A defining member of the new cysteine-cradle family is a transient aECM protein involved in signalling skin damage

Sonntag T, Omi S, Andreeva A, Pujol N.

2024

doi:10.1101/2024.04.11.589058.

Recruitment of trimeric eIF2 by phosphatase non-catalytic subunit PPP1R15B.

Fatalska A, Hodgson G, Freund SMV, Maslen SL, Morgan T, Thorkelsson SR, van Slegtenhorst M, Lorenz S, Andreeva A, Kaat LD, Bertolotti A.

Mol Cell, 2024

doi:10.1016/j.molcel.2023.12.011.

Uncovering new families and folds in the natural protein universe.

Durairaj J, Waterhouse AM, Mets T, Brodiazhenko T, Abdullah M, Studer G, Tauriello G, Akdel M, Andreeva A, Bateman A, Tenson T, Hauryliuk V, Schwede T, Pereira J.

Nature, 2023

doi:10.1038/s41586-023-06622-3.

Activation of the integrated stress response by inhibitors of its kinases.

Szaruga M, Janssen DA, de Miguel C, Hodgson G, Fatalska A, Pitera AP, Andreeva A, Bertolotti A.

Nat Commun, 2023

doi:10.1038/s41467-023-40823-8.

What is hidden in the darkness? Deep-learning assisted large-scale protein family curation uncovers novel protein families and folds

Durairaj J, Waterhouse AM, Mets T, Brodiazhenko T, Abdullah M, Studer G, Akdel M, Andreeva A, Bateman A, Tenson T, Tenson T, Hauryliuk V, Schwede T, Pereira J.

2023

doi:10.1101/2023.03.14.532539.

Structural validation and assessment of AlphaFold2 predictions for centrosomal and centriolar proteins and their complexes.

van Breugel M, Rosa E Silva I, Andreeva A.

Commun Biol, 2022

doi:10.1038/s42003-022-03269-0.

Molecular mechanisms underlying the role of the centriolar CEP164-TTBK2 complex in ciliopathies.

Rosa E Silva I, Binó L, Johnson CM, Rutherford TJ, Neuhaus D, Andreeva A, Čajánek L, van Breugel M.

Structure, 2022

doi:10.1016/j.str.2021.08.007.

Substrate recognition determinants of human eIF2α phosphatases.

Hodgson G, Andreeva A, Bertolotti A.

Open Biol, 2021

doi:10.1098/rsob.210205.

Deaminated purine bypass by DNA polymerase η.

Andreeva A.

Biochem J, 2021

doi:10.1042/bcj20200989.

Genome3D: integrating a collaborative data pipeline to expand the depth and breadth of consensus protein structure annotation.

Sillitoe I, Andreeva A, Blundell TL, Buchan DWA, Finn RD, Gough J, Jones D, Kelley LA, Paysan-Lafosse T, Lam SD, Murzin AG, Pandurangan AP, Salazar GA, Skwark MJ, Sternberg MJE, Velankar S, Orengo C.

Nucleic Acids Res, 2020

doi:10.1093/nar/gkz967.

The SCOP database in 2020: expanded classification of representative family and superfamily domains of known protein structures.

Andreeva A, Kulesha E, Gough J, Murzin AG.

Nucleic Acids Res, 2020

doi:10.1093/nar/gkz1064.

Mechanism of completion of peptidyltransferase centre assembly in eukaryotes.

Kargas V, Castro-Hartmann P, Escudero-Urquijo N, Dent K, Hilcenko C, Sailer C, Zisser G, Marques-Carvalho MJ, Pellegrino S, Wawiórka L, Freund SM, Wagstaff JL, Andreeva A, Faille A, Chen E, Stengel F, Bergler H, Warren AJ.

Elife, 2019

doi:10.7554/elife.44904.

Disease-Associated Mutations in CEP120 Destabilize the Protein and Impair Ciliogenesis.

Joseph N, Al-Jassar C, Johnson CM, Andreeva A, Barnabas DD, Freund SMV, Gergely F, van Breugel M.

Cell Rep, 2018

doi:10.1016/j.celrep.2018.04.100.

Direct binding of CEP85 to STIL ensures robust PLK4 activation and efficient centriole assembly.

Liu Y, Gupta GD, Barnabas DD, Agircan FG, Mehmood S, Wu D, Coyaud E, Johnson CM, McLaughlin SH, Andreeva A, Freund SMV, Robinson CV, Cheung SWT, Raught B, Pelletier L, van Breugel M.

Nat Commun, 2018

doi:10.1038/s41467-018-04122-x.

The Ciliopathy-Associated Cep104 Protein Interacts with Tubulin and Nek1 Kinase.

Al-Jassar C, Andreeva A, Barnabas DD, McLaughlin SH, Johnson CM, Yu M, van Breugel M.

Structure, 2017

doi:10.1016/j.str.2016.11.014.

Crystal Structure of a Group I Energy Coupling Factor Vitamin Transporter S Component in Complex with Its Cognate Substrate.

Josts I, Almeida Hernandez Y, Andreeva A, Tidow H.

Cell Chem Biol, 2016

doi:10.1016/j.chembiol.2016.06.008.

Lessons from making the Structural Classification of Proteins (SCOP) and their implications for protein structure modelling.

Andreeva A.

Biochem Soc Trans, 2016

doi:10.1042/bst20160053.

Consequences of point mutations in melanoma-associated antigen 4 (MAGE-A4) protein: Insights from structural and biophysical studies.

Hagiwara Y, Sieverling L, Hanif F, Anton J, Dickinson ER, Bui TT, Andreeva A, Barran PE, Cota E, Nikolova PV.

Sci Rep, 2016

doi:10.1038/srep25182.

Investigating Protein Structure and Evolution with SCOP2.

Andreeva A, Howorth D, Chothia C, Kulesha E, Murzin AG.

Curr Protoc Bioinformatics, 2015

doi:10.1002/0471250953.bi0126s49.

Genome3D: exploiting structure to help users understand their sequences.

Lewis TE, Sillitoe I, Andreeva A, Blundell TL, Buchan DW, Chothia C, Cozzetto D, Dana JM, Filippis I, Gough J, Jones DT, Kelley LA, Kleywegt GJ, Minneci F, Mistry J, Murzin AG, Ochoa-Montaño B, Oates ME, Punta M, Rackham OJ, Stahlhacke J, Sternberg MJ, Velankar S, Orengo C.

Nucleic Acids Res, 2015

doi:10.1093/nar/gku973.

Tracing the evolution of the p53 tetramerization domain.

Joerger AC, Wilcken R, Andreeva A.

Structure, 2014

doi:10.1016/j.str.2014.07.010.

SCOP2 prototype: a new approach to protein structure mining.

Andreeva A, Howorth D, Chothia C, Kulesha E, Murzin AG.

Nucleic Acids Res, 2014

doi:10.1093/nar/gkt1242.

Crystal structures of the CPAP/STIL complex reveal its role in centriole assembly and human microcephaly.

Cottee MA, Muschalik N, Wong YL, Johnson CM, Johnson S, Andreeva A, Oegema K, Lea SM, Raff JW, van Breugel M.

Elife, 2013

doi:10.7554/elife.01071.

Genome3D: a UK collaborative project to annotate genomic sequences with predicted 3D structures based on SCOP and CATH domains.

Lewis TE, Sillitoe I, Andreeva A, Blundell TL, Buchan DW, Chothia C, Cuff A, Dana JM, Filippis I, Gough J, Hunter S, Jones DT, Kelley LA, Kleywegt GJ, Minneci F, Mitchell A, Murzin AG, Ochoa-Montaño B, Rackham OJ, Smith J, Sternberg MJ, Velankar S, Yeats C, Orengo C.

Nucleic Acids Res, 2013

doi:10.1093/nar/gks1266.

A bimodular mechanism of calcium control in eukaryotes.

Tidow H, Poulsen LR, Andreeva A, Knudsen M, Hein KL, Wiuf C, Palmgren MG, Nissen P.

Nature, 2012

doi:10.1038/nature11539.

Classification of proteins: available structural space for molecular modeling.

Andreeva A.

Methods Mol Biol, 2012

doi:10.1007/978-1-61779-588-6_1.

Structures of SAS-6 suggest its organization in centrioles.

van Breugel M, Hirono M, Andreeva A, Yanagisawa HA, Yamaguchi S, Nakazawa Y, Morgner N, Petrovich M, Ebong IO, Robinson CV, Johnson CM, Veprintsev D, Zuber B.

Science, 2011

doi:10.1126/science.1199325.

Structural classification of proteins and structural genomics: new insights into protein folding and evolution.

Andreeva A, Murzin AG.

Acta Crystallogr Sect F Struct Biol Cryst Commun, 2010

doi:10.1107/s1744309110007177.

The structural basis for catalysis and substrate specificity of a rhomboid protease.

Vinothkumar KR, Strisovsky K, Andreeva A, Christova Y, Verhelst S, Freeman M.

EMBO J, 2010

doi:10.1038/emboj.2010.243.

Mapping the physical and functional interactions between the tumor suppressors p53 and BRCA2.

Rajagopalan S, Andreeva A, Rutherford TJ, Fersht AR.

Proc Natl Acad Sci U S A, 2010

doi:10.1073/pnas.1003689107.

Biophysical characterizations of human mitochondrial transcription factor A and its binding to tumor suppressor p53.

Wong TS, Rajagopalan S, Freund SM, Rutherford TJ, Andreeva A, Townsley FM, Petrovich M, Fersht AR.

Nucleic Acids Res, 2009

doi:10.1093/nar/gkp750.

Adaptive evolution of p53 thermodynamic stability.

Khoo KH, Andreeva A, Fersht AR.

J Mol Biol, 2009

doi:10.1016/j.jmb.2009.08.013.

Interaction between the transactivation domain of p53 and PC4 exemplifies acidic activation domains as single-stranded DNA mimics.

Rajagopalan S, Andreeva A, Teufel DP, Freund SM, Fersht AR.

J Biol Chem, 2009

doi:10.1074/jbc.m109.006429.

Solution structure of the U11-48K CHHC zinc-finger domain that specifically binds the 5' splice site of U12-type introns.

Tidow H, Andreeva A, Rutherford TJ, Fersht AR.

Structure, 2009

doi:10.1016/j.str.2008.11.013.

A fortuitous insight into a common mode of RNA recognition by the dsRNA-specific zinc fingers.

Andreeva A, Murzin AG.

Proc Natl Acad Sci U S A, 2008

doi:10.1073/pnas.0810994106.

A novel CHHC Zn-finger domain found in spliceosomal proteins and tRNA modifying enzymes.

Andreeva A, Tidow H.

Bioinformatics, 2008

doi:10.1093/bioinformatics/btn431.

Data growth and its impact on the SCOP database: new developments.

Andreeva A, Howorth D, Chandonia JM, Brenner SE, Hubbard TJ, Chothia C, Murzin AG.

Nucleic Acids Res, 2008

doi:10.1093/nar/gkm993.

Solution structure of ASPP2 N-terminal domain (N-ASPP2) reveals a ubiquitin-like fold.

Tidow H, Andreeva A, Rutherford TJ, Fersht AR.

J Mol Biol, 2007

doi:10.1016/j.jmb.2007.05.024.

SISYPHUS--structural alignments for proteins with non-trivial relationships.

Andreeva A, Prlić A, Hubbard TJ, Murzin AG.

Nucleic Acids Res, 2007

doi:10.1093/nar/gkl746.

Evolution of protein fold in the presence of functional constraints.

Andreeva A, Murzin AG.

Curr Opin Struct Biol, 2006

doi:10.1016/j.sbi.2006.04.003.

Core domain interactions in full-length p53 in solution.

Veprintsev DB, Freund SM, Andreeva A, Rutledge SE, Tidow H, Cañadillas JM, Blair CM, Fersht AR.

Proc Natl Acad Sci U S A, 2006

doi:10.1073/pnas.0511130103.

Solution structure of the C4 zinc finger domain of HDM2.

Yu GW, Allen MD, Andreeva A, Fersht AR, Bycroft M.

Protein Sci, 2006

doi:10.1110/ps.051927306.

Revised structure of the AbrB N-terminal domain unifies a diverse superfamily of putative DNA-binding proteins.

Bobay BG, Andreeva A, Mueller GA, Cavanagh J, Murzin AG.

FEBS Lett, 2005

doi:10.1016/j.febslet.2005.09.045.

SCOP database in 2004: refinements integrate structure and sequence family data.

Andreeva A, Howorth D, Brenner SE, Hubbard TJ, Chothia C, Murzin AG.

Nucleic Acids Res, 2004

doi:10.1093/nar/gkh039.

Assessment of the CASP4 fold recognition category.

Sippl MJ, Lackner P, Domingues FS, Prlić A, Malik R, Andreeva A, Wiederstein M.

Proteins, 2001

doi:10.1002/prot.10006.

Structure-based evaluation of sequence comparison and fold recognition alignment accuracy.

Domingues FS, Lackner P, Andreeva A, Sippl MJ.

J Mol Biol, 2000

doi:10.1006/jmbi.2000.3615.

Crystallization of type I chloramphenicol acetyltransferase: an approach based on the concept of ionic strength reducers.

Andreeva AE, Borissova BE, Mironova R, Glykos NM, Kotsifaki D, Ivanov I, Krysteva M, Kokkinidis M.

Acta Crystallogr D Biol Crystallogr, 2000

doi:10.1107/s090744499901481x.