A5051424845- Computational Drug Discovery Methods
- Protein Structure and Dynamics
- Enzyme Structure and Function
- Advanced Proteomics Techniques and Applications
- Bioinformatics and Genomic Networks
- Mass Spectrometry Techniques and Applications
- Machine Learning in Materials Science
- RNA and protein synthesis mechanisms
- Genetics, Bioinformatics, and Biomedical Research
- Scientific Computing and Data Management
- X-ray Diffraction in Crystallography
- Geochemistry and Geologic Mapping
- Crystallography and molecular interactions
- Free Radicals and Antioxidants
- Biomedical Text Mining and Ontologies
- Chemical Synthesis and Analysis
- Electron and X-Ray Spectroscopy Techniques
- Research Data Management Practices
- Machine Learning in Bioinformatics
- Advanced Chemical Physics Studies
- Microbial Metabolic Engineering and Bioproduction
- Genomics and Phylogenetic Studies
- Microbial Natural Products and Biosynthesis
- Ion channel regulation and function
- Chemistry and Chemical Engineering
Central European Institute of Technology
2015-2025
Masaryk University
2016-2025
Central European Institute of Technology – Masaryk University
2015-2025
Czech University of Life Sciences Prague
2011
Siemens (Czechia)
2007-2008
University College Dublin
2007-2008
Conway School of Landscape Design
2007-2008
Siemens (Germany)
2007
PDBsum is a web server providing structural information on the entries in Protein Data Bank (PDB). The analyses are primarily image-based and include protein secondary structure, protein-ligand protein-DNA interactions, PROCHECK of quality, many others. 3D structures can be viewed interactively RasMol, PyMOL, JavaScript viewer called 3Dmol.js. Users upload their own PDB files obtain set password-protected for each. freely accessible to all at: http://www.ebi.ac.uk/pdbsum.
The Protein Data Bank (PDB) is the single global archive of experimentally determined three-dimensional (3D) structure data biological macromolecules. Since 2003, PDB has been managed by Worldwide (wwPDB; wwpdb.org), an international consortium that collaboratively oversees deposition, validation, biocuration, and open access dissemination 3D macromolecular data. Core Archive houses atomic coordinates more than 144 000 structural models proteins, DNA/RNA, their complexes with metals small...
Large biomolecular structures are being determined experimentally on a daily basis using established techniques such as crystallography and electron microscopy. In addition, emerging integrative or hybrid methods (I/HM) producing structural models of huge macromolecular machines assemblies, sometimes containing 100s millions non-hydrogen atoms. The performance requirements for visualization analysis tools delivering these data increasing rapidly. Significant progress in developing online,...
Abstract CATH (https://www.cathdb.info) identifies domains in protein structures from wwPDB and classifies these into evolutionary superfamilies, thereby providing structural functional annotations. There are two levels: CATH-B, a daily snapshot of the latest domain superfamily assignments, CATH+, with additional derived data, such as predicted sequence domains, functionally coherent subsets (Functional Families or FunFams). The CATH+ release, version 4.3, significantly increases coverage an...
Channels and pores in biomacromolecules (proteins, nucleic acids their complexes) play significant biological roles, e.g., molecular recognition enzyme substrate specificity.We present an advanced software tool entitled MOLE 2.0, which has been designed to analyze channels pores. Benchmark tests against other available tools showed that 2.0 is by comparison quicker, more robust versatile. As a new feature, estimates physicochemical properties of the identified channels, i.e., hydropathy,...
MOLEonline is an interactive, web-based application for the detection and characterization of channels (pores tunnels) within biomacromolecular structures. The updated version overcomes limitations previous by incorporating recently developed LiteMol Viewer visualization engine providing a simple, fully interactive user experience. enables two modes calculation: one dedicated to analysis while other was specifically designed transmembrane pores. As can use both PDB mmCIF formats, it be...
Abstract The Protein Data Bank in Europe (PDBe), a founding member of the Worldwide (wwPDB), actively participates deposition, curation, validation, archiving and dissemination macromolecular structure data. PDBe supports diverse research communities their use structures by enriching PDB data providing advanced tools services for effective access, visualization analysis. This paper details enrichment at PDBe, including mapping RNA to Rfam, identification molecules that act as cofactors. has...
Life sciences are yielding huge data sets that underpin scientific discoveries fundamental to improvement in human health, agriculture and the environment. In support of these discoveries, a plethora databases tools deployed, technically complex diverse implementations, across spectrum disciplines. The corpus documentation resources is fragmented Web, with much redundancy, has lacked common standard information. outcome scientists must often struggle find, understand, compare use best for...
Scientific research relies on computer software, yet software is not always developed following practices that ensure its quality and sustainability. This manuscript does aim to propose new development best practices, but rather provide simple recommendations encourage the adoption of existing practices. Software promote better improves reproducibility reusability research. These are designed around Open Source values, practical suggestions contribute making source code more discoverable,...
Biomolecular channels play important roles in many biological systems, e.g. enzymes, ribosomes and ion channels. This article introduces a web-based interactive MOLEonline 2.0 application for the analysis of access/egress paths to interior molecular voids. enables platform-independent, easy-to-use analyses (bio)macromolecular channels, tunnels pores. Results are presented clear manner, making their interpretation easy. For each channel, displays 3D graphical representation its profile...
Abstract 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 functional annotations of macromolecular structure data, contained the (PDB). goal PDBe-KB two-fold: (i) to increase visibility reduce fragmentation contributed by specialist data resources, make these more findable, accessible, interoperable reusable (FAIR) (ii) place their...
Enzyme active sites can be connected to the exterior environment by one or more channels passing through protein. Despite our current knowledge of enzyme structure and function, surprisingly little is known about how often are present any structural features such may have in common. Here, we analyze long (i.e. >15 Å) leading 4,306 structures. We find that over 64% enzymes contain two channels, their typical length being 28 Å. show amino acid compositions channel significantly differ both...
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 (PDB). goal of PDBe-KB place macromolecular structure their biological context by developing standardised exchange formats integrating partner into a knowledge graph that can provide valuable insights. Since we described 2019, there have been significant...
Crystallographic studies of ligands bound to biological macromolecules (proteins and nucleic acids) play a crucial role in structure-guided drug discovery design, also provide atomic level insights into the physical chemistry complex formation between ligands. The quality with which small-molecule have been modelled Protein Data Bank (PDB) entries has been, continues be, matter concern for many investigators. Correctly interpreting whether electron density found binding site is compatible...
Partial atomic charges are a well-established concept, useful in understanding and modeling the chemical behavior of molecules, from simple compounds, to large biomolecular complexes with many reactive sites. This paper introduces AtomicChargeCalculator (ACC), web-based application for calculation analysis which respond changes molecular conformation environment. ACC relies on an empirical method rapidly compute accuracy comparable quantum mechanical approaches. Due its efficient...
Strigolactones (SLs) are a relatively recent addition to the list of plant hormones that control different aspects development. SL signalling is perceived by an α/β hydrolase, DWARF 14 (D14). A close homolog D14, KARRIKIN INSENSTIVE2 (KAI2), involved in perception uncharacterized molecule called karrikin (KAR). Recent studies Arabidopsis identified SUPPRESSOR OF MAX2 1 (SMAX1) and SMAX1-LIKE 7 (SMXL7) be potential SCF–MAX2 complex-mediated proteasome targets KAI2 respectively. Genetic on...
Gene expression regulation during tissue development is extremely complex. A key mechanism of gene the recognition regulatory motifs, also known as cis-regulatory elements (CREs), by various proteins in promoter regions. Localization these motifs near transcription start site (TSS) or translation (ATG) crucial for initiation and rate. Transcription levels individual genes, regulated can vary significantly across tissues developmental stages, especially processes like sexual reproduction....
The acid dissociation (ionization) constant pK(a) is one of the fundamental properties organic molecules. We have evaluated different computational strategies and models to predict values substituted phenols using partial atomic charges. Partial charges for 124 phenol molecules were calculated 83 approaches containing seven theory levels (MP2, HF, B3LYP, BLYP, BP86, AM1, PM3), three basis sets (6-31G*, 6-311G, STO-3G), five population analyses (MPA, NPA, Hirshfeld, MK, Löwdin). correlations...
Partial atomic charges describe the distribution of electron density in a molecule and therefore provide clues to chemical behaviour molecules. Recently, these have become popular chemoinformatics, as they are informative descriptors that can be utilised pharmacophore design, virtual screening, similarity searches etc. Especially conformationally-dependent perform very successfully. In particular, their fast accurate calculation via Electronegativity Equalization Method (EEM) seems promising...
Partial atomic charges serve as a simple model for the electrostatic distribution of molecule that drives its interactions with surroundings. Since partial are frequently used in computational chemistry, chemoinformatics and bioinformatics, many approaches calculating them have been introduced. The most applicable fast reasonably accurate empirical charge calculation approaches. Here, we introduce Atomic Charge Calculator II (ACC II), web application enables via all main types molecules. ACC...
ChannelsDB (http://ncbr.muni.cz/ChannelsDB) is a database providing information about the positions, geometry and physicochemical properties of channels (pores tunnels) found within biomacromolecular structures deposited in Protein Data Bank. Channels were from two sources; literature using manual deposition software tool automatically detecting tunnels leading to enzymatic active sites selected cofactors, transmembrane pores. The stores geometrical features (e.g. length radius profile along...
3D macromolecular structural data is growing ever more complex and plentiful in the wake of substantive advances experimental computational structure determination methods including crystallography, cryo-electron microscopy, integrative methods. Efficient means working with for archiving, analyses, visualization are central to facilitating interoperability reusability compliance FAIR Principles. We address two challenges posed by growth size complexity. First, reduced bespoke compression...