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'''AtomicChargeCalculator''', or '''ACC''' is a database of precomputed validation results for all ligands and non-standard residues in the Protein Data Bank (PDB). The molecules deemed relevant for validation are all ligands and non-standard residues with 7 or more heavy atoms. Standard nucleotides, standard amino acids and selenomethionine are not covered. The models from the wwPDB Chemical Component Dictionary (wwPDB CCD) are used as reference structures during validation. The database is updated on a weekly basis.
'''AtomicChargeCalculator''', or '''ACC''' offers an efficient, user-friendly, interactive and platform independent environment for the calculation, visualization and analysis of conformationally dependent, quantum mechanics quality atomic charges in both biomacromolecules and drug-like molecules. ACC computes atomic charges using the Electronegativity Equalization Method, a powerful empirical approach which can provide conformationally dependent, quantum mechanics atomic charges with minimal computational resources.


Below you can find the '''ACC''' user manual, which contains all the information you need in order to make efficient use of '''ACC'''. Additional support is provided on the '''ACC''' web pages. When you first access the '''ACC''' page, you will find basic information in the '''Quick Help''' tab, and useful examples fo database snippets in the '''Samples''' tab. Moreover, various interactive guides are accessible at all times by a green button at the top right corner of some tabs. We recommend that you make use of these as often as you need.
Below you can find the '''ACC''' user manual, which contains all the information you need in order to make efficient use of '''ACC'''. Additional support is provided on the '''ACC''' web pages. When you first access the '''ACC''' page, you will find basic information in the '''Quick Help''' tab, and useful examples in the '''Samples''' tab. Follow the green ? buttons to access the embedded interactive guides that assist you in setting up your calculations and interpreting the results. Many tool tips are available when hovering over various elements of the interface.
 
We hope you make good use of AtomicChargeCalculator.


===[http://www.slideshare.net/lukypravda/validatordb-first-time-user-guide-37728902 First time user guide to ValidatorDB]===
If you are a first time user, we recommend that you go through the basic presentation specifically prepared to help you get oriented.


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===[[ValidatorDB:Introduction | Introduction]]===
===[[ChargeCalculator:Introduction | Introduction]]===
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===[[ValidatorDB:Terminology | Terminology]]===
===[[ChargeCalculator:Terminology | Terminology]]===
* [[ValidatorDB:Terminology#Residue | Residue ]]
# [[ChargeCalculator:Terminology#Structural_elements | Structural elements ]]
* [[ValidatorDB:Terminology#Non-standard_residue | Non-standard residue ]]
## [[ChargeCalculator:Terminology#Atom | Atom ]]
* [[ValidatorDB:Terminology#Ligand | Ligand ]]
## [[ChargeCalculator:Terminology#Molecule | Molecule ]]
* [[ValidatorDB:Terminology#Molecule | Molecule ]]
## [[ChargeCalculator:Terminology#Residue | Residue ]]
* [[ValidatorDB:Terminology#Model | Model ]]
# [[ChargeCalculator:Terminology#Charges | Charges ]]
* [[ValidatorDB:Terminology#Input_motif | Input motif ]]
## [[ChargeCalculator:Terminology#Atomic_charges | Atomic charges ]]
## [[ChargeCalculator:Terminology#Residue_charge | Residue charge]]
## [[ChargeCalculator:Terminology#Molecular_charge | Molecular charge]]
# [[ChargeCalculator:Terminology#Work_flow | Work flow ]]
## [[ChargeCalculator:Terminology#EEM_parameters | EEM parameters ]]
## [[ChargeCalculator:Terminology#Computation_method | Computation_method]]
## [[ChargeCalculator:Terminology#Computation_parameters | Computation_parameters]]


===[[ValidatorDB:Principles | Principles]]===
===[[ChargeCalculator:Principles | Principles]]===
* [[ValidatorDB:Principles#Validation_procedure | Validation procedure ]]
* [[ChargeCalculator:Principles#Validation_procedure | Validation procedure ]]
* [[ValidatorDB:Principles#Validation_analyses | Validation analyses ]]
* [[ChargeCalculator:Principles#Validation_analyses | Validation analyses ]]
* [[ValidatorDB:Principles#Validation_results | Validation results ]]
* [[ChargeCalculator:Principles#Validation_results | Validation results ]]
* [[ValidatorDB:Principles#Validation_reports | Validation reports ]]
* [[ChargeCalculator:Principles#Validation_reports | Validation reports ]]


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===[[ValidatorDB:Database_contents | Database contents]]===  
===[[ChargeCalculator:Database_contents | Database contents]]===  
# [[ValidatorDB:Database_contents#Incomplete_structures | Incomplete structures ]]
# [[ChargeCalculator:Database_contents#Incomplete_structures | Incomplete structures ]]
# [[ValidatorDB:Database_contents#Complete_structures | Complete structures ]]
# [[ChargeCalculator:Database_contents#Complete_structures | Complete structures ]]
## [[ValidatorDB:Database_contents#Wrong_chirality | Wrong chirality ]]
## [[ChargeCalculator:Database_contents#Wrong_chirality | Wrong chirality ]]
## [[ValidatorDB:Database_contents#Correct_chirality | Correct chirality ]]
## [[ChargeCalculator:Database_contents#Correct_chirality | Correct chirality ]]
# [[ValidatorDB:Database_contents#Warnings | Warnings ]]
# [[ChargeCalculator:Database_contents#Warnings | Warnings ]]
# [[ValidatorDB:Database_contents#Processing_warnings | Processing warnings ]]
# [[ChargeCalculator:Database_contents#Processing_warnings | Processing warnings ]]
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===[[ValidatorDB:Database_organization | Database organization]]===
===[[ValidatorDB:Database_organization | Database organization]]===

Revision as of 09:53, 22 November 2014


AtomicChargeCalculator, or ACC offers an efficient, user-friendly, interactive and platform independent environment for the calculation, visualization and analysis of conformationally dependent, quantum mechanics quality atomic charges in both biomacromolecules and drug-like molecules. ACC computes atomic charges using the Electronegativity Equalization Method, a powerful empirical approach which can provide conformationally dependent, quantum mechanics atomic charges with minimal computational resources.

Below you can find the ACC user manual, which contains all the information you need in order to make efficient use of ACC. Additional support is provided on the ACC web pages. When you first access the ACC page, you will find basic information in the Quick Help tab, and useful examples in the Samples tab. Follow the green ? buttons to access the embedded interactive guides that assist you in setting up your calculations and interpreting the results. Many tool tips are available when hovering over various elements of the interface.

We hope you make good use of AtomicChargeCalculator.


Introduction

Terminology

  1. Structural elements
    1. Atom
    2. Molecule
    3. Residue
  2. Charges
    1. Atomic charges
    2. Residue charge
    3. Molecular charge
  3. Work flow
    1. EEM parameters
    2. Computation_method
    3. Computation_parameters

Principles

Database contents

  1. Incomplete structures
  2. Complete structures
    1. Wrong chirality
    2. Correct chirality
  3. Warnings
  4. Processing warnings

Database organization

  1. Synopsis page
    1. Search
    2. Overview
    3. Details by molecule
    4. Details by PDB entry
  2. Specifics page
    1. Overview
    2. Summary
    3. Details
    4. Single molecule report
    5. Processing warnings

Case studies

Technical details

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