David Hoksza
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View article: Hybrid protein–ligand binding residue prediction with protein language models: does the structure matter?
Hybrid protein–ligand binding residue prediction with protein language models: does the structure matter? Open
Motivation Predicting protein–ligand binding sites is crucial in studying protein interactions with applications in biotechnology and drug discovery. Two distinct paradigms have emerged for this purpose: sequence-based methods, which lever…
View article: PrankWeb 4: a modular web server for protein–ligand binding site prediction and downstream analysis
PrankWeb 4: a modular web server for protein–ligand binding site prediction and downstream analysis Open
Knowledge of protein–ligand binding sites (LBSs) is crucial for advancing our understanding of biology and developing practical applications in fields such as medicine or biotechnology. PrankWeb is a web server that allows users to predict…
View article: R2DT: a comprehensive platform for visualizing RNA secondary structure
R2DT: a comprehensive platform for visualizing RNA secondary structure Open
RNA secondary (2D) structure visualization is an essential tool for understanding RNA function. R2DT is a software package designed to visualize RNA 2D structures in consistent, recognizable, and reproducible layouts. The latest release, R…
View article: Unified Visual-Aware Representations for Data Analytics
Unified Visual-Aware Representations for Data Analytics Open
One of the characteristics of big data is its internal complexity and variety manifested in many types of datasets that are to be managed, searched, or analyzed. In their natural forms, some data entities are unstructured, such as texts or…
View article: CryptoBench: cryptic protein–ligand binding sites dataset and benchmark
CryptoBench: cryptic protein–ligand binding sites dataset and benchmark Open
Motivation Structure-based methods for detecting protein–ligand binding sites play a crucial role in various domains, from fundamental research to biomedical applications. However, current prediction methodologies often rely on holo (ligan…
View article: R2DT: a comprehensive platform for visualising RNA secondary structure
R2DT: a comprehensive platform for visualising RNA secondary structure Open
RNA secondary (2D) structure visualisation is an essential tool for understanding RNA function. R2DT is a software package designed to visualise RNA 2D structures in consistent, recognisable, and reproducible layouts. The latest release, R…
View article: Genomics 2 Proteins portal: a resource and discovery tool for linking genetic screening outputs to protein sequences and structures
Genomics 2 Proteins portal: a resource and discovery tool for linking genetic screening outputs to protein sequences and structures Open
View article: CryptoBench: Cryptic protein-ligand binding sites dataset and benchmark
CryptoBench: Cryptic protein-ligand binding sites dataset and benchmark Open
Structure-based methods for detecting protein-ligand binding sites play a crucial role in various domains, from fundamental research to biomedical applications. However, current prediction methodologies often rely on holo (ligand-bound) pr…
View article: Genomics 2 Proteins portal: A resource and discovery tool for linking genetic screening outputs to protein sequences and structures
Genomics 2 Proteins portal: A resource and discovery tool for linking genetic screening outputs to protein sequences and structures Open
Recent advances in AI-based methods have revolutionized the field of structural biology. Concomitantly, high-throughput sequencing and functional genomics technologies have enabled the detection and generation of variants at an unprecedent…
View article: Ahoj Db: A Pdb-Wide Assignment of Apo & Holo Relationships Based on Individual Protein-Ligand Interactions
Ahoj Db: A Pdb-Wide Assignment of Apo & Holo Relationships Based on Individual Protein-Ligand Interactions Open
View article: Visualizations for universal deep-feature representations: survey and taxonomy
Visualizations for universal deep-feature representations: survey and taxonomy Open
In data science and content-based retrieval, we find many domain-specific techniques that employ a data processing pipeline with two fundamental steps. First, data entities are represented by some visualizations, while in the second step, …
View article: Hybrid protein-ligand binding residue prediction with protein language models: Does the structure matter?
Hybrid protein-ligand binding residue prediction with protein language models: Does the structure matter? Open
Background Predicting protein-ligand binding sites is crucial in studying protein interactions with applications in biotechnology and drug discovery. Two distinct paradigms have emerged for this purpose: sequence-based methods, which lever…
View article: Visualization of automatically combined disease maps and pathway diagrams for rare diseases
Visualization of automatically combined disease maps and pathway diagrams for rare diseases Open
Introduction: Investigation of molecular mechanisms of human disorders, especially rare diseases, require exploration of various knowledge repositories for building precise hypotheses and complex data interpretation. Recently, increasingly…
View article: AHoJ: rapid, tailored search and retrieval of apo and holo protein structures for user-defined ligands
AHoJ: rapid, tailored search and retrieval of apo and holo protein structures for user-defined ligands Open
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 conformati…
View article: Delineation of functionally essential protein regions for 242 neurodevelopmental genes
Delineation of functionally essential protein regions for 242 neurodevelopmental genes Open
Neurodevelopmental disorders (NDDs), including severe paediatric epilepsy, autism and intellectual disabilities are heterogeneous conditions in which clinical genetic testing can often identify a pathogenic variant. For many of them, genet…
View article: AHoJ: rapid, tailored search and retrieval of apo and holo protein structures for user-defined ligands
AHoJ: rapid, tailored search and retrieval of apo and holo protein structures for user-defined ligands Open
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 s…
View article: PrankWeb 3: accelerated ligand-binding site predictions for experimental and modelled protein structures
PrankWeb 3: accelerated ligand-binding site predictions for experimental and modelled protein structures Open
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 (h…
View article: PDBe-KB: collaboratively defining the biological context of structural data
PDBe-KB: collaboratively defining the biological context of structural data Open
The Protein Data Bank in Europe – Knowledge Base (PDBe-KB, https://pdbe-kb.org) is an open collaboration between world-leading specialist data resources contributing functional and biophysical annotations derived from or relevant to the Pr…
View article: R2DT is a framework for predicting and visualising RNA secondary structure using templates
R2DT is a framework for predicting and visualising RNA secondary structure using templates Open
View article: Comprehensive characterization of amino acid positions in protein structures reveals molecular effect of missense variants
Comprehensive characterization of amino acid positions in protein structures reveals molecular effect of missense variants Open
Significance Recent large-scale sequencing efforts have enabled the detection of millions of missense variants. Elucidating their functional effect is of crucial importance but challenging. We approach this problem by performing a wide-sca…
View article: RNAcentral 2021: secondary structure integration, improved sequence search and new member databases
RNAcentral 2021: secondary structure integration, improved sequence search and new member databases Open
RNAcentral is a comprehensive database of non-coding RNA (ncRNA) sequences that provides a single access point to 44 RNA resources and >18 million ncRNA sequences from a wide range of organisms and RNA types. RNAcentral now also include…
View article: R2DT: computational framework for template-based RNA secondary structure visualisation across non-coding RNA types
R2DT: computational framework for template-based RNA secondary structure visualisation across non-coding RNA types Open
Non-coding RNAs (ncRNA) are essential for all life, and the functions of many ncRNAs depend on their secondary (2D) and tertiary (3D) structure. Despite proliferation of 2D visualisation software, there is a lack of methods for automatical…
View article: Disease and pathway maps for Rare Diseases
Disease and pathway maps for Rare Diseases Open
In this article we present a workflow for construction of prototype rare disease maps based on the phenotypic description of a rare disease. We use stable disease and phenotype identifiers to i) retrieve disease-associated genes and geneti…
View article: MINERVA, A Platform for the Exploration of Disease Maps
MINERVA, A Platform for the Exploration of Disease Maps Open
Disease maps support the process of discovery of disease mechanisms and help in understanding complex cross-talks of multiple pathways. Their diagrammatic content can be used in a range of visually supported analyses, which requires a prop…
View article: MISCAST: MIssense variant to protein StruCture Analysis web SuiTe
MISCAST: MIssense variant to protein StruCture Analysis web SuiTe Open
Human genome sequencing efforts have greatly expanded, and a plethora of missense variants identified both in patients and in the general population is now publicly accessible. Interpretation of the molecular-level effect of missense varia…
View article: Closing the gap between formats for storing layout information in systems biology
Closing the gap between formats for storing layout information in systems biology Open
The first version of this article listed one of its authors as Jan \nHausenauer rather than Jan Hasenauer. This has now been corrected. The \nauthors regret the error.
View article: PDBe-KB: a community-driven resource for structural and functional annotations
PDBe-KB: a community-driven resource for structural and functional annotations Open
The Protein Data Bank in Europe-Knowledge Base (PDBe-KB, https://pdbe-kb.org) is a community-driven, collaborative resource for literature-derived, manually curated and computationally predicted structural and functional annotations of mac…
View article: Insights into protein structural, physicochemical, and functional consequences of missense variants in 1,330 disease-associated human genes 693259
Insights into protein structural, physicochemical, and functional consequences of missense variants in 1,330 disease-associated human genes 693259 Open
Inference of the structural and functional consequences of amino acid-altering missense variants is challenging and not yet scalable. Clinical and research applications of the colossal number of identified missense variants is thus limited…
View article: Burden analysis of missense variants in 1,330 disease-associated genes on 3D provides insights into the mutation effects
Burden analysis of missense variants in 1,330 disease-associated genes on 3D provides insights into the mutation effects Open
Interpretation of the colossal number of genetic variants identified from sequencing applications is one of the major bottlenecks in clinical genetics, with the inference of the effect of amino acid-substituting missense variants on protei…
View article: Closing the gap between formats for storing layout information in systems biology
Closing the gap between formats for storing layout information in systems biology Open
The understanding of complex biological networks often relies on both a dedicated layout and a topology. Currently, there are three major competing layout-aware systems biology formats, but there are no software tools or software libraries…