GP0.4 from bacteriophage T7: in silico characterisation of its structure and interaction with E. coli FtsZ

por Simpkin, Adam J., Rigden, Daniel J.
Publicado 2016

Structural insights into pink-eyed dilution protein (Oca2)

por Mesdaghi, Shahram, Murphy, David L., Simpkin, Adam J., Rigden, Daniel J.
Publicado 2023

Redeployment of automated MrBUMP search-model identification for map fitting in cryo-EM

por Simpkin, Adam J., Winn, Martyn D., Rigden, Daniel J., Keegan, Ronan M.
Publicado 2021

MrParse: finding homologues in the PDB and the EBI AlphaFold database for molecular replacement and more

por Simpkin, Adam J., Thomas, Jens M. H., Keegan, Ronan M., Rigden, Daniel J.
Publicado 2022

Molecular replacement using structure predictions from databases

por Simpkin, Adam J., Thomas, Jens M. H., Simkovic, Felix, Keegan, Ronan M., Rigden, Daniel J.
Publicado 2019

Helical ensembles outperform ideal helices in molecular replacement

por Sánchez Rodríguez, Filomeno, Simpkin, Adam J., Davies, Owen R., Keegan, Ronan M., Rigden, Daniel J.
Publicado 2020

Ensembles generated from crystal structures of single distant homologues solve challenging molecular-replacement cases in AMPLE

por Rigden, Daniel J., Thomas, Jens M. H., Simkovic, Felix, Simpkin, Adam, Winn, Martyn D., Mayans, Olga, Keegan, Ronan M.
Publicado 2018

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

por Chojnowski, Grzegorz, Simpkin, Adam J., Leonardo, Diego A., Seifert-Davila, Wolfram, Vivas-Ruiz, Dan E., Keegan, Ronan M., Rigden, Daniel J.
Publicado 2021

ConPlot: web-based application for the visualization of protein contact maps integrated with other data

por Sánchez Rodríguez, Filomeno, Mesdaghi, Shahram, Simpkin, Adam J., Burgos-Mármol, J. Javier, Murphy, David L., Uski, Ville, Keegan, Ronan M., Rigden, Daniel J.
Publicado 2021

Pathogenomic analyses of Shigella isolates inform factors limiting shigellosis prevention and control across LMICs

por Bengtsson, Rebecca J., Simpkin, Adam J., Pulford, Caisey V., Low, Ross, Rasko, David A., Rigden, Daniel J., Hall, Neil, Barry, Eileen M., Tennant, Sharon M., Baker, Kate S.
Publicado 2022

Assessment of three-dimensional RNA structure prediction in CASP15

por Das, Rhiju, Kretsch, Rachael C., Simpkin, Adam J., Mulvaney, Thomas, Pham, Phillip, Rangan, Ramya, Bu, Fan, Keegan, Ronan M., Topf, Maya, Rigden, Daniel J., Miao, Zhichao, Westhof, Eric
Publicado 2023

Using Phaser and ensembles to improve the performance of SIMBAD

por Simpkin, Adam J., Simkovic, Felix, Thomas, Jens M. H., Savko, Martin, Lebedev, Andrey, Uski, Ville, Ballard, Charles C., Wojdyr, Marcin, Shepard, William, Rigden, Daniel J., Keegan, Ronan M.
Publicado 2020

Recent developments in MrBUMP: better search-model preparation, graphical interaction with search models, and solution improvement and assessment

por Keegan, Ronan M., McNicholas, Stuart J., Thomas, Jens M. H., Simpkin, Adam J., Simkovic, Felix, Uski, Ville, Ballard, Charles C., Winn, Martyn D., Wilson, Keith S., Rigden, Daniel J.
Publicado 2018

Assessing the utility of CASP14 models for molecular replacement

por Millán, Claudia, Keegan, Ronan M., Pereira, Joana, Sammito, Massimo D., Simpkin, Adam J., McCoy, Airlie J., Lupas, Andrei N., Hartmann, Marcus D., Rigden, Daniel J., Read, Randy J.
Publicado 2021

Predicted models and CCP4

por Simpkin, Adam J., Caballero, Iracema, McNicholas, Stuart, Stevenson, Kyle, Jiménez, Elisabet, Sánchez Rodríguez, Filomeno, Fando, Maria, Uski, Ville, Ballard, Charles, Chojnowski, Grzegorz, Lebedev, Andrey, Krissinel, Eugene, Usón, Isabel, Rigden, Daniel J., Keegan, Ronan M.
Publicado 2023

SIMBAD: a sequence-independent molecular-replacement pipeline

por Simpkin, Adam J., Simkovic, Felix, Thomas, Jens M. H., Savko, Martin, Lebedev, Andrey, Uski, Ville, Ballard, Charles, Wojdyr, Marcin, Wu, Rui, Sanishvili, Ruslan, Xu, Yibin, Lisa, María-Natalia, Buschiazzo, Alejandro, Shepard, William, Rigden, Daniel J., Keegan, Ronan M.
Publicado 2018

CCP4 Cloud for structure determination and project management in macromolecular crystallography

por Krissinel, Eugene, Lebedev, Andrey A., Uski, Ville, Ballard, Charles B., Keegan, Ronan M., Kovalevskiy, Oleg, Nicholls, Robert A., Pannu, Navraj S., Skubák, Pavol, Berrisford, John, Fando, Maria, Lohkamp, Bernhard, Wojdyr, Marcin, Simpkin, Adam J., Thomas, Jens M. H., Oliver, Christopher, Vonrhein, Clemens, Chojnowski, Grzegorz, Basle, Arnaud, Purkiss, Andrew, Isupov, Michail N., McNicholas, Stuart, Lowe, Edward, Triviño, Josep, Cowtan, Kevin, Agirre, Jon, Rigden, Daniel J., Uson, Isabel, Lamzin, Victor, Tews, Ivo, Bricogne, Gerard, Leslie, Andrew G. W., Brown, David G.
Publicado 2022

The CCP4 suite: integrative software for macromolecular crystallography

por Agirre, Jon, Atanasova, Mihaela, Bagdonas, Haroldas, Ballard, Charles B., Baslé, Arnaud, Beilsten-Edmands, James, Borges, Rafael J., Brown, David G., Burgos-Mármol, J. Javier, Berrisford, John M., Bond, Paul S., Caballero, Iracema, Catapano, Lucrezia, Chojnowski, Grzegorz, Cook, Atlanta G., Cowtan, Kevin D., Croll, Tristan I., Debreczeni, Judit É., Devenish, Nicholas E., Dodson, Eleanor J., Drevon, Tarik R., Emsley, Paul, Evans, Gwyndaf, Evans, Phil R., Fando, Maria, Foadi, James, Fuentes-Montero, Luis, Garman, Elspeth F., Gerstel, Markus, Gildea, Richard J., Hatti, Kaushik, Hekkelman, Maarten L., Heuser, Philipp, Hoh, Soon Wen, Hough, Michael A., Jenkins, Huw T., Jiménez, Elisabet, Joosten, Robbie P., Keegan, Ronan M., Keep, Nicholas, Krissinel, Eugene B., Kolenko, Petr, Kovalevskiy, Oleg, Lamzin, Victor S., Lawson, David M., Lebedev, Andrey A., Leslie, Andrew G. W., Lohkamp, Bernhard, Long, Fei, Malý, Martin, McCoy, Airlie J., McNicholas, Stuart J., Medina, Ana, Millán, Claudia, Murray, James W., Murshudov, Garib N., Nicholls, Robert A., Noble, Martin E. M., Oeffner, Robert, Pannu, Navraj S., Parkhurst, James M., Pearce, Nicholas, Pereira, Joana, Perrakis, Anastassis, Powell, Harold R., Read, Randy J., Rigden, Daniel J., Rochira, William, Sammito, Massimo, Sánchez Rodríguez, Filomeno, Sheldrick, George M., Shelley, Kathryn L., Simkovic, Felix, Simpkin, Adam J., Skubak, Pavol, Sobolev, Egor, Steiner, Roberto A., Stevenson, Kyle, Tews, Ivo, Thomas, Jens M. H., Thorn, Andrea, Valls, Josep Triviño, Uski, Ville, Usón, Isabel, Vagin, Alexei, Velankar, Sameer, Vollmar, Melanie, Walden, Helen, Waterman, David, Wilson, Keith S., Winn, Martyn D., Winter, Graeme, Wojdyr, Marcin, Yamashita, Keitaro
Publicado 2023