doc. Mgr. David Bednář, Ph.D.

2020

• CaverDock: A Novel Method for the Fast Analysis of Ligand Transport

  FILIPOVIČ Jiří VÁVRA Ondřej PLHÁK Jan BEDNÁŘ David MARQUES Sérgio Manuel BREZOVSKÝ Jan MATYSKA Luděk DAMBORSKÝ Jiří

  Peer-reviewed scientific article

  IEEE/ACM Transactions on Computational Biology and Bioinformatics, year: 2020, volume: 17, edition: 5, DOI

2019

• Caver Web 1.0: identification of tunnels and channels in proteins and analysis of ligand transport

  ŠTOURAČ Jan VÁVRA Ondřej KOKKONEN Piia Pauliina FILIPOVIČ Jiří RANGEL PAMPLONA PIZARRO PINTO José Gaspar BREZOVSKÝ Jan DAMBORSKÝ Jiří BEDNÁŘ David

  Peer-reviewed scientific article

  Nucleic acids research, year: 2019, volume: 47, edition: W1, DOI

• CaverDock: a molecular docking-based tool to analyse ligand transport through protein tunnels and channels

  VÁVRA Ondřej FILIPOVIČ Jiří PLHÁK Jan BEDNÁŘ David MARQUES Sérgio Manuel BREZOVSKÝ Jan ŠTOURAČ Jan MATYSKA Luděk DAMBORSKÝ Jiří

  Peer-reviewed scientific article

  Bioinformatics, year: 2019, volume: 35, edition: 23, DOI

2018

• CalFitter: a web server for analysis of protein thermal denaturation data

  MAZURENKO Stanislav ŠTOURAČ Jan KUNKA Antonín NEDELJKOVIC S. BEDNÁŘ David PROKOP Zbyněk DAMBORSKÝ Jiří

  Peer-reviewed scientific article

  Nucleic Acids Research, year: 2018, volume: 46, edition: W1, DOI

• CAVER Analyst 2.0: Analysis and Visualization of Channels and Tunnels in Protein Structures and Molecular Dynamics Trajectories

  JURČÍK Adam BEDNÁŘ David BYŠKA Jan MARQUES Sérgio Manuel FURMANOVÁ Katarína DANIEL Lukáš KOKKONEN Piia Pauliina BREZOVSKÝ Jan STRNAD Ondřej ŠTOURAČ Jan PAVELKA Antonín MANAK Martin DAMBORSKÝ Jiří KOZLÍKOVÁ Barbora

  Peer-reviewed scientific article

  Bioinformatics, year: 2018, volume: 34, edition: 20, DOI

• Computer-assisted engineering of hyperstable fibroblast growth factor 2

  DVOŘÁK Pavel BEDNÁŘ David VAŇÁČEK Pavel BÁLEK Lukáš EISELLEOVÁ Lívia ŠTĚPÁNKOVÁ Veronika ŠEBESTOVÁ Eva BOSÁKOVÁ Michaela KONEČNÁ Žaneta MAZURENKO Stanislav KUNKA Antonín VÁŇOVÁ Tereza ZOUFALOVÁ Karolína CHALOUPKOVÁ Radka BREZOVSKÝ Jan KREJČÍ Pavel PROKOP Zbyněk DVOŘÁK Petr DAMBORSKÝ Jiří

  Peer-reviewed scientific article

  Biotechnology and Bioengineering, year: 2018, volume: 115, edition: 4, DOI

• Conformational changes allow processing of bulky substrates by a haloalkane dehalogenase with a small and buried active site

  KOKKONEN Piia Pauliina BEDNÁŘ David DOČKALOVÁ Veronika PROKOP Zbyněk DAMBORSKÝ Jiří

  Peer-reviewed scientific article

  Journal of Biological Chemistry, year: 2018, volume: 293, edition: 29, DOI

• Evolutionary Analysis As a Powerful Complement to Energy Calculations for Protein Stabilization

  BEERENS Koen MAZURENKO Stanislav KUNKA Antonín MARQUES Sérgio Manuel HANSEN N. MUSIL Miloš CHALOUPKOVÁ Radka WATERMAN Jitka BREZOVSKÝ Jan BEDNÁŘ David PROKOP Zbyněk DAMBORSKÝ Jiří

  Peer-reviewed scientific article

  ACS Catalysis, year: 2018, volume: 8, edition: 10, DOI

• HotSpot Wizard 3.0: web server for automated design of mutations and smart libraries based on sequence input information

  SUMBALOVÁ Lenka ŠTOURAČ Jan MARTÍNEK Tomáš BEDNÁŘ David DAMBORSKÝ Jiří

  Peer-reviewed scientific article

  Nucleic Acids Research, year: 2018, volume: 46, edition: W1, DOI

• Molecular Gating of an Engineered Enzyme Captured in Real Time

  KOKKONEN Piia Pauliina SYKORA J. PROKOP Zbyněk GHOSE A. BEDNÁŘ David AMARO M. BEERENS Koen NEVOLOVÁ Šárka SLÁNSKÁ Michaela BREZOVSKÝ Jan DAMBORSKÝ Jiří HOF M.

  Peer-reviewed scientific article

  Journal of the American Chemical Society, year: 2018, volume: 140, edition: 51, DOI