List of works - David Hoksza

2D Pharmacophore Query Generation

article

A Statistical Comparison of SimTandem with State-of-the-Art Peptide Identification Tools

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

scientific article published in 2024

Activity-driven exploration of chemical space with morphing

An application of the metric access methods to the mass spectrometry data

Chemical space visualization using ViFrame

scholarly article published June 2013

Closing the gap between formats for storing layout information in systems biology

scientific article published on 05 July 2019

DDPIn - Distance and density based protein indexing

Density-based classification of protein structures using iterative TM-score

Efficient RNA pairwise structure comparison by SETTER method ⬇️

scientific article published on May 18, 2012

Exploration of Chemical Space by Molecular Morphing

Genomics 2 Proteins portal: A resource and discovery tool for linking genetic screening outputs to protein sequences and structures

scientific article published on 2 January 2024

Improved Alignment of Protein Sequences Based on Common Parts

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

scientific article (publication date: 2015)

Improving the similarity search of tandem mass spectra using metric access methods

MINERVA API and plugins: opening molecular network analysis and visualization to the community

scientific article published on 01 November 2019

MolArt: a molecular structure annotation and visualization tool

scholarly article by David Hoksza published in June 2018

Molpher: a software framework for systematic chemical space exploration

scientific article

MultiSETTER - Multiple RNA Structure Similarity Algorithm

MultiSETTER: web server for multiple RNA structure comparison

scientific article published on 12 August 2015

Multiple 3D RNA Structure Superposition Using Neighbor Joining

scientific article published on May 2015

Non-metric similarity search of tandem mass spectra including posttranslational modifications

On Optimizing the Non-metric Similarity Search in Tandem Mass Spectra by Clustering

On comparison of SimTandem with state-of-the-art peptide identification tools, efficiency of precursor mass filter and dealing with variable modifications

scientific article published on 14 November 2013

On the Parallelization of the SProt Measure and the TM-Score Algorithm

P2RANK: Knowledge-Based Ligand Binding Site Prediction Using Aggregated Local Features

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

scientific article published on 14 August 2018

P3S: Protein Structure Similarity Search

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

scientific article published on 01 July 2019

Protein sequences identification using NM-tree

R2DT is a framework for predicting and visualising RNA secondary structure using templates

scientific article published on 09 June 2021

SETTER - RNA SEcondary sTructure-based TERtiary Structure Similarity Algorithm

SETTER: web server for RNA structure comparison

scientific article

SProt - from local to global protein structure similarity

SProt: sphere-based protein structure similarity algorithm.

scientific article

List of works by David Hoksza

2D Pharmacophore Query Generation

A Statistical Comparison of SimTandem with State-of-the-Art Peptide Identification Tools

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

Activity-driven exploration of chemical space with morphing

An application of the metric access methods to the mass spectrometry data

Chemical space visualization using ViFrame

Closing the gap between formats for storing layout information in systems biology

DDPIn - Distance and density based protein indexing

Density-based classification of protein structures using iterative TM-score

Efficient RNA pairwise structure comparison by SETTER method ⬇️

Exploration of Chemical Space by Molecular Morphing

Genomics 2 Proteins portal: A resource and discovery tool for linking genetic screening outputs to protein sequences and structures

Improved Alignment of Protein Sequences Based on Common Parts

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

Improving the similarity search of tandem mass spectra using metric access methods

MINERVA API and plugins: opening molecular network analysis and visualization to the community

MolArt: a molecular structure annotation and visualization tool

Molpher: a software framework for systematic chemical space exploration

MultiSETTER - Multiple RNA Structure Similarity Algorithm

MultiSETTER: web server for multiple RNA structure comparison

Multiple 3D RNA Structure Superposition Using Neighbor Joining

Non-metric similarity search of tandem mass spectra including posttranslational modifications

On Optimizing the Non-metric Similarity Search in Tandem Mass Spectra by Clustering

On comparison of SimTandem with state-of-the-art peptide identification tools, efficiency of precursor mass filter and dealing with variable modifications

On the Parallelization of the SProt Measure and the TM-Score Algorithm

P2RANK: Knowledge-Based Ligand Binding Site Prediction Using Aggregated Local Features

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

P3S: Protein Structure Similarity Search

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

Protein sequences identification using NM-tree

R2DT is a framework for predicting and visualising RNA secondary structure using templates

SETTER - RNA SEcondary sTructure-based TERtiary Structure Similarity Algorithm

SETTER: web server for RNA structure comparison

SProt - from local to global protein structure similarity

SProt: sphere-based protein structure similarity algorithm.

Scaffold analysis of PubChem database as background for hierarchical scaffold-based visualization

Scaffold-based chemical space exploration

SimTandem: Similarity Search in Tandem Mass Spectra

Similarity search and posttranslational modifications in tandem mass spectra

TRAVeLer: a tool for template-based RNA secondary structure visualization

Template-based prediction of ribosomal RNA secondary structure

Using Neo4j for Mining Protein Graphs: A Case Study

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