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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.


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


===[[ChargeCalculator:Motivation | What can I do with atomic charges?]]===
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===[[ValidatorDB:Introduction | Introduction]]===
===[[ChargeCalculator:FAQ | Frequently Asked Questions]]===
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===[[ChargeCalculator:Introduction | Introduction]]===
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===[[ChargeCalculator:Terminology | Terminology]]===
# [[ChargeCalculator:Terminology#Structural_elements | Structural elements ]]
## [[ChargeCalculator:Terminology#Molecule | Molecule ]]
## [[ChargeCalculator:Terminology#Atom | Atom ]]
## [[ChargeCalculator:Terminology#Residue | Residue ]]
# [[ChargeCalculator:Terminology#Charges | Charges ]]
## [[ChargeCalculator:Terminology#Atomic_charge | Atomic charge ]]
## [[ChargeCalculator:Terminology#Residue_charge | Residue charge]]
## [[ChargeCalculator:Terminology#Molecular_charge | Molecular charge]]
# [[ChargeCalculator:Terminology#Work_flow | Work flow ]]
## [[ChargeCalculator:Terminology#Atom_type | Atom type ]]
## [[ChargeCalculator:Terminology#Atom_type_scheme | Atom type scheme]]
## [[ChargeCalculator:Terminology#EEM_parameters | EEM parameters ]]
## [[ChargeCalculator:Terminology#EEM_parameter_sets | EEM parameter sets ]]
## [[ChargeCalculator:Terminology#Computation_method | Computation method]]
## [[ChargeCalculator:Terminology#Job | Job]]
## [[ChargeCalculator:Terminology#Charge set | Charge set]]


===[[ValidatorDB:Terminology | Terminology]]===
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* [[ValidatorDB:Terminology#Residue | Residue ]]
* [[ValidatorDB:Terminology#Non-standard_residue | Non-standard residue ]]
* [[ValidatorDB:Terminology#Ligand | Ligand ]]
* [[ValidatorDB:Terminology#Molecule | Molecule ]]
* [[ValidatorDB:Terminology#Model | Model ]]
* [[ValidatorDB:Terminology#Input_motif | Input motif ]]


===[[ValidatorDB:Principles | Principles]]===
===[[ChargeCalculator:Job_submission | Job submission]]===  
* [[ValidatorDB:Principles#Validation_procedure | Validation procedure ]]
# [[ChargeCalculator:Job_submission#Upload_molecules | Upload molecules ]]
* [[ValidatorDB:Principles#Validation_analyses | Validation analyses ]]
# [[ChargeCalculator:Job_submission#Setup_computation | Setup computation ]]
* [[ValidatorDB:Principles#Validation_results | Validation results ]]
## [[ChargeCalculator:Job_submission#Set_total_charge | Set total charge ]]
* [[ValidatorDB:Principles#Validation_reports | Validation reports ]]
## [[ChargeCalculator:Job_submission#Pick_EEM_parameters | Pick EEM parameters ]]
## [[ChargeCalculator:Job_submission#Pick_computation_method | Pick computation method ]]
# [[ChargeCalculator:Job_submission#Start_computation | Start computation ]]
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===[[ChargeCalculator:Interpretation_of_results | Interpretation of results]]===
# [[ChargeCalculator:Interpretation_of_results#Synopsis_page | Synopsis page ]]
# [[ChargeCalculator:Interpretation_of_results#Specifics_page | Specifics page ]]
## [[ChargeCalculator:Interpretation_of_results#Summary | Summary ]]
## [[ChargeCalculator:Interpretation_of_results#Raw_data | Raw Data ]]
## [[ChargeCalculator:Interpretation_of_results#Analyze | Analyze ]]
## [[ChargeCalculator:Interpretation_of_results#Compare | Compare ]]
## [[ChargeCalculator:Interpretation_of_results#3D_model | 3D Model ]]
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===[[ValidatorDB:Database_contents | Database contents]]===  
===[[ChargeCalculator:Case_studies | Case studies]]===
# [[ValidatorDB:Database_contents#Incomplete_structures | Incomplete structures ]]
# [[ChargeCalculator:Case_studies#Paracetamol | Paracetamol]]
# [[ValidatorDB:Database_contents#Complete_structures | Complete structures ]]
# [[ChargeCalculator:Case_studies#Apoptosis | Apoptosis]]
## [[ValidatorDB:Database_contents#Wrong_chirality | Wrong chirality ]]
# [[ChargeCalculator:Case_studies#Proteasome | Proteasome]]
## [[ValidatorDB:Database_contents#Correct_chirality | Correct chirality ]]
 
# [[ValidatorDB:Database_contents#Warnings | Warnings ]]
# [[ValidatorDB:Database_contents#Processing_warnings | Processing warnings ]]
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===[[ValidatorDB:Database_organization | Database organization]]===
 
# [[ValidatorDB:Database_organization#Synopsis_page | Synopsis page ]]
===[[ChargeCalculator:Technical_details | Technical details ]]===
## [[ValidatorDB:Database_organization#Search | Search ]]
# [[ChargeCalculator:Technical_details#Requirements | Requirements]]
## [[ValidatorDB:Database_organization#Overview | Overview ]]
# [[ChargeCalculator:Technical_details#Limitations_and_troubleshooting | Limitations and troubleshooting]]
## [[ValidatorDB:Database_organization#Details_by_molecule | Details by molecule ]]
 
## [[ValidatorDB:Database_organization#Details_by_PDB_entry | Details by PDB entry ]]
# [[ValidatorDB:Database_organization#Specifics_page | Specifics page ]]
## [[ValidatorDB:Database_organization#Overview_2 | Overview ]]
## [[ValidatorDB:Database_organization#Summary | Summary ]]
## [[ValidatorDB:Database_organization#Details | Details ]]
## [[ValidatorDB:Database_organization#Single_molecule_report | Single molecule report ]]
## [[ValidatorDB:Database_organization#Processing_warnings | Processing warnings ]]
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===[[ValidatorDB:CaseStudies | Case studies]]===
===[[ChargeCalculator:Theoretical_background | Theoretical background ]]===
# [[ChargeCalculator:Theoretical_background#EEM | EEM ]]
# [[ChargeCalculator:Theoretical_background#EEM_Cutoff | EEM Cutoff ]]
# [[ChargeCalculator:Theoretical_background#EEM_Cutoff_Cover | EEM Cutoff Cover ]]


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===[[ValidatorDB:Technical_details | Technical details ]]===
 
===[[ChargeCalculator:Index | Index ]]===

Latest revision as of 00:29, 26 December 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.

What can I do with atomic charges?

[edit]

Frequently Asked Questions

[edit]

Introduction

[edit]

Terminology

[edit]
  1. Structural elements
    1. Molecule
    2. Atom
    3. Residue
  2. Charges
    1. Atomic charge
    2. Residue charge
    3. Molecular charge
  3. Work flow
    1. Atom type
    2. Atom type scheme
    3. EEM parameters
    4. EEM parameter sets
    5. Computation method
    6. Job
    7. Charge set

Job submission

[edit]
  1. Upload molecules
  2. Setup computation
    1. Set total charge
    2. Pick EEM parameters
    3. Pick computation method
  3. Start computation

Interpretation of results

[edit]
  1. Synopsis page
  2. Specifics page
    1. Summary
    2. Raw Data
    3. Analyze
    4. Compare
    5. 3D Model

Case studies

[edit]
  1. Paracetamol
  2. Apoptosis
  3. Proteasome

Technical details

[edit]
  1. Requirements
  2. Limitations and troubleshooting

Theoretical background

[edit]
  1. EEM
  2. EEM Cutoff
  3. EEM Cutoff Cover

Index

[edit]
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