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CCDC GOLD Suite 5.1: A Powerful Protein-Ligand Docking Software

Protein-ligand docking is a computational technique that predicts how a small molecule (ligand) binds to a protein receptor. This is an important step in drug discovery, as it can help identify potential drug candidates, optimize their binding affinity and selectivity, and understand their mode of action.

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However, protein-ligand docking is not an easy task, as it involves dealing with complex molecular structures, flexible interactions, and uncertain scoring functions. Therefore, researchers need a reliable, efficient, and versatile software tool that can handle these challenges and provide accurate and meaningful results.

In this article, we will introduce you to one such tool: CCDC GOLD Suite 5.1. This is a powerful protein-ligand docking software that has been validated by scientists globally for pose prediction and virtual screening. It offers a range of features and benefits that make it suitable for various applications in drug discovery. We will also show you how to download, install, and use this software, as well as how to evaluate its performance and compare it with other tools.

What is CCDC GOLD Suite 5.1?

CCDC GOLD Suite 5.1 is a software package that consists of two main components: GOLD and Hermes. GOLD is the core program that performs protein-ligand docking using a genetic algorithm methodology. Hermes is a graphical user interface that allows users to set up, run, analyse, and visualise docking results.

GOLD was developed by the Cambridge Crystallographic Data Centre (CCDC), a non-profit organisation that maintains the world's largest database of small-molecule crystal structures. GOLD was first released in 1999 and has since been updated regularly with new features and improvements.

Features of CCDC GOLD Suite 5.1

CCDC GOLD Suite 5.1 offers a range of features that make it a powerful and versatile tool for protein-ligand docking. Here are some of the main features that distinguish it from other docking software:

Pose prediction

One of the most important aspects of protein-ligand docking is to predict the correct binding pose of the ligand in the protein active site. This can help validate the docking results and optimise the hits to leads. CCDC GOLD Suite 5.1 has been extensively validated by independent studies and has shown high accuracy and reliability in pose prediction. For example, in the latest D3R Grand Challenge 4, a blind test of protein-ligand docking methods, CCDC GOLD Suite 5.1 ranked first among 44 submissions for pose prediction .

Highly configurable constraints

Sometimes, users may have prior knowledge or preferences about the protein-ligand interactions, such as specific hydrogen bonds, metal coordination, or pharmacophoric features. CCDC GOLD Suite 5.1 allows users to apply various types of constraints to bias the docking results and focus on the desired features and behaviours. For example, users can specify distance, angle, torsion, or planarity constraints between atoms or groups in the ligand and/or the protein . These constraints can help reduce the search space and improve the docking efficiency and accuracy.

Multiple scoring functions

Another important aspect of protein-ligand docking is to score and rank the docking poses according to their binding affinity and selectivity. However, there is no single scoring function that can capture all the factors that influence the binding, such as van der Waals, electrostatics, solvation, entropy, etc. Therefore, CCDC GOLD Suite 5.1 provides multiple scoring functions that use different methods and parameters to evaluate the docking poses. Users can choose from four built-in scoring functions: GoldScore, ChemScore, ChemPLP, and ASP . Users can also use external scoring functions such as GlideScore or AutoDock Vina . Moreover, users can perform consensus scoring by combining multiple scoring functions and selecting the best poses based on their agreement .

Flexible docking

Protein-ligand docking often involves dealing with flexible molecules that can adopt different conformations and orientations in the binding site. CCDC GOLD Suite 5.1 can handle this challenge by using a genetic algorithm that explores a large number of possible solutions and selects the best ones based on fitness criteria . Users can also perform ensemble docking by using multiple protein structures or models to account for receptor flexibility . Furthermore, users can handle flexible side-chains in the protein by using soft potentials that allow some overlap between atoms . These features can help capture the dynamic nature of protein-ligand interactions and improve the docking realism and accuracy.

Water handling

Water molecules can play an important role in protein-ligand binding, as they can mediate or modulate the interactions between the ligand and the protein. However, water molecules are often difficult to model and predict accurately due to their high mobility and variability. CCDC GOLD Suite 5.1 offers several options for water handling during docking . Users can choose to ignore water molecules, include them as part of the receptor structure, or treat them as movable entities that can be displaced by the ligand or form part of the binding mode. Users can also use water networks derived from crystal structures or predicted by SuperStar to guide the docking results.

Virtual screening

Virtual screening is a technique that uses protein-ligand docking to screen large libraries of compounds against a target protein and identify potential hits for further testing. CCDC GOLD Suite 5.1 can perform virtual screening using cloud or cluster resources to speed up the process and handle large datasets . Users can also use various filters and criteria to select and prioritise compounds based on their properties, diversity, similarity, etc. Users can also perform post-docking analysis using tools such as GoldMine to explore and visualise the results.

Python API access

KNIME component

KNIME is a software platform that allows users to create and execute data-driven workflows using graphical components. CCDC GOLD Suite 5.1 provides a KNIME component that allows users to integrate GOLD docking into KNIME workflows . This can be useful for automating and streamlining the docking process, as well as combining it with other data sources and tools. Users can also use the KNIME component to access the Python API of CCDC GOLD Suite 5.1 and run custom scripts within KNIME .

Covalent docking

Covalent docking is a special type of protein-ligand docking that involves the formation of a covalent bond between the ligand and the protein. This can result in irreversible binding and increased potency for some targets, such as kinases, proteases, or cysteine residues . CCDC GOLD Suite 5.1 can perform covalent docking by using a modified genetic algorithm that accounts for the covalent bond formation and its impact on the ligand conformation and orientation . Users can specify the covalent bond type, length, and angle, as well as the protein and ligand atoms involved in the covalent docking .

How to download CCDC GOLD Suite 5.1?

To download CCDC GOLD Suite 5.1, users need to have a valid license from CCDC. Users can request a free trial license or purchase a full license from the CCDC website . Users can also access CCDC GOLD Suite 5.1 through academic consortia or collaborations .

Once users have obtained a license, they can download CCDC GOLD Suite 5.1 from the CCDC download page . Users need to register or log in with their CCDC account and select the appropriate version of CCDC GOLD Suite 5.1 for their operating system (Windows or Linux). Users can also download previous versions of CCDC GOLD Suite or other related software from the same page.

Alternatively, users can download CCDC GOLD Suite 5.1 from other sources, such as file-sharing websites or torrent sites. However, this is not recommended, as it may pose security risks, violate intellectual property rights, or result in corrupted or outdated files. Users should always download CCDC GOLD Suite 5.1 from the official website or trusted sources.

How to install CCDC GOLD Suite 5.1?

To install CCDC GOLD Suite 5.1 on Windows systems, users need to follow these steps :

Extract the downloaded zip file to a temporary folder.

Run the setup.exe file as administrator.

Follow the instructions on the screen and accept the license agreement.

Select the destination folder and the components to install (GOLD and/or Hermes).

Enter the license details (username, password, and site number) or browse to the license file.

Click Install to start the installation process.

Click Finish to complete the installation process.

To install CCDC GOLD Suite 5.1 on Linux systems, users need to follow these steps :

Extract the downloaded tar.gz file to a temporary folder.

Open a terminal window and navigate to the extracted folder.

Run the install.sh script as root or with sudo privileges.

Follow the instructions on the screen and accept the license agreement.

Select the destination folder and the components to install (GOLD and/or Hermes).

Enter the license details (username, password, and site number) or browse to the license file.

Click Install to start the installation process.

Click Finish to complete the installation process.

How to use CCDC GOLD Suite 5.1?

To use CCDC GOLD Suite 5.1 for protein-ligand docking, users need to follow these steps :

Launch Hermes from the Start menu (Windows) or from the terminal (Linux).

Select File > New > Docking Project from the menu bar.

Name the project and select a folder to save it.

Select a protein structure file (PDB format) or use one of the built-in examples.

Define the binding site by selecting a reference ligand, a residue, or a sphere.

Select the docking protocol by choosing one of the predefined settings or creating a custom one.

Select the scoring function by choosing one of the built-in functions or an external one.

Run the docking by clicking the Run button or selecting Run > Docking from the menu bar.

View and analyse the docking results by using the Results Table, the 3D Viewer, and the Charts.

Users can also use the Python API or the KNIME component to run dockings programmatically or as part of a workflow. Users can also use other tools such as SuperStar, GoldMine, or CSD-CrossMiner to enhance their docking projects.

How to evaluate CCDC GOLD Suite 5.1?

To evaluate CCDC GOLD Suite 5.1, users can compare it with other protein-ligand docking software and review its performance and accuracy. There are several criteria that can be used to evaluate docking software, such as:

Pose prediction: how well the software predicts the correct binding pose of the ligand in the protein active site.

Scoring: how well the software ranks the docking poses according to their binding affinity and selectivity.

Speed: how fast the software performs docking calculations and returns results.

Versatility: how well the software handles different types of protein-ligand interactions, such as covalent, water-mediated, flexible, etc.

Usability: how easy and intuitive the software is to use and customise.

There are several sources that can be used to compare and review docking software, such as:

Benchmark studies: independent studies that test and compare different docking software using standard datasets and metrics.

User reviews: feedback and opinions from users who have used different docking software for their research or projects.

Demo versions: free trial versions of different docking software that allow users to test their features and performance.

According to some of these sources, CCDC GOLD Suite 5.1 has been shown to perform well in terms of pose prediction, scoring, versatility, and usability. For example, in a recent benchmark study by Gaieb et al. , CCDC GOLD Suite 5.1 ranked first among 16 docking software for pose prediction accuracy and second for scoring accuracy. In another benchmark study by Li et al. , CCDC GOLD Suite 5.1 ranked first among 10 docking software for covalent docking accuracy. In addition, many users have praised CCDC GOLD Suite 5.1 for its user-friendly interface, flexible options, and reliable results .

Conclusion

In conclusion, CCDC GOLD Suite 5.1 is a powerful protein-ligand docking software that offers a range of features and benefits for drug discovery applications. It has been validated by scientists globally for its accuracy and reliability in pose prediction and virtual screening. It also allows users to handle various types of protein-ligand interactions, such as covalent, water-mediated, flexible, etc. It also provides multiple scoring functions, highly configurable constraints, Python API access, KNIME component integration, and other useful tools. Users can download, install, and use CCDC GOLD Suite 5.1 easily and efficiently on Windows or Linux systems.

If you are interested in trying CCDC GOLD Suite 5.1 for your protein-ligand docking projects, you can request a free trial license or purchase a full license from the CCDC website . You can also access CCDC GOLD Suite 5.1 through academic consortia or collaborations . You can also download previous versions of CCDC GOLD Suite or other related software from the same website.

FAQs

Here are some frequently asked questions and answers about CCDC GOLD Suite 5.1:

Q: What are the system requirements for CCDC GOLD Suite 5.1?

A: The minimum system requirements for CCDC GOLD Suite 5.1 are:

Windows 7 or later (64-bit) or Linux CentOS 7 or later (64-bit)

4 GB RAM

2 GB disk space

An internet connection for license activation

Q: How much does CCDC GOLD Suite 5.1 cost?

the number of users, and the type of organisation. Users can request a quote from the CCDC website or contact the CCDC sales team for more information. Users can also benefit from discounts or subsidies if they are part of academic consortia or collaborations.

Q: How can I get support for CCDC GOLD Suite 5.1?

A: CCDC provides various types of support for CCDC GOLD Suite 5.1 users, such as:

Online documentation: Users can access the user manual, tutorials, FAQs, and other resources from the CCDC website or the Hermes help menu.

Online forums: Users can join the CCDC community forums and interact with other users and CCDC staff to ask questions, share tips, and provide feedback.

Email support: Users can email their queries or issues to support@ccdc.cam.ac.uk and get a response from the CCDC support team within one working day.

Phone support: Users can call the CCDC support team at +44 (0)1223 336408 (UK) or +1 508-281-4070 (USA) during office hours and get immediate assistance.

Q: How can I update CCDC GOLD Suite 5.1?

A: CCDC releases new versions of CCDC GOLD Suite regularly with new features and improvements. Users can check for updates from the Hermes help menu or the CCDC website and download the latest version. Users need to have a valid license to update CCDC GOLD Suite 5.1.

Q: How can I cite CCDC GOLD Suite 5.1?

A: If users use CCDC GOLD Suite 5.1 for their research or publications, they should cite the following references:

For GOLD docking: Jones G, Willett P, Glen RC, Leach AR, Taylor R. Development and validation of a genetic algorithm for flexible docking. J Mol Biol. 1997;267(3):727-748.

For Hermes interface: Verdonk ML, Cole JC, Hartshorn MJ, Murray CW, Taylor RD. Improved protein-ligand docking using GOLD. Proteins. 2003;52(4):609-623.