P
Petr Škoda
Researcher at Charles University in Prague
Publications - 34
Citations - 498
Petr Škoda is an academic researcher from Charles University in Prague. The author has contributed to research in topics: Virtual screening & Linked data. The author has an hindex of 9, co-authored 34 publications receiving 285 citations. Previous affiliations of Petr Škoda include University of Economics, Prague.
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Journal ArticleDOI
PrankWeb: a web server for ligand binding site prediction and visualization.
TL;DR: PrankWeb is an online resource providing an interface to P2Rank, a state-of-the-art method for ligand binding site prediction based on the prediction of local chemical neighborhood ligandability centered on points placed on a solvent-accessible protein surface.
Journal ArticleDOI
PDBe-KB: a community-driven resource for structural and functional annotations
Mihaly Varadi,John M. Berrisford,Mandar Deshpande,Sreenath Nair,Aleksandras Gutmanas,David R. Armstrong,Lukáš Pravda,Bissan Al-Lazikani,Stephen Anyango,Geoffrey J. Barton,Karel Berka,Tom L. Blundell,Neera Borkakoti,Jose M. Dana,Sayoni Das,Sucharita Dey,Patrizio Di Micco,Franca Fraternali,Toby J. Gibson,Manuela Helmer-Citterich,David Hoksza,David Hoksza,Liang-Chin Huang,Rishabh Jain,Harry Jubb,Christos C. Kannas,Natarajan Kannan,Jaroslav Koča,Radoslav Krivak,Manjeet Kumar,Emmanuel D. Levy,Fábio Madeira,Mallur S. Madhusudhan,Henry J Martell,Stuart A. MacGowan,Jake E McGreig,Saqib Mir,Abhik Mukhopadhyay,Luca Parca,Typhaine Paysan-Lafosse,Leandro G Radusky,António J. M. Ribeiro,Luis Serrano,Ian Sillitoe,Gulzar Singh,Petr Škoda,Radka Svobodová,Jonathan D. Tyzack,Alfonso Valencia,Eloy Villasclaras Fernandez,Wim F. Vranken,Mark N. Wass,Janet M. Thornton,Michael J.E. Sternberg,Christine A. Orengo,Sameer Velankar +55 more
TL;DR: The guidelines of this collaborative effort, the current status of contributed data, and the PDBe-KB infrastructure, which includes the data exchange format, the deposition system for added value annotations, the distributable database containing the assembledData, and programmatic access endpoints are described.
Journal ArticleDOI
Molpher: a software framework for systematic chemical space exploration.
TL;DR: Molpher is an open-source software framework for the design of virtual chemical libraries focused on a particular mechanistic class of compounds that produces a path of structurally-related compounds through a process the authors term ‘molecular morphing’.
Posted ContentDOI
PrankWeb: web server for ligand binding-site prediction and visualization
TL;DR: PrankWeb is an online resource providing an interface to P2Rank, a state-of-the-art ligand binding site prediction method which is based on the prediction of ligandability of local chemical neighborhoods centered on points placed on a solvent accessible surface of a protein.
Journal ArticleDOI
PDBe-KB: collaboratively defining the biological context of structural data
Mihaly Varadi,Stephen Anyango,David R. Armstrong,John M. Berrisford,Preeti Choudhary,Mandar Deshpande,Nurul Nadzirin,Sreenath Nair,Lukáš Pravda,Ahsan Tanweer,Bissan Al-Lazikani,Claudia Andreini,Geoffrey J. Barton,David Bednar,Karel Berka,Tom L. Blundell,Kelly P Brock,José María Carazo,Jiri Damborsky,Alessia David,Sucharita Dey,Roland L. Dunbrack,Juan Fernandez Recio,Franca Fraternali,Toby J. Gibson,Manuela Helmer-Citterich,David Hoksza,Thomas A. Hopf,David Jakubec,Natarajan Kannan,Radoslav Krivak,Manjeet Kumar,Emmanuel D. Levy,Nir London,Jose Ramon Macias,Madhusudhan M Srivatsan,Debora S. Marks,Lennart Martens,Stuart A McGowan,Jake E McGreig,Vivek Modi,R. Gonzalo Parra,Gerardo Pepe,Damiano Piovesan,Jaime Prilusky,Valeria Putignano,Leandro G Radusky,Pathmanaban Ramasamy,Atilio O Rausch,Nathalie Reuter,Luis A Rodriguez,Nathan J Rollins,Antonio Rosato,Pawel Rubach,Luis Serrano,Gulzar Singh,Petr Škoda,Carlos Oscar S. Sorzano,Jan Stourac,Joanna I. Sulkowska,Radka Svobodová,Natalia Tichshenko,Silvio C. E. Tosatto,Wim F. Vranken,Mark N. Wass,Dandan Xue,Daniel Zaidman,Janet M. Thornton,Michael J.E. Sternberg,Christine A. Orengo,Sameer Velankar +70 more