Vyhledávání publikací

Vybrané publikace/výsledky

Electronegativity Equalization Method - Fast Method For Charge Calculation (2009)
Fast methods of atomic charge calculation: parameterization of EEM for applicability to metal containing proteins (2010)
Fast methods of atomic charge calculation: parameterization of EEM for applicability to proteins (2010)
QSPR Designer - a program to design and evaluate QSPR models. Case study on pKa prediction (2010)
SiteBinder – software tool for superimposing multiple structural motives (2010)
Predicting pKa values of substituted phenols from atomic charges. (2011)
QSPR modeling – algorithms, challenges and IT solutions (2011)
Docking study of matrix metalloproteinase inhibitors (2011)
Comparison of protein structural motifs – challenges and algorithms. Improved approach and case studies (2011)
Fast methods of atomic charge calculation: the Electronegativity Equalization Method for proteins. (2011)
Predicting pK(a) values of substituted phenols from atomic charges: Comparison of different quantum mechanical methods and charge distribution schemes (2011)
How the methodology of 3D structure preparation influences the quality of QSPR models? (2011)
Searching for tunnels of proteins - comparison of approaches and available software tools (2011)
SiteBinder – an improved approach for comparing multiple protein structural motifs. Case studies on biologically important motifs (2011)
QSPR Designer – Employ your own descriptors in the automated QSAR modeling process (2011)
SiteBinder – an improved software superimposing multiple protein structural motifs and its applications (2011)
Zpracování dat z vysoce výkonných sekvenátorů (2011)
SiteBinder: An improved approach for comparing multiple protein structural motifs (2012)
MOLEonline 2.0: Interactive Web-based Analysis of Biomacromolecular Channels (2012)
Charge Profile Analysis Reveals That Activation of Pro-apoptotic Regulators Bax and Bak Relies on Charge Transfer Mediated Allosteric Regulation (2012)
ROLE OF CHARGE TRANSFER IN THE ACTIVATION OF PRO-APOPTOTIC REGULATORS BAX AND BAK (2012)
BH3-ONLY PROTEINS - FROM STRUCTURE TO FUNCTION (2012)
Protein Politics: How Neutral is Neutral? (2012)
Quantum Mechanical Evaluation of Charge Transfer inside Proteins (2012)
Predicting pKa values from EEM atomic charges (2013)
MOLE 2.0: advanced approach for analysis of biomacromolecular channels (2013)
Rapid Calculation of Accurate Atomic Charges for Proteins via the Electronegativity Equalization Method (2013)
Advanced implementation of atomic charge calculation with electronegativity equalization (2013)
MotiveValidator: interactive web-based validation of ligand and residue structure in biomolecular complexes (2014)
Predikce pKa pro nově navržené molekuly léků (2012)
Jaký vliv na přesnost QSPR modelů má metodika přípravy 3D struktury? Případová studie pro predikci pKa. (2014)
QM quality atomic charges for proteins (2013)
Empirical charges for chemoinformatics applications (2013)
Predicting pKa values of substituted phenols by QSPR models which employ EEM atomic charges (2012)
Web server for the rapid calculation of empirical atomic charges with QM accuracy (2014)
NEEMP – Tool for parameterization of empirical charge calculation method EEM (2014)
Atomic charge based descriptors and their applications in QSAR (2014)
How the methodology of 3D structure preparation influences the quality of pKa prediction? (2014)
MOLE 2.0: Improved Approach for Analysis of Biomacromolecular Channels and Pores (2013)
MotiveQuery: Language and Web Service for Fast Identification of Protein Structural Motifs in the Entire Protein Data Bank (2014)
Ligand structures in the Protein Data Bank – can we trust them? (2014)
Anatomy of enzymatic channels and algorithm for its detection (2014)
MOLE: Pokročilý nástroj pro vyhledávání a charakterizaci tunelů (2014)
ValidatorDB: database of up-to-date validation results for ligands and non-standard residues from the Protein Data Bank (2015)
Anatomy of Enzyme Channels (2014)
Consistency of sugar structures and their annotation in the PDB (2014)
MotiveValidator: software for validation of ligand and residue structures in biomolecular complexes (2014)
ValidatorDB: database of validation results for ligands and non-standard residues from the Protein Data Bank (2014)
Anatomy of protein channels (2015)
PatternQuery: web application for fast detection of biomacromolecular structural patterns in the entire Protein Data Bank (2015)
How Does the Methodology of 3D Structure Preparation Influence the Quality of pK(a) Prediction? (2015)
MotiveQuery: Web application for fast detection of biomacromolecular fragments in the entire Protein Data Bank (2015)
MOLE 2.5: Improved Tool for Analysis of Ligand-Accessible Channels (2015)
WebChemistry: a platform for the detection, validation, comparison, and characterization of structural patterns in biomacromolecules (2015)
PatternQuery: Web application for fast detection of biomacromolecular structural patterns in the entire Protein Data Bank (2015)
ValidatorDB: database of up-to-date validation results for ligands and non-standard residues from the Protein Data Bank (2015)
AtomicChargeCalculator: Interactive Web-based calculation of atomic charges in large biomolecular complexes and drug like molecules (2015)
High-quality and universal empirical atomic charges for chemoinformatics applications (2015)
Tools and data services registry: a community effort to document bioinformatics resources (2016)
NEEMP – nástroj pro parametrizaci EEM (2016)
Detekce biomolekulárních substruktur pomocí PatternQuery (2016)
Parametrizace ekvalizace elektronegativity metodou diferenciální evoluce (2016)
NEEMP: software for validation, accurate calculation and fast parameterization of EEM charges (2016)
The Eighth Central European Conference “Chemistry towards Biology”: Snapshot (2016)
Structural Bioinformatics Tools for Drug Design: Extraction of Biologically Relevant Information from Structural Databases (2016)
Outcome of the First wwPDB/CCDC/D3R Ligand Validation Workshop (2016)
Top 10 metrics for life science software good practices [version 1; referees: 2 approved] (2016)
Quo Vadis, Biomacromolecular Structure Quality (2017)
Biomacromolecular structure quality – improvement or stagnation? (2017)
ChrgDescCalc.py – nástroj na výpočet nábojových deskriptorů (2016)
Využití nábojových deskriptorů v chemoinformatice (2016)
Trends in biomacromolecular structure quality (2017)
Do trends in biomacromolecular structure quality inspire optimism? (2017)
Trends in quality and properties of biomacromolecular complexes (2017)
PDBsum: Structural summaries of PDB entries (2018)
ChannelsDB: database of biomacromolecular tunnels and pores (2018)
Exploring Trends in Quality of Biomacromolecular Structure Data (2017)
bio.tools Sum (2017)
LiteMol suite: interactive web-based visualization of large-scale macromolecular structure data (2017)
Four simple recommendations to encourage best practices in research software (2017)
Validation and analyses of biomacromolecular ligand conformations (2017)
Connection of saccharide database UnicarbKb with common databases of molecular structures (2017)
Worldwide Protein Data Bank validation information: usage and trends (2018)
Validation of ligands in macromolecular structures determined by X-ray crystallography (2018)
Bringing validation information closer to the user (2018)
Validation information in the Protein Data Bank: What is it and why should you care? (2018)
Connection of glycoinformatics databases with Pubchem (2018)
Empirical methods for calculation of partial atomic charges – applicability for proteins? (2018)
MOLEonline: a web-based tool for analyzing channels, tunnels and pores (2018 update) (2018)
bio.tools Sum – tool for exploration of summary information about bioinformatics services in bio.tools (2018)
Molecular evolution and diversification of the SMXL gene family (2018)
Secondary Structure Elements-Annotations and Schematic 2D Visualizations Stable for Individual Protein Families (2018)
Annotation of protein secondary structure elements for whole protein families (2018)
CCL - Charge Calculation Language (2018)
ValTrendsDB: Viewing structure quality from macro and micro perspective (2018)
SugarSketcher: Quick and Intuitive Online Glycan Drawing (2018)
Protein Data Bank: the single global archive for 3D macromolecular structure data (2019)
Automated family-wide annotation of secondary structure elements (2019)
ValTrendsDB: bringing Protein Data Bank validation information closer to the user (2019)
Interactive exploration of trends in biomacromolecule structure quality with ValTrendsDB (2019)
ValTrendsDB: bringing Protein Data Bank validation information closer to the user (2019)
ValTrendsDB: Database of biomacromolecular structure validation trends (2019)
The bio.tools registry of software tools and data resources for the life sciences (2019)
AtomicChargeCalculator II (2019)
Partial atomic charges for proteins (2019)
Exploring trends in quality and features of biomacromolecular complexes with ValTrendsDB (2019)
ValTrendsDB: Enabling comparison of quality and features of biomacromolecular complexes to the global trend (2019)
Family-wide annotation and schematic 2D visualization of secondary structure elements (2018)
Protein family based 2D Diagrams of Secondary Structure Elements (2018)
Mapping and 2D visualization of secondary structure elements in cytochromes (2017)
Automatická anotácia sekundárnych štruktúr v cytochrómoch P450 a hodnotenie ich štruktúrnej podobnosti (2016)
Cytochrome P450 structure anatomy – recognition and analysis of secondary structure elements (2017)
Automated Annotation of Secondary Structure Elements for Entire Protein Families (2018)
Creation and visualization of secondary structure consensus for protein families (2019)
Lesson development for Open Source Software best practices adoption (2018)
Interactive 3D Macromolecular Structure Data Mining with MolQL and Litemol Suite (2018)
Atomic Charge Calculator II: web-based tool for the calculation of partial atomic charges (2020)
SQE charge calculation and its applicability for proteins (2020)
BinaryCIF and CIFTools-Lightweight, efficient and extensible macromolecular data management (2020)
High-performance macromolecular data delivery and visualization for the web (2020)
CATH: increased structural coverage of functional space (2021)
Molecular Evolution and Diversification of Proteins Involved in miRNA Maturation Pathway (2020)
PDBe-KB: a community-driven resource for structural and functional annotations (2020)
PDBe: improved findability of macromolecular structure data in the PDB (2020)
Optimized SQE atomic charges for peptides accessible via a web application (2021)
CoverView: clear atom-level visualization of electron density coverage of PDB structures to assist validation (2022)
Mol* Viewer: modern web app for 3D visualization and analysis of large biomolecular structures (2021)
Uncovering of cytochrome P450 anatomy by SecStrAnnotator (2021)
Visualization and Analysis of Protein Structures with LiteMol Suite (2020)
2DProts: database of family-wide protein secondary structure diagrams (2021)
The EurOPDX Data Portal: an open platform for patient-derived cancer xenograft data sharing and visualization (2022)
Partial atomic charges for proteins (2021)
QM-like partial atomic charges for proteins available online (2021)
PDBe-KB: collaboratively defining the biological context of structural data (2022)
Atomic Charge Calculator II – a web service for calculating partial atomic charges (2022)
QM-like partial atomic charges for AlphaFold available online (2022)
Prediction of QM-like partial atomic charges for alphafold (2022)
OverProt: secondary structure consensus for protein families (2022)
Acknowledging and citing core facilities Key contributions to data lifecycle should be recognised in the scientific literature (2022)
PDBe and PDBe-KB: Providing high-quality, up-to-date and integrated resources of macromolecular structures to support basic and applied research and education (2022)
International Conference on Research Infrastructures 2022. Proceedings Report (2022)
CF Day Meeting (2022)
Automatic storing, sharing and archiving datasets with Onedata (2022)
Automating scientific dataset management and processing using Onedata (2022)
Alphacharges - a web service for calculating QM-like partial atomic charges for AlphaFold proteins (2022)
αCharges: partial atomic charges for AlphaFold structures in high quality (2023)
A survey of the European Open Science Cloud services for expanding the capacity and capabilities of multidisciplinary scientific applications (2023)
An Evaluation of EDAM Coverage in the Tools Ecosystem and Prototype Integration of Galaxy and Workflowhub Systems. (2023)
Building OpenStack Cloud with Kubernetes as Undercloud (2023)
Easy Deployment of Dask and Jupyter Notebooks on Managed Kubernetes (2023)
Cloudification of scientific experimental data using Onedata (2023)
COMPUTER-AIDED MODEL DESIGN OF EMPIRICAL METHODS FOR CALCULATING PARTIAL ATOMIC CHARGES (2021)
Mol* Volumes and Segmentations: visualization and interpretation of cell imaging data alongside macromolecular structure data and biological annotations (2023)
Zpracování dat na CEITECu (2023)
Enhancing Data Accessibility: Strategies and Tools for Effective Metadata Management (2023)
Beskar Cloud: OpenStack Deployment on Top of Kubernetes (2023)
Management of life-science data and their metadata (2023)
New ways of protein family visualization in AlphaFold era (2023)
ChannelsDB 2.0: A Comprehensive Database of Protein Tunnels and Pores in AlphaFold Era (2023)
Onedata4Sci: Life-science experimental datasets management system (2023)
ChannelsDB 2.0: a comprehensive database of protein tunnels and pores in AlphaFold era (2024)
Annotating Macromolecular Complexes in the Protein Data Bank: Improving the FAIRness of Structure Data (2023)
Journal metrics and structures: A dynamic interplay (2023)
Exploring the relationship between structural quality and journal impact factor (2023)
Introduction to Onedata at CEITEC MU and in Czech National Repository Platform (2023)
Introduction to the new generation EGI container execution platform (2024)
AlphaFind: Discover structure similarity across the entire known proteome (2024)
CF Day 2023 (2024)
EMDB-the Electron Microscopy Data Bank (2023)
Data workflows at CEITEC MU (2024)
MAFILDB - technická realizace (2024)
PDBe and PDBe-KB: Providing high-quality, up-to-date and integrated resources of macromolecular structures to support basic and applied research and education (2022)
AlphaFind: discover structure similarity across the proteome in AlphaFold DB (2024)
Hands-on experience with big data transfer via iRODS and Onedata (2024)
Research Data Management at CEITEC MU (2024)
Conformational study of small carbon rings in ligands (2023)
Invesigating the rare conformation of small rings in ligands (2023)
Validation of cycle conformation in small molecules (2022)
Validation of cycle conformation in Protein Data Bank (2020)
Rare ring conformations in PDB: Facts or wishful thinking? (2024)
AlphaFind — discover structure similarity across the proteome in AlphaFold DB (2024)
LMI-10: Protein structural embeddings of AlphaFold DB (2024)
GraSR: Protein structural embeddings of AlphaFold DB (2024)
LMI-30: Protein structural embeddings of AlphaFold DB (2024)
Data Management and FAIRification in MAFIL (2024)
AlphaFind — discover structure similarity across the proteome in AlphaFold DB (2024)
AlphaFind (2024)
Fast, structure-based searching in a large-scale protein data repository (2024)
3D-af-Surfer: Protein structural embeddings of AlphaFold DB (2024)
AlphaFind: Discover structure similarity across the entire known proteome – data and model (2024)
RBP-Tar – a searchable database for experimental RBP binding sites (2024)
Data Management of Biological Imaging Data (2024)
Scientific Dataset Management System for the Research Institute Based on Onedata (2024)

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