantity of residues evaluated | AA type(3L) | frequencies
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---------------------------------------------------------------------------------------------------------------
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Polar option
 
---------------------------------------------------------------------------------------------------------------
 
P |  total quantity of residues evaluated | AA type(3L) | frequencies | Polar frequency |
 
---------------------------------------------------------------------------------------------------------------
 
  
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'''Non polar output file format '''
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---------------------------------------------------------------------------------------------------------------
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total quantity of residues evaluated | AA type(3L) | frequencies
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---------------------------------------------------------------------------------------------------------------
  
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.  
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 +
'''Polar output file format '''
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---------------------------------------------------------------------------------------------------------------
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P |  total quantity of residues evaluated | AA type(3L) | frequencies | Polar frequency |
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---------------------------------------------------------------------------------------------------------------
 +
 +
 
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To obtain the solv.par file used for  pdb2energy, frst, etc applications, you need to use the following line with all the pdbs in the TOP500H database.  
 
  ./pdb2solv -i ../samples/119L.pdb  
 
  ./pdb2solv -i ../samples/119L.pdb  
  
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More reference "Victor/Frst function for model quality Estimation" GenTHREADER: an efficient and reliable protein fold recognition method for genomic sequences1 David T. Jones
 
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)
 
The TOP500H database was used to create the file (solv.par)
 +
 +
for a detailed example see [[pdb2solv example]]
  
 
==How to obtain the torsion angles from the PDB residues==
 
==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.  
 
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  
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'''Structure of the pdb filelist '''
 
Uses the first chain for each pdb  
 
Uses the first chain for each pdb  
PDBID  
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PDBID  
PDBID  
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PDBID  
PDBID  
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PDBID  
  
 
To use the corresponding chain for each pdb, need to use the --complete option  
 
To use the corresponding chain for each pdb, need to use the --complete option  
PDBID(complete name of the corresponding file) chain  
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PDBID(complete name of the corresponding file) chain  
PDBID chain  
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PDBID chain  
PDBID chain  
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PDBID chain  
 
if many chains from the same pdb are input, just repeat the PDBid and use a different 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.  
 
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
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./pdb2tor -I ../samples/filelist2_ --complete
  
  
OUTPUT FORMAT (default option)  
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'''Output format''' (-A option, Give per residue phi, psi, omega, chi, pre-psi and pre-psi angle)  
 
---------------------------------------------------------------------------------------------------------------  
 
---------------------------------------------------------------------------------------------------------------  
 
AA Type(one letter format)  | Number | pre-phi | pre-psi | phi | psi | omega |  chi1  | chi2  
 
AA Type(one letter format)  | Number | pre-phi | pre-psi | phi | psi | omega |  chi1  | chi2  
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OUTPUT FORMAT (using -r option)  
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'''Output format''' (using -r option)  
 
---------------------------------------------------------------------------------------------------------------  
 
---------------------------------------------------------------------------------------------------------------  
 
Numbers of lines in the file  
 
Numbers of lines in the file  
 
---------------------------------------------------------------------------------------------------------------  
 
---------------------------------------------------------------------------------------------------------------  
 
phi | psi | AA type | pre phi | pre psi | omega | #carbons | chi1 | chi2  
 
phi | psi | AA type | pre phi | pre psi | omega | #carbons | chi1 | chi2  
---------------------------------------------------------------------------------------------------------------  
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---------------------------------------------------------------------------------------------------------------
  
 +
for a detailed example see [[pdb2tor example]]
  
 
==How to obtain normalized energy from a PDB==
 
==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.  
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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.  
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 +
'''Input data by default'''
  
INPUT DEFAULT DATA
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tor.par , created by [[Features#How to obtain the torsion angles from the PDB residues|pdb2tor]] using TOP500H database.
tor.par , created by pdb2tor using TOP500H database
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To calculate the normalized energy multiple PDBs and PDB chain(s) can be used
 
To calculate the normalized energy multiple PDBs and PDB chain(s) can be used
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  ./pdb2torenergy -i ../samples/1IHQ.pdb -c A  
 
  ./pdb2torenergy -i ../samples/1IHQ.pdb -c A  
  
 
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for a detailed example see [[pdb2torenergy example]]
  
 
==How to obtain FRST value from a PDB==
 
==How to obtain FRST value from a PDB==
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To calculate the average over many pdb files  
 
To calculate the average over many pdb files  
 
  ./frst -I ../samples/filelist
 
  ./frst -I ../samples/filelist
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 +
for a detailed example see [[frst example]]
  
 
==How to obtain TAP value from a PDB==
 
==How to obtain TAP value from a PDB==
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  ./pdb2tap -i ../samples/1IHQ.pdb -P sal --allchains --nmr  
 
  ./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
 
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
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 +
for a detailed example see [[pdb2tap example]]

Revision as of 14:07, 15 July 2014

Remember that before trying any of the following applications the environment variables should be set

export VICTOR_ROOT=/<your_folder>/victor2.0/  
export PATH=$PATH:/<your_folder>/victor2.0/bin/ 

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:

Solvation potential=R*T*ln(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, considering 30 maximum binds possible (by default test.out, use -o option to set a name)


Non polar output file format

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


Polar output file format

--------------------------------------------------------------------------------------------------------------- 
P |  total quantity of residues evaluated | AA type(3L) | frequencies | Polar frequency | 
--------------------------------------------------------------------------------------------------------------- 

To obtain the solv.par file used for pdb2energy, frst, etc applications, you need to use the following line with 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)

for a detailed example see pdb2solv example

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/filelist2_ --complete 


Output format (-A option, Give per residue phi, psi, omega, chi, pre-psi and pre-psi angle)


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


!Total file analyzed: Number of files analyzed


Output format (using -r option)


Numbers of lines in the file


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


for a detailed example see pdb2tor example

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 data by default

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 

for a detailed example see pdb2torenergy example

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

for a detailed example see frst example

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 crystallography. 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.

INITIAL 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 available 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 application 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

for a detailed example see pdb2tap example