Publications

2024

• Procházka, D; Slanináková, T; Olha, J; Rosinec, A; Gresová, K; Jánosová, M; Cillík, J; Porubská, J; Svobodová, R; Dohnal, V; Antol, M, 2024: AlphaFind: discover structure similarity across the proteome in AlphaFold DB. NUCLEIC ACIDS RESEARCH 52(W1), doi: 10.1093/nar/gkae397
• Vollmar, M; Tirunagari, S; Harrus, D; Armstrong, D; Gáborová, R; Gupta, D; Afonso, MQL; Evans, G; Velankar, S, 2024: Dataset from a human-in-the-loop approach to identify functionally important protein residues from literature. SCIENTIFIC DATA 11(1), doi: 10.1038/s41597-024-03841-9

2023

• Appasamy, SD; Berrisford, J; Gaborova, R; Nair, S; Anyango, S; Grudinin, S; Deshpande, M; Armstrong, D; Pidruchna, I; Ellaway, JIJ; Leines, GD; Gupta, D; Harrus, D; Varadi, M; Velankar, S, 2023: Annotating Macromolecular Complexes in the Protein Data Bank: Improving the FAIRness of Structure Data. SCIENTIFIC DATA 10(1), doi: 10.1038/s41597-023-02778-9
• Schindler, O; Berka, K; Cantara, A; Krenek, A; Tichy, D; Racek, T; Svobodová, R, 2023: αCharges: partial atomic charges for AlphaFold structures in high quality. NUCLEIC ACIDS RESEARCH 51(W1), p. W11 - W16, doi: 10.1093/nar/gkad349
• Chareshneu, A; Midlik, A; Ionescu, CM; Rose, A; Horsky, V; Cantara, A; Svobodová, R; Berka, K; Sehnal, D, 2023: Mol* Volumes and Segmentations: visualization and interpretation of cell imaging data alongside macromolecular structure data and biological annotations. NUCLEIC ACIDS RESEARCH 51(W1), p. W326 - W330, doi: 10.1093/nar/gkad411
• Spackova, A; Vavra, O; Racek, T; Bazgier, V; Sehnal, D; Damborsky, J; Svobodova, R; Bednar, D; Berka, K, 2023: ChannelsDB 2.0: a comprehensive database of protein tunnels and pores in AlphaFold era. NUCLEIC ACIDS RESEARCH , doi: 10.1093/nar/gkad1012
• Turner, J; Abbott, S; Fonseca, N; Carrijo, L; Duraisamy, AK; Salih, O; Wang, Z; Kleywegt, GJ; Morris, KL; Patwardhan, A; Burley, SK; Crichlow, G; Feng, ZK; Flatt, JW; Ghosh, S; Hudson, BP; Lawson, CL; Liang, YH; Peisach, E; Persikova, I; Sekharan, M; Shao, CH; Young, J; Velankar, S; Armstrong, D; Bage, M; Bueno, WM; Evans, G; Gaborova, R; Ganguly, S; Gupta, D; Harrus, D; Tanweer, A; Bansal, M; Rangannan, V; Kurisu, G; Cho, H; Ikegawa, Y; Kengaku, Y; Kim, JY; Niwa, S; Sato, J; Takuwa, A; Yu, J; Hoch, JC; Baskaran, K; Xu, WQ; Zhang, WZ; Ma, XD, 2023: EMDB-the Electron Microscopy Data Bank. NUCLEIC ACIDS RESEARCH , doi: 10.1093/nar/gkad1019

2022

• Varadi, M; Anyango, S; Armstrong, D; Berrisford, J; Choudhary, P; Deshpande, M; Nadzirin, N; Nair, SS.; Pravda, L; Tanweer, A; Al-Lazikani, ; Andreini, C; Barton, GJ; Bednar, D; Berka, K; Blundell, T; Brock, K.; Maria Carazo, J; Damborsky, J; David, A; Dey, S; Dunbrack, R; Fernandez RJ; Fraternali, F; Gibson, T; Helmer-Citterich, M; Hoksza, D; Hopf, T; Jakubec, D; Kannan, N; Krivak, R; Kumar, M; Levy, ED; Lon don,N; Macias, JR; Srivatsan, MM; Marks, DS; Martens, L; McGowan, SA; McGreig, JE; Modi, V; Gonzalo PR; Pepe, G; Piovesan, D; Prilusky, J; Putignano, V; Radusky, LG; Ramasamy, P; Rausch, AO; Reuter, N; Rodriguez, LA; Rollins, NJ; Rosato, A; Serrano, L; Singh, G; Skoda, P; Sorzano, COS; Stourac, J; Sulkowska, JI; Svobodova, R; Tichshenko, N; Tosatto, SCE; Vranken, W; Wass, MN; Xue, D; Zaidman, D; Thornton, J; Sternberg, M; Orengo, C; Velankar, S, 2022: PDBe-KB: collaboratively defining the biological context of structural data. NUCLEIC ACIDS RESEARCH 50(D1), p. D534 - D542, doi: 10.1093/nar/gkab988
• Varadi, M; Anyango, S; Appasamy, SD; Armstrong, D; Bage, M; Berrisford, J; Choudhary, P; Bertoni, D; Deshpande, M; Leines, GD; Ellaway, J; Evans, G; Gaborova, R; Gupta, D; Gutmanas, A; Harrus, D; Kleywegt, GJ; Bueno, WM; Nadzirin, N; Nair, S; Pravda, L; Afonso, MQL; Sehnal, D; Tanweer, A; Tolchard, J; Abrams, C; Dunlop, R; Velankar, S, 2022: PDBe and PDBe-KB: Providing high-quality, up-to-date and integrated resources of macromolecular structures to support basic and applied research and education. PROTEIN SCIENCE 31(10), doi: 10.1002/pro.4439
• Midlik, A; Varekova, IH; Hutar, J; Chareshneu, A; Berka, K; Svobodova, R, 2022: OverProt: secondary structure consensus for protein families. BIOINFORMATICS 38(14), p. 3648 - 3650, doi: 10.1093/bioinformatics/btac384

2021

• Varekova, IH; Hutar, J; Midlik, A; Horsky, V; Hladka, E; Svobodova, R; Berka, K, 2021: 2DProts: database of family-wide protein secondary structure diagrams. BIOINFORMATICS 37(23), p. 4599 - 4601, doi: 10.1093/bioinformatics/btab505