Mgr. Jan Dvorský, Ph.D.

2024

• A computational workflow for analysis of missense mutations in precision oncology

  KHAN Rayyan Tariq POKORNÁ Petra DVORSKÝ Jan BORKO Simeon AREFIEV Ihor PLANAS IGLESIAS Joan DOBIÁŠ Adam RANGEL PAMPLONA PIZARRO PINTO José Gaspar SZOTKOWSKÁ Veronika ŠTĚRBA Jaroslav SLABÝ Ondřej DAMBORSKÝ Jiří MAZURENKO Stanislav BEDNÁŘ David

  Article in Periodical

  JOURNAL OF CHEMINFORMATICS, year: 2024, volume: 16, edition: 1, DOI

• Large-scale annotation of biochemically relevant pockets and tunnels in cognate enzyme-ligand complexes

  VÁVRA Ondřej TYZACK J. HADDADI Faraneh DVORSKÝ Jan DAMBORSKÝ Jiří MAZURENKO Stanislav THORNTON J.M. BEDNÁŘ David

  Article in Periodical

  Journal of Cheminformatics, year: 2024, volume: 16, edition: 1, DOI

• PredictONCO: a web tool supporting decision-making in precision oncology by extending the bioinformatics predictions with advanced computing and machine learning

  ŠTOURAČ Jan BORKO Simeon KHAN Rayyan Tariq POKORNÁ Petra DOBIÁŠ Adam PLANAS IGLESIAS Joan MAZURENKO Stanislav RANGEL PAMPLONA PIZARRO PINTO José Gaspar SZOTKOWSKÁ Veronika ŠTĚRBA Jaroslav SLABÝ Ondřej DAMBORSKÝ Jiří BEDNÁŘ David

  Article in Periodical

  Briefings in Bioinformatics, year: 2024, volume: 25, edition: 1, DOI

• Visual Support for the Loop Grafting Workflow on Proteins

  OPÁLENÝ Filip ULBRICH Pavol PLANAS IGLESIAS Joan BYŠKA Jan ŠTOURAČ Jan BEDNÁŘ David FURMANOVÁ Katarína KOZLÍKOVÁ Barbora

  Article in Periodical

  IEEE Transactions on Visualization and Computer Graphics, year: 2024

2023

• pyCaverDock: Python implementation of the popular tool for analysis of ligand transport with advanced caching and batch calculation support

  VÁVRA Ondřej BERANEK Jakub ŠTOURAČ Jan SURKOVSKY Martin FILIPOVIČ Jiří DAMBORSKÝ Jiří MARTINOVIC Jan BEDNÁŘ David

  Article in Periodical

  Bioinformatics, year: 2023, volume: 39, edition: 8, DOI

2022

• CalFitter 2.0: Leveraging the power of singular value decomposition to analyse protein thermostability

  KUNKA Antonín LACKO David ŠTOURAČ Jan DAMBORSKÝ Jiří PROKOP Zbyněk MAZURENKO Stanislav

  Article in Periodical

  Nucleic acids research, year: 2022, volume: 50, edition: W1, DOI

• Caver Web 1.2

  MUSIL Miloš JEŽÍK Andrej HAMŠÍKOVÁ Marie ŠTOURAČ Jan GALGONEK Jakub VONDÁŠEK jiří BEDNÁŘ David DAMBORSKÝ Jiří

  Year: 2022

• Fully automated virtual screening pipeline of FDA-approved drugs using Caver Web

  MUSIL Miloš JEŽÍK Andrej HAMŠÍKOVÁ Marie ŠTOURAČ Jan GALGONEK Jakub EYRILMEZ Saltuk Mustafa VONDRASEK Jiri DAMBORSKÝ Jiří BEDNÁŘ David

  Article in Periodical

  Computational and Structural Biotechnology Journal, year: 2022, volume: 20, edition: November 2022, DOI

• LoopGrafter: a web tool for transplanting dynamical loops for protein engineering

  PLANAS IGLESIAS Joan OPÁLENÝ Filip ULBRICH Pavol ŠTOURAČ Jan SANUSI Zainab Kemi RANGEL PAMPLONA PIZARRO PINTO José Gaspar SMITH Andrea BYŠKA Jan DAMBORSKÝ Jiří KOZLÍKOVÁ Barbora BEDNÁŘ David

  Article in Periodical

  Nucleic acids research, year: 2022, volume: 50, edition: W1, DOI

• Nástroj LoopGrafter

  PLANAS IGLESIAS Joan OPÁLENÝ Filip ULBRICH Pavol ŠTOURAČ Jan SANUSI Zainab Kemi RANGEL PAMPLONA PIZARRO PINTO José Gaspar SCHENKMAYEROVÁ A. BYŠKA Jan DAMBORSKÝ Jiří KOZLÍKOVÁ Barbora BEDNÁŘ David

  Year: 2022, type: