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

  Article in Periodical

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

• Decoding the intricate network of molecular interactions of a hyperstable engineered biocatalyst

  MARKOVÁ Klára CHMELOVÁ Klaudia MARQUES Sérgio Manuel CARPENTIER Philippe BEDNÁŘ David DAMBORSKÝ Jiří MAREK Martin

  Article in Periodical

  Chemical Science, year: 2020, volume: 11, edition: 41, DOI

• DockVis: Visual Analysis of Molecular Docking Trajectories

  FURMANOVÁ Katarína VÁVRA Ondřej KOZLÍKOVÁ Barbora DAMBORSKÝ Jiří VONÁSEK Vojtěch BEDNÁŘ David BYŠKA Jan

  Article in Periodical

  Computer Graphics Forum, year: 2020, volume: 39, edition: 6, DOI

• EnzymeMiner: automated mining of soluble enzymes with diverse structures, catalytic properties and stabilities

  HON Jiří BORKO Simeon ŠTOURAČ Jan PROKOP Zbyněk ZENDULKA Jaroslav BEDNÁŘ David MARTINEK Tomas DAMBORSKÝ Jiří

  Article in Periodical

  Nucleic acids research, year: 2020, volume: 48, edition: W1, DOI

• Structures of hyperstable ancestral haloalkane dehalogenases show restricted conformational dynamics

  BABKOVÁ Petra DUNAJOVÁ Zuzana CHALOUPKOVÁ Radka DAMBORSKÝ Jiří BEDNÁŘ David MAREK Martin

  Article in Periodical

  Computational and Structural Biotechnology Journal, year: 2020, volume: 18, edition: 2020, DOI

• The impact of tunnel mutations on enzymatic catalysis depends on the tunnel-substrate complementarity and the rate-limiting step

  KOKKONEN Piia Pauliina SLÁNSKÁ Michaela DOČKALOVÁ Veronika RANGEL PAMPLONA PIZARRO PINTO José Gaspar MARQUEZ SANCHEZ - CARNERERO Esther Maria DAMBORSKÝ Jiří KLÁN Petr PROKOP Zbyněk BEDNÁŘ David

  Article in Periodical

  Computational and Structural Biotechnology Journal, year: 2020, volume: 18, edition: 2020, DOI

• Thermostable FGF2 Polypeptide, Use Thereof

  DVOŘÁK Petr KREJČÍ Pavel BÁLEK Lukáš EISELLEOVÁ Lívia KONEČNÁ Žaneta DVOŘÁK Pavel BEDNÁŘ David BREZOVSKÝ Jan ŠEBESTOVÁ Eva CHALOUPKOVÁ Radka ŠTĚPÁNKOVÁ Veronika VAŇÁČEK Pavel PROKOP Zbyněk DAMBORSKÝ Jiří BOSÁKOVÁ Michaela

  Patent

  Publisher: European Patent Office, state: Germany, patent's number: EP3380508, year: 2020

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

  Article in Periodical

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

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

  ŠTOURAČ Jan VAVRA O. KOKKONEN Piia Pauliina FILIPOVIČ Jiří FONSECA PINTO Gabriela Filipa SCHENKMAYEROVÁ Andrea DAMBORSKÝ Jiří BEDNÁŘ David

  Conference abstract

  Year: 2019, type: Conference abstract

• 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

  Article in Periodical

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