Outcomes of the EMDataResource Cryo-EM Ligand modeling challenge.

Lawson C, Kryshtafovych A, Pintilie G, Burley S, Cerny J, Chen V, Emsley P, Gobbi A, Joachimiak A, Noreng S, Prisant M, Read R, Richardson J, Rohou A, Schneider B, Sellers B, Chao C, Sourial E, Williams C, Williams C, Yang Y, Abbaraju V, Afonine PV, Baker M, Bond P, Blundell T, Burnley T, Campbell A, Cao R, Cheng J, Chojnowski G, Cowtan K, Dimaio F, Esmaeeli R, Giri N, Grubmüller H, Hoh SW, Hou J, Hryc C, Hunte C, Igaev M, Joseph A, Kao W, Kihara D, Kumar D, Lang L, Lin S, Subramaniya SRMV, Mittal S, Mondal A, Moriarty N, Muenks A, Murshudov G, Nicholls R, Olek M, Palmer C, Perez A, Pohjolainen E, Pothula K, Rowley C, Sarkar D, Schäfer L, Schlicksup C, Schroeder G, Shekhar M, Si D, Singharoy A, Sobolev O, Terashi G, Vaiana A, Vedithi S, Verburgt J, Wang X, Warshamanage R, Winn M, Weyand S, Yamashita K, Zhao M, Schmid M, Berman H, Chiu W

Research square, 2024

doi:10.21203/rs.3.rs-3864137/v1.

RNA 3D structure modeling by fragment assembly with small-angle X-ray scattering restraints.

Chojnowski G, Zaborowski R, Magnus M, Mukherjee S, Bujnicki JM

Bioinformatics (Oxford, England), 2023

doi:10.1093/bioinformatics/btad527.

Predicted models and CCP4.

Simpkin AJ, Caballero I, McNicholas S, Stevenson K, Jiménez E, Sánchez Rodríguez F, Fando M, Uski V, Ballard C, Chojnowski G, Lebedev A, Krissinel E, Usón I, Rigden DJ, Keegan RM

Acta crystallographica. Section D, Structural biology, 2023

doi:10.1107/s2059798323006289.

DoubleHelix: nucleic acid sequence identification, assignment and validation tool for cryo-EM and crystal structure models.

Chojnowski G

Nucleic acids research, 2023

doi:10.1093/nar/gkad553.

Sequence-assignment validation in protein crystal structure models with checkMySequence.

Chojnowski G

Acta crystallographica. Section D, Structural biology, 2023

doi:10.1107/s2059798323003765.

Asymmetric horseshoe-like assembly of peroxisomal yeast oxalyl-CoA synthetase.

Bürgi J, Lill P, Giannopoulou EA, Jeffries CM, Chojnowski G, Raunser S, Gatsogiannis C, Wilmanns M

Biological chemistry, 2023

doi:10.1515/hsz-2022-0273.

AlphaPulldown-a Python package for protein-protein interaction screens using AlphaFold-Multimer.

Yu D, Chojnowski G, Rosenthal M, Kosinski J

Bioinformatics , 2022

doi:10.1093/bioinformatics/btac749.

Using deep-learning predictions of inter-residue distances for model validation.

Sánchez Rodríguez F, Chojnowski G, Keegan RM, Rigden DJ

Acta crystallographica. Section D, Structural biology, 2022

doi:10.1107/s2059798322010415.

CCP4 Cloud for structure determination and project management in macromolecular crystallography.

Krissinel E, Lebedev AA, Uski V, Ballard CB, Keegan RM, Kovalevskiy O, Nicholls RA, Pannu NS, Skubák P, Berrisford J, Fando M, Lohkamp B, Wojdyr M, Simpkin AJ, Thomas JMH, Oliver C, Vonrhein C, Chojnowski G, Basle A, Purkiss A, Isupov MN, McNicholas S, Lowe E, Triviño J, Cowtan K, Agirre J, Rigden DJ, Uson I, Lamzin V, Tews I, Bricogne G, Leslie AGW, Brown DG

Acta crystallographica. Section D, Structural biology, 2022

doi:10.1107/s2059798322007987.

Sequence-assignment validation in cryo-EM models with checkMySequence.

Chojnowski G

Acta crystallographica. Section D, Structural biology, 2022

doi:10.1107/s2059798322005009.

Crystal structures of the molecular class A β-lactamase TEM-171 and its complexes with tazobactam.

Grigorenko VG, Petrova TE, Carolan C, Rubtsova MY, Uporov IV, Pereira J, Chojnowski G, Samygina VR, Lamzin VS, Egorov AM

Acta crystallographica. Section D, Structural biology, 2022

doi:10.1107/s2059798322004879.

Cryo-EM and artificial intelligence visualize endogenous protein community members.

Skalidis I, Kyrilis FL, Tüting C, Hamdi F, Chojnowski G, Kastritis PL

Structure (London, England : 1993), 2022

doi:10.1016/j.str.2022.01.001.

findMySequence: a neural-network-based approach for identification of unknown proteins in X-ray crystallography and cryo-EM

Chojnowski G, Simpkin AJ, Leonardo DA, Seifert-Davila W, Vivas-Ruiz DE, Keegan RM, Rigden DJ

IUCrJ, 2022

doi:10.1107/S2052252521011088.

Structure of the mycobacterial ESX-5 type VII secretion system pore complex.

Beckham KSH, Ritter C, Chojnowski G, Ziemianowicz DS, Mullapudi E, Rettel M, Savitski MM, Mortensen SA, Kosinski J, Wilmanns M

Science advances, 2021

doi:10.1126/sciadv.abg9923.

Cryo-EM model validation recommendations based on outcomes of the 2019 EMDataResource challenge.

Lawson CL, Kryshtafovych A, Adams PD, Afonine PV, Baker ML, Barad BA, Bond P, Burnley T, Cao R, Cheng J, Chojnowski G, Cowtan K, Dill KA, DiMaio F, Farrell DP, Fraser JS, Herzik MA, Hoh SW, Hou J, Hung LW, Igaev M, Joseph AP, Kihara D, Kumar D, Mittal S, Monastyrskyy B, Olek M, Palmer CM, Patwardhan A, Perez A, Pfab J, Pintilie GD, Richardson JS, Rosenthal PB, Sarkar D, Schäfer LU, Schmid MF, Schröder GF, Shekhar M, Si D, Singharoy A, Terashi G, Terwilliger TC, Vaiana A, Wang L, Wang Z, Wankowicz SA, Williams CJ, Winn M, Wu T, Yu X, Zhang K, Berman HM, Chiu W

Nature methods, 2021

doi:10.1038/s41592-020-01051-w.

The accuracy of protein models automatically built into cryo-EM maps with ARP/wARP.

Chojnowski G, Sobolev E, Heuser P, Lamzin VS

Acta crystallographica. Section D, Structural biology, 2021

doi:10.1107/S2059798320016332.

Megahertz single-particle imaging at the European XFEL.

Sobolev E, Zolotarev S, Giewekemeyer K, Bielecki J, Okamoto K, Reddy HKN, Andreasson J, Ayyer K, Barak I, Bari S, Barty A, Bean R, Bobkov S, Chapman HN, Chojnowski G, Daurer BJ, Dorner K, Ekeberg T, Fluckiger L, Galzitskaya O, Gelisio L, Hauf S, Hogue BG, Horke DA, Hosseinizadeh A, Ilyin V, Jung C, Kim C, Kim Y, Kirian RA, Kirkwood H, Kulyk O, Kupper J, Letrun R, Loh ND, Lorenzen K, Messerschmidt M, Muhlig K, Ourmazd A, Raab N, Rode AV, Rose M, Round A, Sato T, Schubert R, Schwander P, Sellberg JA, Sikorski M, Silenzi A, Song CY, Spence JCH, Stern S, Sztuk-Dambietz J, Teslyuk A, Timneanu N, Trebbin M, Uetrecht C, Weinhausen B, Williams GJ, Xavier PL, Xu C, Vartanyants IA, Lamzin VS, Mancuso A, Maia FRNC

COMMUNICATIONS PHYSICS, 2020

doi:10.1038/s42005-020-0362-y.

The use of local structural similarity of distant homologues for crystallographic model building from a molecular-replacement solution.

Chojnowski G, Choudhury K, Heuser P, Sobolev E, Pereira J, Oezugurel U, Lamzin VS

Acta crystallographica. Section D, Structural biology, 2020

doi:10.1107/S2059798320000455.

Sequence assignment for low-resolution modelling of protein crystal structures.

Chojnowski G, Pereira J, Lamzin VS

Acta crystallographica. Section D, Structural biology, 2019

doi:10.1107/S2059798319009392.

West-Life: A Virtual Research Environment for structural biology.

Morris C, Andreetto P, Bancic B, .Bonvind AMJJ, Chojnowski G, Canoe L, Carazo JH, Conesa P, Daenke S, Damaskos G, Giachettic A, Haley NEC, Hekkelmang ML, Heuser P, Joosten RP, Kouřil D, Křenek A, Kulháneka T, Lamzin VS, Nadzirin N, Perrakis A, Rosato A, Sanderson F, Segura J, Schaarschmidt J, Sobolev E, Traldi S, Trellet ME, Velankar S, Verlato M, Winn M

2019

doi:10.1016/j.yjsbx.2019.100006.

Impact of the structural integrity of the three-way junction of adenovirus VAI RNA on PKR inhibition.

Dzananovic E, Astha E, Chojnowski G, Deo S, Booy EP, Padilla-Meier P, McEleney K, Bujnicki JM, Patel TR, McKenna SA

PloS one, 2017

doi:10.1371/journal.pone.0186849.

Structural studies of RNA-protein complexes: A hybrid approach involving hydrodynamics, scattering, and computational methods.

Patel TR, Chojnowski G, Astha, Koul A, McKenna SA, Bujnicki JM

Methods (San Diego, Calif.), 2016

doi:10.1016/j.ymeth.2016.12.002.