Search Results - "Galgonek, Jakub"

The LOTUS initiative for open knowledge management in natural products research by Rutz, Adriano, Sorokina, Maria, Galgonek, Jakub, Mietchen, Daniel, Willighagen, Egon, Gaudry, Arnaud, Graham, James G, Stephan, Ralf, Page, Roderic, Vondrášek, Jiří, Steinbeck, Christoph, Pauli, Guido F, Wolfender, Jean-Luc, Bisson, Jonathan, Allard, Pierre-Marie

“…Contemporary bioinformatic and chemoinformatic capabilities hold promise to reshape knowledge management, analysis and interpretation of data in natural…”
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IDSM ChemWebRDF: SPARQLing small-molecule datasets by Galgonek, Jakub, Vondrášek, Jiří

“…The Resource Description Framework (RDF), together with well-defined ontologies, significantly increases data interoperability and usability. The SPARQL query…”
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A comparison of approaches to accessing existing biological and chemical relational databases via SPARQL by Galgonek, Jakub, Vondrášek, Jiří

“…Current biological and chemical research is increasingly dependent on the reusability of previously acquired data, which typically come from various sources…”
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Toward Ab Initio Protein Folding: Inherent Secondary Structure Propensity of Short Peptides from the Bioinformatics and Quantum-Chemical Perspective by Culka, Martin, Galgonek, Jakub, Vymětal, Jiří, Vondrášek, Jiří, Rulíšek, Lubomír

“…By combining bioinformatics with quantum-chemical calculations, we attempt to address quantitatively some of the physical principles underlying protein…”
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Sachem: a chemical cartridge for high-performance substructure search by Kratochvíl, Miroslav, Vondrášek, Jiří, Galgonek, Jakub

“…Background Structure search is one of the valuable capabilities of small-molecule databases. Fingerprint-based screening methods are usually employed to…”
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Correction to: Interoperable chemical structure search service by Kratochvíl, Miroslav, Vondrášek, Jiří, Galgonek, Jakub

“…It was highlighted that the original article [1] contained an error in the last paragraph of the section ‘Structure search using SPARQL’, specifically in the…”
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Interoperable chemical structure search service by Kratochvíl, Miroslav, Vondrášek, Jiří, Galgonek, Jakub

“…Motivation The existing connections between large databases of chemicals, proteins, metabolites and assays offer valuable resources for research in fields…”
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Fully automated virtual screening pipeline of FDA-approved drugs using Caver Web by Musil, Milos, Jezik, Andrej, Jankujova, Marie, Stourac, Jan, Galgonek, Jakub, Mustafa Eyrilmez, Saltuk, Vondrasek, Jiri, Damborsky, Jiri, Bednar, David

“…[Display omitted] Protein tunnels are essential in transporting small molecules into the active sites of enzymes. Tunnels' geometrical and physico-chemical…”
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The IDSM mass spectrometry extension: searching mass spectra using SPARQL by Galgonek, Jakub, Vondrášek, Jiří

“…The Integrated Database of Small Molecules (IDSM) integrates data from small-molecule datasets, making them accessible through the SPARQL query language. Its…”
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Amino Acid Interactions (INTAA) web server v2.0: a single service for computation of energetics and conservation in biomolecular 3D structures by Vymětal, Jiří, Jakubec, David, Galgonek, Jakub, Vondrášek, Jiří

“…Abstract Interactions among amino acid residues are the principal contributor to the stability of the three-dimensional structure of a protein. The Amino Acid…”
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Amino Acid Interaction (INTAA) web server by Galgonek, Jakub, Vymetal, Jirí, Jakubec, David, Vondrášek, Jirí

“…Large biomolecules-proteins and nucleic acids-are composed of building blocks which define their identity, properties and binding capabilities. In order to…”
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Computational methods for the description of pharmacologically relevant platinum complexes--molecular structure and bond dissociation by Kokoschka, Malte, Galgonek, Jakub, Vondrasek, Jiri, Hobza, Pavel

“…Cancer is after cardiovascular disease the most frequent cause of death in Europe. In 28 of 53 countries considered in this area it is already the leading…”
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What are the minimal folding seeds in proteins? Experimental and theoretical assessment of secondary structure propensities of small peptide fragments by Osifová, Zuzana, Kalvoda, Tadeáš, Galgonek, Jakub, Culka, Martin, Vondrášek, Ji í, Bou, Petr, Bednárová, Lucie, Andrushchenko, Valery, Dra ínský, Martin, Rulíšek, Lubomír

“…Certain peptide sequences, some of them as short as amino acid triplets, are significantly overpopulated in specific secondary structure motifs in folded…”
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On InChI and evaluating the quality of cross-reference links by Galgonek, Jakub, Vondrášek, Jiří

“…Background There are many databases of small molecules focused on different aspects of research and its applications. Some tasks may require integration of…”
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SProt: sphere-based protein structure similarity algorithm by Galgonek, Jakub, Hoksza, David, Skopal, Tomáš

“…Similarity search in protein databases is one of the most essential issues in computational proteomics. With the growing number of experimentally resolved…”
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Advanced SPARQL querying in small molecule databases by Galgonek, Jakub, Hurt, Tomáš, Michlíková, Vendula, Onderka, Petr, Schwarz, Jan, Vondrášek, Jiří

“…Background In recent years, the Resource Description Framework (RDF) and the SPARQL query language have become more widely used in the area of cheminformatics…”
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SProt - from local to global protein structure similarity by Galgonek, J, Hoksza, D

“…Similarity search in protein databases is one of the most essential issues in proteomics. With the growing number of experimentally solved protein structures,…”
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Density-based classification of protein structures using iterative TM-score by Hoksza, D., Galgonek, J.

“…Finding similarity between a pair of protein structures is one of the fundamental tasks in many areas of bioinformatical research such as protein structure…”
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On the Effectiveness of Distances Measuring Protein Structure Similarity by Galgonek, Jakub, Hokzsa, David

“…Determining similarity between two protein structures is one of the most fundamental problems in contemporary structural bioinformatics. With the increasing…”
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