Ресурсы
Mirrors of Protein Data Banks
- PDB (The base of protein structures. Syncronization with WorldWide Protein Data Bank)
- HSSP
- FSSP
- DSSP (DSSP, program [Kabsch and Sander (1983)Biopolymers, 22, 2577–2637] for localization of secondary structure elements and energy of hydrogen connections in main chain)
- SCOP (Structure Classification of Proteins)
Our Resources
- PDB (PDB в обработке М.Лобанова — ручное обновление, исправление ошибок)
- IsUnstruct предсказание неструктурированных участков белковой цепи по аминокислотной последовательности
- OGU предсказание неструктурированных участков белковой цепи по аминокислотной последовательности
- Compact база данных по кинетике сворачивания белковых структур
Nucleic Acids Res. 2009 Jan; 37(Database issue):D342-6 - KineticDB база данных по кинетике сворачивания белковых структур
Nucleic Acids Res. 2009 Jan; 37(Database issue):D342-6 - Fold Amyloid Base база данных амилоидогенных фрагментов, известных из экспериментальных данных
- Fold Amyloid сервер для предсказания амилоидогенных участков по аминокислотной последовательности
- ComSin base of protein structures in bound (Complex) and unbound (Single) states in relation to their intrinsic disorder.
Nucleic Acids Res. 2010 Jan;38(Database issue): D283-7. http://www.pathguide.org/fullrecord.php?DBID=321 - OG3 предсказание границ доменов по аминокислотной последовательности
- BM_OG предсказание границ доменов по аминокислотной последовательности
- H-Protection предсказание защищенности аминокислотных остатков от водородно-дейтериевого обмена
- Thermo- and mesophilic Database of structural pairs of proteins from thermo- and mesophilic organisms
- Phi-values Experimentally measured and theoretically predicted phi-values.
Pereyaslavets LB, Sokolovsky IV, Galzitskaya OV. FoldNucleus: web server for the prediction of RNA and protein folding nuclei from their 3D structures. Bioinformatics. 2015 Oct 15;31(20):3374-6. doi: 10.1093/bioinformatics/btv369. - Ideal-base Database of 3D structures of «ideally» folded proteins.
Garbuzynskiy S.O., Lobanov M.Yu., Galzitskaya O.V. (2004). To be folded or to be unfolded? Protein Science, v.13 (11), pp. 2871-2877. - scop_1.61 Database of 3D structures with identity below 80%.
Galzitskaya O.V., Garbuzynskiy S.O., Lobanov M.Yu. (2006). Prediction of natively unfolded regions in protein chains. Molecular Biology, v.40 (2), pp. 298-304. - Natively unfolded Database of natively unfolded proteins.
Galzitskaya O.V., Garbuzynskiy S.O., Lobanov M.Yu. (2006). Prediction of natively unfolded regions in protein chains. Molecular Biology, v.40 (2), pp. 298-304. - Folded 559 Database of 559 globular proteins.
Galzitskaya O.V., Garbuzynskiy S.O., Lobanov M.Yu. (2006). Prediction of natively unfolded regions in protein chains. Molecular Biology, v.40 (2), pp. 298-304. - Folded 80 Database of 80 globular proteins.
Galzitskaya O.V., Garbuzynskiy S.O., Lobanov M.Yu. (2006). Prediction of natively unfolded regions in protein chains. Molecular Biology, v.40 (2), pp. 298-304. - HRAP Database HRAP.
Nucleic Acids Res. 2014 Jan;42(Database issue):D273-8. doi: 10.1093/nar/gkt927. Lobanov MY, Sokolovskiy IV, Galzitskaya OV. HRaP: database of occurrence of HomoRepeats and patterns in proteomes. - HRADIS Database HRADIS.
Lobanov MY, Klus P, Sokolovsky IV, Tartaglia GG, Galzitskaya OV. Non-random distribution of homo-repeats: links with biological functions and human diseases, Sci Rep. 2016 Jun 3;6:26941. doi: 10.1038/srep26941. - foldnucleus Server foldnucleus.
Pereyaslavets LB, Sokolovsky IV, Galzitskaya OV. Bioinformatics. 2015 Oct 15;31(20):3374-6. doi: 10.1093/bioinformatics/btv369. FoldNucleus: web server for the prediction of RNA and protein folding nuclei from their 3D structures. - foldhandedness Server foldhandedness.
Pereyaslavets LB, Glyakina AV, Dovidchenko NV, Sokolovskiy IV, Galzitskaya OV. What handedness and angles between helices has the studied three-helical protein domain? Bioinformatics. 2015 Mar 15;31(6):963-5. doi: 10.1093/bioinformatics/btu737. - Clustered PDB Server Clustered PDB.
Lobanov M.Yu., Galzitskaya O.V., Likhachev I.V. - Antimicrob-I Prediction of antibacterial regions in the protein chain.
Lobanov M.Yu., Galzitskaya O.V., Likhachev I.V. - Antimicrob-II Prediction of antibacterial regions in the protein chain.
Lobanov M.Yu., Galzitskaya O.V., Likhachev I.V. - C.A.R.P. Contacts of Aromatic Residues in Proteins.
Galzitskaya O.V., Lobanov M.Yu., Likhachev I.V. - Production Scale
M.Y. Lobanov, M.V. Slizen, N.V. Dovidchenko, A.V. Panfilov, A.A. Surin, I.V. Likhachev, O.V. Galzitskaya. Comparison of deep learning models with simple method to assess the problem of antimicrobial peptides prediction. Molecular Informatics 2023, 42, e202200181