CCDC ConQuest: A Powerful Tool for Searching the Cambridge Structural Database
If you are interested in exploring the structural knowledge of small molecules and their interactions, you might want to check out CCDC ConQuest, a software tool that allows you to perform advanced 3D searching of structures in the Cambridge Structural Database (CSD). The CSD is the world's largest and most comprehensive curated repository of organic and metal-organic crystal structures, containing over one million entries from X-ray and neutron diffraction analyses. CCDC ConQuest provides easy and convenient access to this wealth of information, enabling you to carry out more advanced searches than WebCSD, including context and criteria matching. In this article, we will introduce you to the features and benefits of CCDC ConQuest, show you how to download and install it, and guide you through some examples of how to use it for your research.
What is CCDC ConQuest?
CCDC ConQuest is a software tool that allows you to search the CSD using a variety of options, such as chemical substructure, reference, unit cell, and text terms. You can also search by known polymorphs and subsets, such as metal-organic frameworks (MOFs), co-crystals, or pharmaceuticals. CCDC ConQuest lets you specify chemical constraints, such as charge, hybridization state, and cyclicity, as well as 3D geometric parameters, such as bond lengths, angles, torsions, and ring puckering. You can also explore intermolecular contacts, such as hydrogen bonds, halogen bonds, pi-pi interactions, and pharmacophoric patterns. Moreover, you can link your proprietary data to the CSD entries, so you can get a complete picture of your system of interest.
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One of the main advantages of CCDC ConQuest is that it is integrated with the CCDC suite of software tools that use powerful algorithms for further analysis of your search results. These tools include Mercury, GOLD, Mogul, IsoStar, and more. You can seamlessly export your search results to these tools and perform tasks such as crystal structure visualisation, protein-ligand docking, molecular geometry analysis, intermolecular interaction analysis, and more. We will discuss these tools in more detail later in this article.
How to download and install CCDC ConQuest
To download and install CCDC ConQuest, you need to have a current licence for the CSD data and software. If you are an academic user, you can register for free . Once you have your licence details, you can follow these steps:
Go to the page on the CCDC website.
Click on "Request Download Links" and enter your licence details.
You will receive an email with links to download the full CSD portfolio, including the database and all software tools.
Click on the link for CCDC ConQuest and save the file to your computer.
Run the installer and follow the instructions on the screen.
Once the installation is complete, launch CCDC ConQuest from your desktop or start menu.
You can also watch a step-by-step video tutorial .
How to use CCDC ConQuest for advanced 3D searching of structuresHow to use CCDC ConQuest for advanced 3D searching of structures
CCDC ConQuest offers a user-friendly interface that allows you to perform various types of searches on the CSD. You can access the search options from the toolbar or the menu bar. Here are some examples of how to use CCDC ConQuest for advanced 3D searching of structures:
Chemical substructure search
A chemical substructure search allows you to find all structures in the CSD that contain a specific fragment or group of atoms. You can draw the substructure using the built-in sketcher or import it from a file. You can also specify additional chemical constraints, such as charge, hybridization state, and cyclicity. To perform a chemical substructure search, follow these steps:
Click on the "Substructure" icon on the toolbar or select "Search > Substructure" from the menu bar.
Draw or import your substructure in the sketcher window. You can use the tools on the left panel to modify your drawing.
Click on the "Constraints" tab to add any chemical constraints to your substructure. You can use the drop-down menus and checkboxes to select the options you want.
Click on the "Search" button to start the search. You will see a progress bar and a message indicating how many hits have been found.
When the search is complete, you will see a list of hits in the results window. You can sort, filter, and export the hits as you wish.
You can also watch a video tutorial .
3D geometric search
A 3D geometric search allows you to find all structures in the CSD that match a specific 3D shape or configuration of atoms. You can define the 3D geometry using coordinates, bond lengths, angles, torsions, and ring puckering. You can also specify a tolerance range for each parameter. To perform a 3D geometric search, follow these steps:
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Click on the "Geometry" icon on the toolbar or select "Search > Geometry" from the menu bar.
Enter or import your 3D geometry in the geometry window. You can use the tools on the left panel to modify your input.
Click on the "Tolerances" tab to add any tolerance ranges to your geometry. You can use the sliders and text boxes to adjust the values.
Click on the "Search" button to start the search. You will see a progress bar and a message indicating how many hits have been found.
When the search is complete, you will see a list of hits in the results window. You can sort, filter, and export the hits as you wish.
You can also watch a video tutorial .
Intermolecular contact search
An intermolecular contact search allows you to find all structures in the CSD that have specific types of interactions between molecules, such as hydrogen bonds, halogen bonds, pi-pi interactions, and pharmacophoric patterns. You can define the intermolecular contacts using atom types, distances, angles, and other criteria. To perform an intermolecular contact search, follow these steps:
Click on the "Contact" icon on the toolbar or select "Search > Contact" from the menu bar.
Select the type of contact you want to search for from the drop-down menu. You will see a list of predefined templates for common types of contacts.
Select one of the templates or create your own by clicking on "New". You can edit the template by changing the atom types, distances, angles, and other criteria.
Click on the "Search" button to start the search. You will see a progress bar and a message indicating how many hits have been found.
When the search is complete, you will see a list of hits in the results window. You can sort, filter, and export the hits as you wish.
You can also watch a video tutorial .
Text and numeric database search
A text and numeric database search allows you to find all structures in Text and numeric database search
A text and numeric database search allows you to find all structures in the CSD that match a specific text or numeric term, such as author name, journal title, year of publication, unit cell parameters, space group, and more. You can combine multiple terms using logical operators, such as AND, OR, and NOT. To perform a text and numeric database search, follow these steps:
Click on the "Text/Numeric" icon on the toolbar or select "Search > Text/Numeric" from the menu bar.
Enter or select your text or numeric term in the text/numeric window. You can use the drop-down menus and checkboxes to choose the options you want.
If you want to add more terms, click on the "Add Term" button and repeat the previous step. You can also change the logical operator between the terms by clicking on it.
Click on the "Search" button to start the search. You will see a progress bar and a message indicating how many hits have been found.
When the search is complete, you will see a list of hits in the results window. You can sort, filter, and export the hits as you wish.
You can also watch a video tutorial .
Link to proprietary data
If you have your own data that you want to link to the CSD entries, you can use the "Link Data" feature of CCDC ConQuest. This allows you to associate any external data, such as biological activity, solubility, melting point, etc., with the CSD structures. You can then use this data to filter or sort your search results. To link your proprietary data to the CSD entries, follow these steps:
Prepare your data in a CSV file with the following format: The first column should contain the CSD refcode of the structure you want to link to. The second column should contain the name of the data field you want to link. The third column should contain the value of the data field. You can have multiple data fields for each structure, but each field should have a unique name.
Click on the "Link Data" icon on the toolbar or select "Search > Link Data" from the menu bar.
Browse and select your CSV file and click on "Open". You will see a message confirming that your data has been linked successfully.
To use your linked data in your searches, click on the "Linked Data" tab in the search window and select the data field you want to use. You can enter or select a value or range for your data field and click on "Search".
You will see a list of hits that match your linked data criteria in the results window. You can sort, filter, and export the hits as you wish.
You can also watch a video tutorial .
How to analyse and visualise search results with CCDC software tools
Once you have performed your searches with CCDC ConQuest, you can further analyse and visualise your search results with other CCDC software tools that are integrated with ConQuest. These tools include Mercury, GOLD, Mogul, IsoStar, and more. You can easily export your search results to these tools and perform tasks such as crystal structure visualisation, protein-ligand docking, molecular geometry analysis, intermolecular interaction analysis, and more. Here are some examples of how to use these tools with your search results:
Mercury: Crystal structure visualisation and analysis
Mercury is a software tool that allows you to visualise and analyse crystal structures in 2D and 3D. You can use Mercury to explore various aspects of crystal structures, such as symmetry elements, packing motifs, hydrogen bonding networks, coordination geometries, thermal ellipsoids, and more. You can also generate publication-quality graphics and animations of crystal structures using Mercury. To use Mercury with your search results from ConQuest, follow these steps:
Select one or more structures from your search results in ConQuest.
Click on the "Mercury" icon on the toolbar or select "Tools > Mercury" from the menu bar.
You will see a new window with Mercury launched and your selected structures loaded.
You can use the tools on the left panel to manipulate and analyse your structures in 2D and 3D.
You can also use the menus on the top bar to access more features and options in Mercury.
You can also watch a video tutorial .
<h3 GOLD: Protein-ligand docking and scoring
GOLD is a software tool that allows you to perform protein-ligand docking and scoring using a genetic algorithm. You can use GOLD to predict the binding modes and affinities of small molecules to protein targets, as well as to rank and compare different ligands. You can also use GOLD to perform virtual screening of large compound libraries against protein targets. To use GOLD with your search results from ConQuest, follow these steps:
Select one or more structures from your search results in ConQuest that contain a ligand and a protein.
Click on the "GOLD" icon on the toolbar or select "Tools > GOLD" from the menu bar.
You will see a new window with GOLD launched and your selected structures loaded.
You can use the tools on the left panel to set up and run your docking and scoring calculations.
You can also use the menus on the top bar to access more features and options in GOLD.
You can also watch a video tutorial .
Mogul: Molecular geometry analysis
Mogul is a software tool that allows you to analyse the molecular geometry of small molecules using statistical data from the CSD. You can use Mogul to check the validity and quality of your structures, as well as to compare and optimise different conformations. You can also use Mogul to generate idealised geometries for new molecules or fragments. To use Mogul with your search results from ConQuest, follow these steps:
Select one or more structures from your search results in ConQuest that contain a small molecule.
Click on the "Mogul" icon on the toolbar or select "Tools > Mogul" from the menu bar.
You will see a new window with Mogul launched and your selected structures loaded.
You can use the tools on the left panel to analyse and modify your structures using bond lengths, angles, torsions, and ring puckering data from the CSD.
You can also use the menus on the top bar to access more features and options in Mogul.
You can also watch a video tutorial .
IsoStar: Intermolecular interaction analysis
IsoStar is a software tool that allows you to analyse the intermolecular interactions of small molecules using statistical data from the CSD and the Protein Data Bank (PDB). You can use IsoStar to explore how different functional groups interact with each other in various environments, such as in crystals, in solution, or in protein binding sites. You can also use IsoStar to generate pharmacophore models for drug design. To use IsoStar with your search results from ConQuest, follow these steps:
Select one or more structures from your search results in ConQuest that contain a small molecule.
Click on the "IsoStar" icon on the toolbar or select "Tools > IsoStar" from the menu bar.
You will see a new window with IsoStar launched and your selected structures loaded.
You can use the tools on the left panel to select a central group and a contact group for your interaction analysis.
You can also use the menus on the top bar to access more features and options in IsoStar.
You can also watch a video tutorial .
Conclusion
In this article, we have introduced you to CCDC ConQuest, a powerful tool for searching the Cambridge Structural Database (CSD). We have shown you how to download and install CCDC ConQuest, and how to use it for advanced 3D searching of structures using various options, such as chemical substructure, 3D geometry, intermolecular contact, text and numeric database, and link to proprietary data. We have also shown you how to analyse and visualise your search results with other CCDC software tools that are integrated with ConQuest, such as Mercury, GOLD, Mogul, IsoStar, and more. We hope you have found this article useful and informative, and that you will enjoy exploring the structural knowledge of small molecules and their interactions with CCDC ConQuest.
FAQs
Q: How can I get a licence for CCDC ConQuest?
A: If you are an academic user, you can register for free .
Q: How can I Q: How can I update CCDC ConQuest to the latest version?
A: You can check for updates by clicking on the "Help" menu and selecting "Check for Updates". You will see a message telling you if there is a new version available. If there is, you can download and install it by following the instructions on the screen.
Q: How can I get help and support for CCDC ConQuest?
A: You can access the online help and documentation by clicking on the "Help" menu and selecting "ConQuest Help". You can also visit the or by phone at +44 (0)1223 336408.
Q: How can I cite CCDC ConQuest in my publications?
A: You can cite CCDC ConQuest using the following reference: Groom, C. R., Bruno, I. J., Lightfoot, M. P., & Ward, S. C. (2016). The Cambridge Structural Database. Acta Crystallographica Section B: Structural Science, Crystal Engineering and Materials, 72(2), 171-179.
Q: How can I share my search results with others?
A: You can export your search results to various formats, such as CIF, SDF, MOL2, PDB, PDF, CSV, and more. You can also save your search results as a ConQuest file (.cqs) that can be opened by other users of ConQuest. To export or save your search results, click on the "File" menu and select "Export" or "Save As".
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