| Year |
Citation |
Score |
| 2024 |
Beton JG, Mulvaney T, Cragnolini T, Topf M. Cryo-EM structure and B-factor refinement with ensemble representation. Nature Communications. 15: 444. PMID 38200043 DOI: 10.1038/s41467-023-44593-1 |
0.33 |
|
| 2023 |
Sweeney A, Mulvaney T, Maiorca M, Topf M. ChemEM: Flexible Docking of Small Molecules in Cryo-EM Structures. Journal of Medicinal Chemistry. PMID 38157562 DOI: 10.1021/acs.jmedchem.3c01134 |
0.318 |
|
| 2023 |
Mulvaney T, Kretsch RC, Elliott L, Beton JG, Kryshtafovych A, Rigden DJ, Das R, Topf M. CASP15 cryo-EM protein and RNA targets: Refinement and analysis using experimental maps. Proteins. 91: 1935-1951. PMID 37994556 DOI: 10.1002/prot.26644 |
0.334 |
|
| 2023 |
Malhotra S, Mulvaney T, Cragnolini T, Sidhu H, Joseph AP, Beton JG, Topf M. RIBFIND2: Identifying rigid bodies in protein and nucleic acid structures. Nucleic Acids Research. PMID 37670532 DOI: 10.1093/nar/gkad721 |
0.325 |
|
| 2023 |
Mulvaney T, Kretsch RC, Elliott L, Beton J, Kryshtafovych A, Rigden DJ, Das R, Topf M. CASP15 cryoEM protein and RNA targets: refinement and analysis using experimental maps. Biorxiv : the Preprint Server For Biology. PMID 37609268 DOI: 10.1101/2023.08.07.552287 |
0.321 |
|
| 2021 |
Cragnolini T, Kryshtafovych A, Topf M. Cryo-EM targets in CASP14. Proteins. PMID 34398978 DOI: 10.1002/prot.26216 |
0.32 |
|
| 2021 |
Malhotra S, Joseph AP, Thiyagalingam J, Topf M. Assessment of protein-protein interfaces in cryo-EM derived assemblies. Nature Communications. 12: 3399. PMID 34099703 DOI: 10.1038/s41467-021-23692-x |
0.309 |
|
| 2021 |
Cragnolini T, Sweeney A, Topf M. Automated Modeling and Validation of Protein Complexes in Cryo-EM Maps. Methods in Molecular Biology (Clifton, N.J.). 2215: 189-223. PMID 33368005 DOI: 10.1007/978-1-0716-0966-8_9 |
0.327 |
|
| 2020 |
Sinnott M, Malhotra S, Madhusudhan MS, Thalassinos K, Topf M. Combining Information from Crosslinks and Monolinks in the Modeling of Protein Structures. Structure (London, England : 1993). PMID 32531204 DOI: 10.1016/J.Str.2020.05.012 |
0.68 |
|
| 2020 |
Atherton J, Jiang K, Stangier MM, Luo Y, Hua S, Houben K, van Hooff JJE, Joseph AP, Scarabelli G, Grant BJ, Roberts AJ, Topf M, Steinmetz MO, Baldus M, Moores CA, et al. Author Correction: A structural model for microtubule minus-end recognition and protection by CAMSAP proteins. Nature Structural & Molecular Biology. PMID 32355336 DOI: 10.1038/S41594-020-0382-Z |
0.353 |
|
| 2020 |
Peña A, Sweeney A, Cook AD, Topf M, Moores CA. Structure of Microtubule-Trapped Human Kinesin-5 and Its Mechanism of Inhibition Revealed Using Cryoelectron Microscopy. Structure (London, England : 1993). PMID 32084356 DOI: 10.1016/J.Str.2020.01.013 |
0.325 |
|
| 2020 |
Joseph AP, Lagerstedt I, Jakobi A, Burnley T, Patwardhan A, Topf M, Winn M. Comparing Cryo-EM Reconstructions and Validating Atomic Model Fit Using Difference Maps. Journal of Chemical Information and Modeling. PMID 32043355 DOI: 10.1021/Acs.Jcim.9B01103 |
0.427 |
|
| 2019 |
Ignatiou A, Brasilès S, El Sadek Fadel M, Bürger J, Mielke T, Topf M, Tavares P, Orlova EV. Structural transitions during the scaffolding-driven assembly of a viral capsid. Nature Communications. 10: 4840. PMID 31649265 DOI: 10.1038/S41467-019-12790-6 |
0.346 |
|
| 2019 |
Kryshtafovych A, Malhotra S, Monastyrskyy B, Cragnolini T, Joseph AP, Chiu W, Topf M. Cryo-EM targets in CASP13: overview and evaluation of results. Proteins. PMID 31576602 DOI: 10.1002/Prot.25817 |
0.425 |
|
| 2019 |
Malhotra S, Träger S, Dal Peraro M, Topf M. Modelling structures in cryo-EM maps. Current Opinion in Structural Biology. 58: 105-114. PMID 31394387 DOI: 10.1016/J.Sbi.2019.05.024 |
0.456 |
|
| 2019 |
Hernández Durán A, Greco TM, Vollmer B, Cristea IM, Grünewald K, Topf M. Protein interactions and consensus clustering analysis uncover insights into herpesvirus virion structure and function relationships. Plos Biology. 17: e3000316. PMID 31199794 DOI: 10.1371/Journal.Pbio.3000316 |
0.327 |
|
| 2019 |
Topf M. Modeling Protein Monomers and Complexes using Restraints from Crosslinking Mass Spectrometry Biophysical Journal. 116. DOI: 10.1016/J.Bpj.2018.11.1790 |
0.308 |
|
| 2019 |
Cook AD, Roberts AJ, Topf M, Moores CA. The Cryo-EM Structure and Activity of Kinesin-5 from Plasmodium falciparum: Mechanistic Lessons from a Parasite Kinesin Biophysical Journal. 116: 308a. DOI: 10.1016/J.Bpj.2018.11.1671 |
0.3 |
|
| 2018 |
Menny A, Serna M, Boyd CM, Gardner S, Joseph AP, Morgan BP, Topf M, Brooks NJ, Bubeck D. CryoEM reveals how the complement membrane attack complex ruptures lipid bilayers. Nature Communications. 9: 5316. PMID 30552328 DOI: 10.2210/Pdb6H04/Pdb |
0.327 |
|
| 2018 |
Bullock JMA, Sen N, Thalassinos K, Topf M. Modeling Protein Complexes Using Restraints from Crosslinking Mass Spectrometry. Structure (London, England : 1993). PMID 29804821 DOI: 10.1016/J.Str.2018.04.016 |
0.383 |
|
| 2018 |
Bullock JMA, Thalassinos K, Topf M. Jwalk and MNXL web server: model validation using restraints from crosslinking mass spectrometry. Bioinformatics (Oxford, England). 34: 3584-3585. PMID 29741581 DOI: 10.1093/Bioinformatics/Bty366 |
0.337 |
|
| 2018 |
Newcombe J, Chatzidaki A, Sheppard TD, Topf M, Millar NS. Diversity of Nicotinic Acetylcholine Receptor Positive Allosteric Modulators Revealed by Mutagenesis and a Revised Structural Model. Molecular Pharmacology. 93: 128-140. PMID 29196491 DOI: 10.1124/Mol.117.110551 |
0.347 |
|
| 2018 |
Atherton J, Jiang K, Stangier M, Luo Y, Hua S, Houben K, Scarabelli G, Joseph A, Roberts A, Grant B, Topf M, Steinmetz M, Baldus M, Akhmanova A, Moores C. Structural Model for Preferential Microtubule Minus End Binding by CAMSAP CKK Domains Biophysical Journal. 114: 507a-508a. DOI: 10.1016/J.Bpj.2017.11.2773 |
0.338 |
|
| 2017 |
Atherton J, Jiang K, Stangier MM, Luo Y, Hua S, Houben K, van Hooff JJE, Joseph AP, Scarabelli G, Grant BJ, Roberts AJ, Topf M, Steinmetz MO, Baldus M, Moores CA, et al. A structural model for microtubule minus-end recognition and protection by CAMSAP proteins. Nature Structural & Molecular Biology. PMID 28991265 DOI: 10.1038/Nsmb.3483 |
0.344 |
|
| 2017 |
Deville C, Carroni M, Franke KB, Topf M, Bukau B, Mogk A, Saibil HR. Structural pathway of regulated substrate transfer and threading through an Hsp100 disaggregase. Science Advances. 3: e1701726. PMID 28798962 DOI: 10.1126/Sciadv.1701726 |
0.331 |
|
| 2017 |
Joseph AP, Polles G, Alber F, Topf M. Integrative modelling of cellular assemblies. Current Opinion in Structural Biology. 46: 102-109. PMID 28735107 DOI: 10.1016/J.Sbi.2017.07.001 |
0.383 |
|
| 2017 |
Joseph AP, Lagerstedt I, Patwardhan A, Topf M, Winn M. Improved metrics for comparing structures of macromolecular assemblies determined by 3D electron-microscopy. Journal of Structural Biology. PMID 28552721 DOI: 10.1016/J.Jsb.2017.05.007 |
0.387 |
|
| 2016 |
Ashford P, Hernandez A, Greco TM, Buch A, Sodeik B, Cristea IM, Grunewald K, Shepherd A, Topf M. HVint: A strategy for identifying novel protein-protein interactions in herpes simplex virus type 1. Molecular & Cellular Proteomics : McP. PMID 27384951 DOI: 10.1074/Mcp.M116.058552 |
0.318 |
|
| 2016 |
Bullock JM, Schwab J, Thalassinos K, Topf M. The importance of non-accessible crosslinks and solvent accessible surface distance in modelling proteins with restraints from crosslinking mass spectrometry. Molecular & Cellular Proteomics : McP. PMID 27150526 DOI: 10.1074/Mcp.M116.058560 |
0.365 |
|
| 2016 |
Zeev-Ben-Mordehai T, Vasishtan D, Hernández Durán A, Vollmer B, White P, Prasad Pandurangan A, Siebert CA, Topf M, Grünewald K. Two distinct trimeric conformations of natively membrane-anchored full-length herpes simplex virus 1 glycoprotein B. Proceedings of the National Academy of Sciences of the United States of America. PMID 27035968 DOI: 10.1073/Pnas.1523234113 |
0.344 |
|
| 2016 |
Joseph AP, Malhotra S, Burnley T, Wood C, Clare DK, Winn M, Topf M. Refinement of atomic models in high resolution EM reconstructions using Flex-EM and local assessment. Methods (San Diego, Calif.). PMID 26988127 DOI: 10.1016/J.Ymeth.2016.03.007 |
0.435 |
|
| 2015 |
Pandurangan AP, Vasishtan D, Alber F, Topf M. γ-TEMPy: Simultaneous Fitting of Components in 3D-EM Maps of Their Assembly Using a Genetic Algorithm. Structure (London, England : 1993). 23: 2365-76. PMID 26655474 DOI: 10.1016/J.Str.2015.10.013 |
0.738 |
|
| 2015 |
Farabella I, Vasishtan D, Joseph AP, Pandurangan AP, Sahota H, Topf M. TEMPy: a Python library for assessment of three-dimensional electron microscopy density fits. Journal of Applied Crystallography. 48: 1314-1323. PMID 26306092 DOI: 10.1107/S1600576715010092 |
0.743 |
|
| 2015 |
Sali A, Berman HM, Schwede T, Trewhella J, Kleywegt G, Burley SK, Markley J, Nakamura H, Adams P, Bonvin AM, Chiu W, Peraro MD, Di Maio F, Ferrin TE, Grünewald K, ... ... Topf M, et al. Outcome of the First wwPDB Hybrid/Integrative Methods Task Force Workshop. Structure (London, England : 1993). PMID 26095030 DOI: 10.1016/J.Str.2015.05.013 |
0.512 |
|
| 2015 |
Lukoyanova N, Kondos SC, Farabella I, Law RH, Reboul CF, Caradoc-Davies TT, Spicer BA, Kleifeld O, Traore DA, Ekkel SM, Voskoboinik I, Trapani JA, Hatfaludi T, Oliver K, Hotze EM, ... ... Topf M, et al. Conformational changes during pore formation by the perforin-related protein pleurotolysin. Plos Biology. 13: e1002049. PMID 25654333 DOI: 10.1371/Journal.Pbio.1002049 |
0.414 |
|
| 2014 |
Leung C, Dudkina NV, Lukoyanova N, Hodel AW, Farabella I, Pandurangan AP, Jahan N, Pires Damaso M, Osmanovi? D, Reboul CF, Dunstone MA, Andrew PW, Lonnen R, Topf M, Saibil HR, et al. Stepwise visualization of membrane pore formation by suilysin, a bacterial cholesterol-dependent cytolysin. Elife. 3: e04247. PMID 25457051 DOI: 10.7554/Elife.04247 |
0.725 |
|
| 2014 |
Mortensen M, Iqbal F, Pandurangan AP, Hannan S, Huckvale R, Topf M, Baker JR, Smart TG. Photo-antagonism of the GABAA receptor. Nature Communications. 5: 4454. PMID 25072879 DOI: 10.1038/Ncomms5454 |
0.674 |
|
| 2014 |
Pandurangan AP, Shakeel S, Butcher SJ, Topf M. Combined approaches to flexible fitting and assessment in virus capsids undergoing conformational change. Journal of Structural Biology. 185: 427-39. PMID 24333899 DOI: 10.1016/J.Jsb.2013.12.003 |
0.756 |
|
| 2013 |
Thalassinos K, Pandurangan AP, Xu M, Alber F, Topf M. Conformational States of macromolecular assemblies explored by integrative structure calculation. Structure (London, England : 1993). 21: 1500-8. PMID 24010709 DOI: 10.1016/J.Str.2013.08.006 |
0.733 |
|
| 2013 |
Maurer UE, Zeev-Ben-Mordehai T, Pandurangan AP, Cairns TM, Hannah BP, Whitbeck JC, Eisenberg RJ, Cohen GH, Topf M, Huiskonen JT, Grünewald K. The structure of herpesvirus fusion glycoprotein B-bilayer complex reveals the protein-membrane and lateral protein-protein interaction. Structure (London, England : 1993). 21: 1396-405. PMID 23850455 DOI: 10.1016/J.Str.2013.05.018 |
0.708 |
|
| 2013 |
Redzej A, Ilangovan A, Lang S, Gruber CJ, Topf M, Zangger K, Zechner EL, Waksman G. Structure of a translocation signal domain mediating conjugative transfer by type IV secretion systems. Molecular Microbiology. 89: 324-33. PMID 23710762 DOI: 10.1111/Mmi.12275 |
0.325 |
|
| 2013 |
Yuan S, Topf M, Reubold TF, Eschenburg S, Akey CW. Changes in Apaf-1 conformation that drive apoptosome assembly. Biochemistry. 52: 2319-27. PMID 23521171 DOI: 10.1021/Bi301721G |
0.373 |
|
| 2012 |
Pandurangan AP, Topf M. RIBFIND: a web server for identifying rigid bodies in protein structures and to aid flexible fitting into cryo EM maps. Bioinformatics (Oxford, England). 28: 2391-3. PMID 22796953 DOI: 10.1093/Bioinformatics/Bts446 |
0.752 |
|
| 2012 |
Seitsonen JJ, Shakeel S, Susi P, Pandurangan AP, Sinkovits RS, Hyvönen H, Laurinmäki P, Ylä-Pelto J, Topf M, Hyypiä T, Butcher SJ. Structural analysis of coxsackievirus A7 reveals conformational changes associated with uncoating. Journal of Virology. 86: 7207-15. PMID 22514349 DOI: 10.1128/Jvi.06425-11 |
0.718 |
|
| 2012 |
Pandurangan AP, Topf M. Finding rigid bodies in protein structures: Application to flexible fitting into cryoEM maps. Journal of Structural Biology. 177: 520-31. PMID 22079400 DOI: 10.1016/J.Jsb.2011.10.011 |
0.751 |
|
| 2011 |
Vasishtan D, Topf M. Scoring functions for cryoEM density fitting. Journal of Structural Biology. 174: 333-43. PMID 21296161 DOI: 10.1016/J.Jsb.2011.01.012 |
0.411 |
|
| 2011 |
Yuan S, Yu X, Topf M, Dorstyn L, Kumar S, Ludtke SJ, Akey CW. Structure of the Drosophila apoptosome at 6.9 å resolution. Structure (London, England : 1993). 19: 128-40. PMID 21220123 DOI: 10.1016/J.Str.2010.10.009 |
0.383 |
|
| 2011 |
Beck M, Topf M, Frazier Z, Tjong H, Xu M, Zhang S, Alber F. Exploring the spatial and temporal organization of a cell's proteome. Journal of Structural Biology. 173: 483-96. PMID 21094684 DOI: 10.1016/J.Jsb.2010.11.011 |
0.346 |
|
| 2011 |
Yuan S, Yu X, Topf M, Dorstyn L, Kumar S, Ludtke SJ, Akey CW. Structure of the Drosophila apoptosome at 6.9 angstrom resolution Structure. 19: 128-140. DOI: 10.2210/Pdb4V4L/Pdb |
0.369 |
|
| 2010 |
Zhang S, Vasishtan D, Xu M, Topf M, Alber F. A fast mathematical programming procedure for simultaneous fitting of assembly components into cryoEM density maps. Bioinformatics (Oxford, England). 26: i261-8. PMID 20529915 DOI: 10.1093/Bioinformatics/Btq201 |
0.418 |
|
| 2010 |
Yuan S, Yu X, Topf M, Ludtke SJ, Wang X, Akey CW. Structure of an apoptosome-procaspase-9 CARD complex. Structure (London, England : 1993). 18: 571-83. PMID 20462491 DOI: 10.1016/J.Str.2010.04.001 |
0.393 |
|
| 2010 |
Rawi R, Whitmore L, Topf M. CHOYCE: a web server for constrained homology modelling with cryoEM maps. Bioinformatics (Oxford, England). 26: 1673-4. PMID 20444836 DOI: 10.1093/Bioinformatics/Btq237 |
0.417 |
|
| 2010 |
Gartmann M, Blau M, Armache JP, Mielke T, Topf M, Beckmann R. Mechanism of eIF6-mediated inhibition of ribosomal subunit joining. The Journal of Biological Chemistry. 285: 14848-51. PMID 20356839 DOI: 10.1074/Jbc.C109.096057 |
0.353 |
|
| 2009 |
Taylor DJ, Devkota B, Huang AD, Topf M, Narayanan E, Sali A, Harvey SC, Frank J. Comprehensive molecular structure of the eukaryotic ribosome. Structure (London, England : 1993). 17: 1591-604. PMID 20004163 DOI: 10.1016/J.Str.2009.09.015 |
0.534 |
|
| 2009 |
Lasker K, Topf M, Sali A, Wolfson HJ. Inferential optimization for simultaneous fitting of multiple components into a CryoEM map of their assembly. Journal of Molecular Biology. 388: 180-94. PMID 19233204 DOI: 10.1016/J.Jmb.2009.02.031 |
0.601 |
|
| 2008 |
Connell SR, Topf M, Qin Y, Wilson DN, Mielke T, Fucini P, Nierhaus KH, Spahn CM. A new tRNA intermediate revealed on the ribosome during EF4-mediated back-translocation. Nature Structural & Molecular Biology. 15: 910-5. PMID 19172743 DOI: 10.1038/Nsmb.1469 |
0.389 |
|
| 2008 |
Serysheva II, Ludtke SJ, Baker ML, Cong Y, Topf M, Eramian D, Sali A, Hamilton SL, Chiu W. Subnanometer-resolution electron cryomicroscopy-based domain models for the cytoplasmic region of skeletal muscle RyR channel. Proceedings of the National Academy of Sciences of the United States of America. 105: 9610-5. PMID 18621707 DOI: 10.1073/Pnas.0803189105 |
0.521 |
|
| 2008 |
Booth CR, Meyer AS, Cong Y, Topf M, Sali A, Ludtke SJ, Chiu W, Frydman J. Mechanism of lid closure in the eukaryotic chaperonin TRiC/CCT. Nature Structural & Molecular Biology. 15: 746-53. PMID 18536725 DOI: 10.1038/Nsmb.1436 |
0.529 |
|
| 2008 |
Chandramouli P, Topf M, Ménétret JF, Eswar N, Cannone JJ, Gutell RR, Sali A, Akey CW. Structure of the mammalian 80S ribosome at 8.7 A resolution. Structure (London, England : 1993). 16: 535-48. PMID 18400176 DOI: 10.1016/J.Str.2008.01.007 |
0.594 |
|
| 2008 |
Alber F, Förster F, Korkin D, Topf M, Sali A. Integrating diverse data for structure determination of macromolecular assemblies. Annual Review of Biochemistry. 77: 443-77. PMID 18318657 DOI: 10.1146/Annurev.Biochem.77.060407.135530 |
0.569 |
|
| 2008 |
Topf M, Lasker K, Webb B, Wolfson H, Chiu W, Sali A. Protein structure fitting and refinement guided by cryo-EM density. Structure (London, England : 1993). 16: 295-307. PMID 18275820 DOI: 10.1016/J.Str.2007.11.016 |
0.611 |
|
| 2008 |
Cong Y, Topf M, Sali A, Matsudaira P, Dougherty M, Chiu W, Schmid MF. Crystallographic conformers of actin in a biologically active bundle of filaments. Journal of Molecular Biology. 375: 331-6. PMID 18022194 DOI: 10.1016/J.Jmb.2007.10.027 |
0.501 |
|
| 2007 |
Serysheva I, Ludtke S, Baker M, Cong Y, Topf M, Sali A, Hamilton S, Chiu W. Single Particle Cryo-EM of RyR1 Channel at Subnanometer Resolution Microscopy and Microanalysis. 13. DOI: 10.1017/S1431927607071401 |
0.433 |
|
| 2006 |
Topf M, Baker ML, Marti-Renom MA, Chiu W, Sali A. Refinement of protein structures by iterative comparative modeling and cryoEM density fitting Journal of Molecular Biology. 357: 1655-1668. PMID 16490207 DOI: 10.1016/J.Jmb.2006.01.062 |
0.613 |
|
| 2005 |
Topf M, Sali A. Combining electron microscopy and comparative protein structure modeling. Current Opinion in Structural Biology. 15: 578-85. PMID 16118050 DOI: 10.1016/J.Sbi.2005.08.001 |
0.592 |
|
| 2005 |
Topf M, Baker ML, John B, Chiu W, Sali A. Structural characterization of components of protein assemblies by comparative modeling and electron cryo-microscopy Journal of Structural Biology. 149: 191-203. PMID 15681235 DOI: 10.1016/J.Jsb.2004.11.004 |
0.616 |
|
| 2005 |
Sali A, Topf M, Baker ML, Chiu W. Structure of protein assemblies by comparative modeling and electron microscopy Acta Crystallographica Section a Foundations of Crystallography. 61: c3-c3. DOI: 10.1107/S0108767305099897 |
0.57 |
|
| 2004 |
Shacham S, Marantz Y, Bar-Haim S, Kalid O, Warshaviak D, Avisar N, Inbal B, Heifetz A, Fichman M, Topf M, Naor Z, Noiman S, Becker OM. PREDICT modeling and in-silico screening for G-protein coupled receptors. Proteins. 57: 51-86. PMID 15326594 DOI: 10.1002/Prot.20195 |
0.345 |
|
| 2004 |
Russell RB, Alber F, Aloy P, Davis FP, Korkin D, Pichaud M, Topf M, Sali A. A structural perspective on protein-protein interactions. Current Opinion in Structural Biology. 14: 313-24. PMID 15193311 DOI: 10.1016/J.Sbi.2004.04.006 |
0.565 |
|
| 2003 |
Clifton IJ, Doan LX, Sleeman MC, Topf M, Suzuki H, Wilmouth RC, Schofield CJ. Crystal structure of carbapenem synthase (CarC). The Journal of Biological Chemistry. 278: 20843-50. PMID 12611886 DOI: 10.1074/Jbc.M213054200 |
0.301 |
|
| 2002 |
Topf M, Várnai P, Schofield CJ, Richards WG. Molecular dynamics simulations of the acyl-enzyme and the tetrahedral intermediate in the deacylation step of serine proteases. Proteins. 47: 357-69. PMID 11948789 DOI: 10.1002/Prot.10097 |
0.314 |
|
| 2001 |
Shacham S, Topf M, Avisar N, Glaser F, Marantz Y, Bar-Haim S, Noiman S, Naor Z, Becker OM. Modeling the 3D structure of GPCRs from sequence. Medicinal Research Reviews. 21: 472-83. PMID 11579443 DOI: 10.1002/Med.1019 |
0.368 |
|
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