AHoJ-DB: A PDB-wide Assignment of apo & holo Relationships Based on Individual Protein-Ligand Interactions.

A single protein structure is rarely sufficient to capture the conformational variability of a protein. Both bound and unbound (holo and apo) forms of a protein are essential for understanding its geometry and making meaningful comparisons. Nevertheless, docking or drug design studies often still consider only single protein structures in their holo form, which are for the most part rigid. With the recent explosion in the field of structural biology, large, curated datasets are urgently needed. Here, we use a previously developed application (AHoJ) to perform a comprehensive search for apo-holo pairs for 468,293 biologically relevant protein-ligand interactions across 27,983 proteins. In each search, the binding pocket is captured and mapped across existing structures within the same UniProt, and the mapped pockets are annotated as apo or holo, based on the presence or absence of ligands. We assemble the results into a database, AHoJ-DB (www.apoholo.cz/db), that captures the variability of proteins with identical sequences, thereby exposing the agents responsible for the observed differences in geometry. We report several metrics for each annotated pocket, and we also include binding pockets that form at the interface of multiple chains. Analysis of the database shows that about 24% of the binding sites occur at the interface of two or more chains and that less than 50% of the total binding sites processed have an apo form in the PDB. These results can be used to train and evaluate predictors, discover potentially druggable proteins, and reveal protein- and ligand-specific relationships that were previously obscured by intermittent or partial data. Availability: www.apoholo.cz/db.

AHoJ: rapid, tailored search and retrieval of apo and holo protein structures for user-defined ligands.

SUMMARY: Understanding the mechanism of action of a protein or designing better ligands for it, often requires access to a bound (holo) and an unbound (apo) state of the protein. Resources for the quick and easy retrieval of such conformations are severely limited. Apo-Holo Juxtaposition (AHoJ), is a web application for retrieving apo-holo structure pairs for user-defined ligands. Given a query structure and one or more user-specified ligands, it retrieves all other structures of the same protein that feature the same binding site(s), aligns them, and examines the superimposed binding sites to determine whether each structure is apo or holo, in reference to the query. The resulting superimposed datasets of apo-holo pairs can be visualized and downloaded for further analysis. AHoJ accepts multiple input queries, allowing the creation of customized apo-holo datasets. AVAILABILITY AND IMPLEMENTATION: Freely available for non-commercial use at http://apoholo.cz. Source code available at https://github.com/cusbg/AHoJ-project. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

PrankWeb 3: accelerated ligand-binding site predictions for experimental and modelled protein structures.

Knowledge of protein-ligand binding sites (LBSs) enables research ranging from protein function annotation to structure-based drug design. To this end, we have previously developed a stand-alone tool, P2Rank, and the web server PrankWeb (https://prankweb.cz/) for fast and accurate LBS prediction. Here, we present significant enhancements to PrankWeb. First, a new, more accurate evolutionary conservation estimation pipeline based on the UniRef50 sequence database and the HMMER3 package is introduced. Second, PrankWeb now allows users to enter UniProt ID to carry out LBS predictions in situations where no experimental structure is available by utilizing the AlphaFold model database. Additionally, a range of minor improvements has been implemented. These include the ability to deploy PrankWeb and P2Rank as Docker containers, support for the mmCIF file format, improved public REST API access, or the ability to batch download the LBS predictions for the whole PDB archive and parts of the AlphaFold database.

PrankWeb: a web server for ligand binding site prediction and visualization.

PrankWeb is an online resource providing an interface to P2Rank, a state-of-the-art method for ligand binding site prediction. P2Rank is a template-free machine learning method based on the prediction of local chemical neighborhood ligandability centered on points placed on a solvent-accessible protein surface. Points with a high ligandability score are then clustered to form the resulting ligand binding sites. In addition, PrankWeb provides a web interface enabling users to easily carry out the prediction and visually inspect the predicted binding sites via an integrated sequence-structure view. Moreover, PrankWeb can determine sequence conservation for the input molecule and use this in both the prediction and result visualization steps. Alongside its online visualization options, PrankWeb also offers the possibility of exporting the results as a PyMOL script for offline visualization. The web frontend communicates with the server side via a REST API. In high-throughput scenarios, therefore, users can utilize the server API directly, bypassing the need for a web-based frontend or installation of the P2Rank application. PrankWeb is available at http://prankweb.cz/, while the web application source code and the P2Rank method can be accessed at https://github.com/jendelel/PrankWebApp and https://github.com/rdk/p2rank, respectively.

P2Rank: machine learning based tool for rapid and accurate prediction of ligand binding sites from protein structure.

BACKGROUND: Ligand binding site prediction from protein structure has many applications related to elucidation of protein function and structure based drug discovery. It often represents only one step of many in complex computational drug design efforts. Although many methods have been published to date, only few of them are suitable for use in automated pipelines or for processing large datasets. These use cases require stability and speed, which disqualifies many of the recently introduced tools that are either template based or available only as web servers. RESULTS: We present P2Rank, a stand-alone template-free tool for prediction of ligand binding sites based on machine learning. It is based on prediction of ligandability of local chemical neighbourhoods that are centered on points placed on the solvent accessible surface of a protein. We show that P2Rank outperforms several existing tools, which include two widely used stand-alone tools (Fpocket, SiteHound), a comprehensive consensus based tool (MetaPocket 2.0), and a recent deep learning based method (DeepSite). P2Rank belongs to the fastest available tools (requires under 1 s for prediction on one protein), with additional advantage of multi-threaded implementation. CONCLUSIONS: P2Rank is a new open source software package for ligand binding site prediction from protein structure. It is available as a user-friendly stand-alone command line program and a Java library. P2Rank has a lightweight installation and does not depend on other bioinformatics tools or large structural or sequence databases. Thanks to its speed and ability to make fully automated predictions, it is particularly well suited for processing large datasets or as a component of scalable structural bioinformatics pipelines.

Improving protein-ligand binding site prediction accuracy by classification of inner pocket points using local features.

BACKGROUND: Protein-ligand binding site prediction from a 3D protein structure plays a pivotal role in rational drug design and can be helpful in drug side-effects prediction or elucidation of protein function. Embedded within the binding site detection problem is the problem of pocket ranking - how to score and sort candidate pockets so that the best scored predictions correspond to true ligand binding sites. Although there exist multiple pocket detection algorithms, they mostly employ a fairly simple ranking function leading to sub-optimal prediction results. RESULTS: We have developed a new pocket scoring approach (named PRANK) that prioritizes putative pockets according to their probability to bind a ligand. The method first carefully selects pocket points and labels them by physico-chemical characteristics of their local neighborhood. Random Forests classifier is subsequently applied to assign a ligandability score to each of the selected pocket point. The ligandability scores are finally merged into the resulting pocket score to be used for prioritization of the putative pockets. With the used of multiple datasets the experimental results demonstrate that the application of our method as a post-processing step greatly increases the quality of the prediction of Fpocket and ConCavity, two state of the art protein-ligand binding site prediction algorithms. CONCLUSIONS: The positive experimental results show that our method can be used to improve the success rate, validity and applicability of existing protein-ligand binding site prediction tools. The method was implemented as a stand-alone program that currently contains support for Fpocket and Concavity out of the box, but is easily extendible to support other tools. PRANK is made freely available at http://siret.ms.mff.cuni.cz/prank.