Publications

2026

• AlphaFind v2: similarity search in AlphaFold DB and TED domains across structural contexts

  SLANINÁKOVÁ Terézia ROŠINEC Adrián ČILLÍK Jakub KŘENEK Aleš GREŠOVÁ Katarína PORUBSKÁ Jana MARŠÁLKOVÁ Eva OĽHA Jaroslav PROCHÁZKA David HEJTMÁNEK Lukáš DOHNAL Vlastislav BERKA Karel SVOBODOVÁ Radka ANTOL Matej

  Peer-reviewed scientific article

  NUCLEIC ACIDS RESEARCH, year: 2026, DOI

• Analysis of cyclohexane, cyclopentane, and benzene conformations in ligands for PDB X-ray structures using the Hill-Reilly approach

  BUČEKOVÁ Gabriela DOSHCHENKO Viktoriia SVOBODA Tomáš PORUBSKÁ Jana CHARESHNEU Aliaksei RAČEK Tomáš HORSKÝ Vladimír SVOBODOVÁ Radka SCHINDLER Ondřej

  Peer-reviewed scientific article

  Journal of Cheminformatics, year: 2026, volume: 18, edition: 1, DOI

• Atomic Charge Calculator III: a modern platform for calculating partial atomic charges

  RAČEK Tomáš PILÁT Martin SCHINDLER Ondřej BUČEKOVÁ Gabriela TICHÝ Dominik BERKA Karel SVOBODOVÁ Radka

  Peer-reviewed scientific article

  Nucleic Acids Research, year: 2026, DOI

• bio.tools: an expanded web service for research software in the life sciences

  MENDES Ana I S IENASESCU Hans ANDERSEN Christian A T CALHOUN Erin CHMURA Piotr J COLLIER Keiler GOGA Iosif GUSTAFSSON Ove J R KALAŠ Matúš KIERKEGAARD Mads NIELSEN Niclas K JAANISO Erik JENSEN Jennifer R B LUDL Adriaan-Alexander MÉNAGER Hervé PALMBLAD Magnus MAGYAR Zsófia RAČEK Tomáš ROŠINEC Adrián RUSZ Filip STEEGHS-TURCHINA Mariia SZMIGIEL Aleksandra SVOBODOVÁ Radka SCHWÄMMLE Veit

  Peer-reviewed scientific article

  Nucleic Acids Research, year: 2026, DOI

• Foldify: Web Application for Protein Structure Prediction

  ĎURÁČIOVÁ Romana CAPANDOVÁ Michaela BERKA Karel SVOBODOVÁ Radka SLANINÁKOVÁ Terézia KOVÁČ Kristián ANTOL Matej HEJTMÁNEK Lukáš

  Peer-reviewed scientific article

  Journal of Chemical Information and Modeling, year: 2026, volume: 66, edition: 13, DOI

• PROPTIMUS LIVE: local constrained α-carbon optimization of proteins

  SVOBODA Tomáš MIKUŠ Michal BOHUŠ Lukáš RAČEK Tomáš BUČEKOVÁ Gabriela TICHÝ Dominik BERKA Karel SVOBODOVÁ Radka SCHINDLER Ondřej

  Peer-reviewed scientific article

  Nucleic Acids Research, year: 2026, volume: 54, edition: W1, DOI

2025

• GOLEM: A tool for visualizing the distribution of Gene regulatOry eLEMents within the plant promoters with a focus on male gametophyte

  NEVOSÁD Lukáš KLODOVÁ Božena RUDOLF Jiří RAČEK Tomáš PŘEROVSKÁ Tereza KUSOVÁ Alžbeta SVOBODOVÁ Radka HONYS David PROCHÁZKOVÁ SCHRUMPFOVÁ Petra

  Peer-reviewed scientific article

  Plant Journal, year: 2025, volume: 121, edition: 5, DOI

• Gromacs MetaDump: a tool for extracting GROMACS simulation metadata

  ROŠINEC Adrián SLANINÁKOVÁ Terézia PAVLÍK Tomáš RANDIAK Róbert SVOBODA Tomáš RAČEK Tomáš BUČEKOVÁ Gabriela SCHINDLER Ondřej ANTOL Matej KŘENEK Aleš BERKA Karel SVOBODOVÁ Radka

  Peer-reviewed scientific article

  Journal of Cheminformatics, year: 2025, volume: 17, edition: 1, DOI

• MOLEonline: a web-based tool for analysing channels, tunnels and pores (2025 update)

  RAČEK Tomáš VEĽKÝ Dušan BUČEKOVÁ Gabriela SCHINDLER Ondřej HUTAŘOVÁ VAŘEKOVÁ Ivana ŠPAČKOVÁ Anna BAZGIER Václav BERKA Karel SVOBODOVÁ Radka

  Peer-reviewed scientific article

  Bioinformatics, year: 2025, volume: 41, edition: 9, DOI

• PDBCharges: Quantum-Mechanical Partial Atomic Charges for PDB Structures

  SCHINDLER Ondřej SVOBODA Tomáš ROŠINEC Adrián RAČEK Tomáš BUČEKOVÁ Gabriela TICHÝ Dominik BERKA Karel SVOBODOVÁ Radka

  Peer-reviewed scientific article

  Nucleic Acids Research, year: 2025, volume: 53, edition: W1, DOI