المؤلفون: Simpkin, Adam J, Mesdaghi, Shahram, Rodríguez, Filomeno Sánchez, Elliott, Luc, Murphy, David L, Kryshtafovych, Andriy, Keegan, Ronan M, Rigden, Daniel J

المصدر: Proteins Structure Function and Bioinformatics. 91(12)

مصطلحات موضوعية: Biochemistry and Cell Biology, Biological Sciences, Furylfuramide, Computational Biology, Models, Molecular, Proteins, Sequence Alignment, CASP15, machine learning, molecular replacement, protein modelling, protein structure prediction, structural bioinformatics, Mathematical Sciences, Information and Computing Sciences, Bioinformatics, Biological sciences, Mathematical sciences

وصف الملف: application/pdf

URL الوصول: https://escholarship.org/uc/item/4sk2p3s7
https://escholarship.org/content/qt4sk2p3s7/qt4sk2p3s7.pdf

المؤلفون: Pratt, Olivia S., Elliott, Luc G., Haon, Margaux, Mesdaghi, Shahram, Price, Rebecca M., Simpkin, Adam J., Rigden, Daniel J.

المساهمون: Biotechnology and Biological Sciences Research Council

المصدر: Computational and Structural Biotechnology Journal ; volume 27, page 467-477 ; ISSN 2001-0370

الاتاحة: https://doi.org/10.1016/j.csbj.2025.01.016
https://api.elsevier.com/content/article/PII:S2001037025000200?httpAccept=text/xml
https://api.elsevier.com/content/article/PII:S2001037025000200?httpAccept=text/plain

المؤلفون: Agirre, Jon, Atanasova, Mihaela, Bagdonas, Haroldas, Ballard, Charles B., Basle, Arnaud, Beilsten-Edmands, James, Borges, Rafael J., Brown, David G., Burgos-Marmol, 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 E., 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., Jimenez, 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, Maly, Martin, McCoy, Airlie J., McNicholas, Stuart J., Medina, Ana, Millan, 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, Rodriguez, Filomeno Sanchez, 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, Trivino Valls, Josep, Uski, Ville, Uson, Isabel, Vagin, Alexei, Velankar, Sameer, Vollmar, Melanie, Walden, Helen, Waterman, David, Wilson, Keith S., Winn, Martyn D., Winter, Graeme, Wojdyr, Marcin, Yamashita, Keitaro

المصدر: Acta Crystallographica Section D. 79:449-461

مصطلحات موضوعية: Collaborative Computational Project No. 4, CCP4, crystallography software, macromolecular crystallography

وصف الملف: electronic

URL الوصول: https://urn.kb.se/resolve?urn=urn:nbn:se:liu:diva-196856
https://liu.diva-portal.org/smash/get/diva2:1791221/FULLTEXT01.pdf

المؤلفون: Simpkin, Adam J, Rodríguez, Filomeno Sánchez, Mesdaghi, Shahram, Kryshtafovych, Andriy, Rigden, Daniel J

المصدر: Proteins Structure Function and Bioinformatics. 89(12)

مصطلحات موضوعية: Biochemistry and Cell Biology, Biological Sciences, Generic health relevance, Computational Biology, Models, Molecular, Protein Conformation, Proteins, Sequence Analysis, Protein, Software, CASP, function prediction, refinement, structure prediction, Mathematical Sciences, Information and Computing Sciences, Bioinformatics, Biological sciences, Mathematical sciences

وصف الملف: application/pdf

URL الوصول: https://escholarship.org/uc/item/1hs7q9xt
https://escholarship.org/content/qt1hs7q9xt/qt1hs7q9xt.pdf

المؤلفون: Simpkin, Adam

مصطلحات موضوعية: 572

URL الوصول: https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.803918

المؤلفون: 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

وصف الملف: text

Relation: https://eprints.gla.ac.uk/299893/1/299893.pdf; Agirre, J. et al. (2023) The CCP 4 suite: integrative software for macromolecular crystallography. Acta Crystallographica. Section D: Structural Biology , D79(6), pp. 449-461. (doi:10.1107/S2059798323003595 )

الاتاحة: https://eprints.gla.ac.uk/299893/
https://eprints.gla.ac.uk/299893/1/299893.pdf

المؤلفون: 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

المساهمون: Stanford Bio-X, National Institutes of Health, Howard Hughes Medical Institute, Biotechnology and Biological Sciences Research Council, National Natural Science Foundation of China, National Key Research and Development Program of China, Agence Nationale de la Recherche

المصدر: Proteins: Structure, Function, and Bioinformatics ; volume 91, issue 12, page 1747-1770 ; ISSN 0887-3585 1097-0134

الاتاحة: http://dx.doi.org/10.1002/prot.26602
https://onlinelibrary.wiley.com/doi/pdf/10.1002/prot.26602

المؤلفون: Mesdaghi, Shahram, Murphy, David L., Simpkin, Adam J., Rigden, Daniel J.

المساهمون: none to report

المصدر: Bioscience Reports ; volume 43, issue 7 ; ISSN 0144-8463 1573-4935

الاتاحة: http://dx.doi.org/10.1042/bsr20230060
https://portlandpress.com/bioscirep/article-pdf/doi/10.1042/BSR20230060/948451/bsr-2023-0060.pdf

المؤلفون: Keegan, Ronan M.^1,2 (AUTHOR), Simpkin, Adam J.¹ (AUTHOR), Rigden, Daniel J.¹ (AUTHOR) drigden@liv.ac.uk

المصدر: Acta Crystallographica: Section D, Structural Biology. Nov2024, Vol. 80 Issue 11, p766-779. 14p.

مصطلحات موضوعية: *PROTEIN structure prediction, *CRYSTAL structure, *OPEN-ended questions, *FORECASTING

المؤلفون: 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

وصف الملف: text

Relation: https://eprints.soton.ac.uk/471374/1/ai5007.pdf; 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 and Brown, David G (2022) CCP4 Cloud for structure determination and project management in macromolecular crystallography. Acta Crystallographica Section D: Structural Biology, 78 (Pt 9), 1079-1089. (doi:10.1107/S2059798322007987 ).

الاتاحة: https://eprints.soton.ac.uk/471374/
https://eprints.soton.ac.uk/471374/1/ai5007.pdf

المؤلفون: 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

المصدر: Nature microbiology ; 7 ; 2 ; 251 ; 261 ; United Kingdom ; United States ; England

Relation: Nature Microbiology; http://hdl.handle.net/10713/17929

الاتاحة: http://hdl.handle.net/10713/17929
https://doi.org/10.1038/s41564-021-01054-z

المؤلفون: Pereira, Joana, Simpkin, Adam J., Hartmann, Marcus D., Rigden, Daniel J., Keegan, Ronan M., Lupas, Andrei N.

المساهمون: Biotechnology and Biological Sciences Research Council, Volkswagen Foundation

المصدر: Proteins: Structure, Function, and Bioinformatics ; volume 89, issue 12, page 1687-1699 ; ISSN 0887-3585 1097-0134

الاتاحة: http://dx.doi.org/10.1002/prot.26171
https://onlinelibrary.wiley.com/doi/pdf/10.1002/prot.26171
https://onlinelibrary.wiley.com/doi/full-xml/10.1002/prot.26171

المؤلفون: 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.

المساهمون: Max-Planck-Gesellschaft, Wellcome, Biotechnology and Biological Sciences Research Council

المصدر: Proteins: Structure, Function, and Bioinformatics ; volume 89, issue 12, page 1752-1769 ; ISSN 0887-3585 1097-0134

الاتاحة: http://dx.doi.org/10.1002/prot.26214
https://onlinelibrary.wiley.com/doi/pdf/10.1002/prot.26214
https://onlinelibrary.wiley.com/doi/full-xml/10.1002/prot.26214

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

المساهمون: Valencia, Alfonso, Biotechnology and Biological Sciences Research Council

المصدر: Bioinformatics ; volume 37, issue 17, page 2763-2765 ; ISSN 1367-4803 1367-4811

مصطلحات موضوعية: Computational Mathematics, Computational Theory and Mathematics, Computer Science Applications, Molecular Biology, Biochemistry, Statistics and Probability

الاتاحة: http://dx.doi.org/10.1093/bioinformatics/btab049
http://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btab049/37768058/btab049.pdf
https://academic.oup.com/bioinformatics/article-pdf/37/17/2763/50339273/btab049.pdf

المؤلفون: Simpkin, Adam J, Caballero, Iracema, McNicholas, Stuart, Stevenson, Kyle, Jimenez, Elisabet, Rodriguez, Filomneno Sanchez, Fando, Maria, Uski, Ville, Ballard, Charles, Chojnowski, Grzegorz, Lebedev, Andrey, Krissinel, Eugene, Uson, Isabel, Rigden, Daniel J, Keegan, Ronan M

Relation: Collapse authors list. Simpkin, Adam J orcid:0000-0003-1883-9376 , Caballero, Iracema, McNicholas, Stuart, Stevenson, Kyle, Jimenez, Elisabet, Rodriguez, Filomneno Sanchez, Fando, Maria, Uski, Ville, Ballard, Charles, Chojnowski, Grzegorz et al (show 5 more authors) , Lebedev, Andrey, Krissinel, Eugene, Uson, Isabel, Rigden, Daniel J orcid:0000-0002-7565-8937 and Keegan, Ronan M (2023) Predicted models and CCP 4. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY, 79 (Pt 9). pp. 806-819.

الاتاحة: http://livrepository.liverpool.ac.uk/3173282/
https://doi.org/10.1107/s2059798323006289

المؤلفون: 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

المصدر: Proteins: Structure, Function, and Bioinformatics ; volume 91, issue 12 ; ISSN 0887-3585 1097-0134

الاتاحة: http://dx.doi.org/10.1002/prot.26640
https://onlinelibrary.wiley.com/doi/pdf/10.1002/prot.26640

المؤلفون: Rigden, Daniel, Simpkin, Adam, Mesdaghi, Shahram, Rodríguez, Filomeno Sánchez, Elliott, Luc, Murphy, David, Kryshtafovych, Andriy, Keegan, Ronan

الاتاحة: http://dx.doi.org/10.22541/au.168495671.14377331/v1

المؤلفون: Simpkin, Adam, J, Simkovic, Felix, Thomas, Jens, 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

المساهمون: University of Liverpool, Synchrotron SOLEIL (SSOLEIL), Centre National de la Recherche Scientifique (CNRS), STFC Rutherford Appleton Laboratory (RAL), Science and Technology Facilities Council (STFC), Global Phasing Ltd, Weill Medical College of Cornell University New York, Argonne National Laboratory Lemont (ANL), University of Melbourne, The Walter and Eliza Hall Institute of Medical Research (WEHI), Molecular and structural microbiology / Microbiología Molecular y Estructural Montevideo, Institut Pasteur de Montevideo, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP), The development of SIMBAD has been supported by the BBSRC CCP4 grant BB/L009544/1, the University of Liverpool and Synchrotron SOLEIL. GM/CA@APS has been funded in whole or in part with Federal funds from the National Cancer Institute (ACB-12002) and the National Institute of General Medical Sciences (AGM-12006). This research used resources of the Advanced Photon Source, a US Department of Energy (DOE) Office of Science User Facility operated for the DOE Office of Science by Argonne National Laboratory under Contract No. DE-AC02-06CH11357. The work on cytokine/cyanase was supported by grant APP1004945 from the Australian National Health and Medical Research Council (NHMRC) and was made possible at WEHI through Victorian State Government Operational Infrastructure Support and the Australian NHMRC Independent Research Institutes Infrastructure Support Scheme. M-NL received a postdoctoral fellowship from the ANII (Agencia Nacional de Investigación e Innovación, Uruguay).

المصدر: ISSN: 2059-7983 ; EISSN: 2059-7983.

مصطلحات موضوعية: molecular replacement pipeline, SIMBAD, contaminant, lattice search, structure solution, [CHIM.CRIS]Chemical Sciences/Cristallography

Relation: info:eu-repo/semantics/altIdentifier/pmid/29968670; pasteur-02554316; https://pasteur.hal.science/pasteur-02554316; https://pasteur.hal.science/pasteur-02554316/document; https://pasteur.hal.science/pasteur-02554316/file/simpkin_18.pdf; PUBMED: 29968670; PUBMEDCENTRAL: PMC6038384

الاتاحة: https://pasteur.hal.science/pasteur-02554316
https://pasteur.hal.science/pasteur-02554316/document
https://pasteur.hal.science/pasteur-02554316/file/simpkin_18.pdf
https://doi.org/10.1107/S2059798318005752

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

المصدر: Acta Crystallographica Section D Structural Biology. 2018, 74(3), pp. 183-193. ISSN 2059-7983. Available under: doi:10.1107/S2059798318002310

مصطلحات موضوعية: ddc:570

وصف الملف: application/pdf

Relation: http://nbn-resolving.de/urn:nbn:de:bsz:352-2-17l0q6kaqdr8l1; http://dx.doi.org/10.1107/S2059798318002310; 50108424X

الاتاحة: http://nbn-resolving.de/urn:nbn:de:bsz:352-2-17l0q6kaqdr8l1
https://doi.org/10.1107/S2059798318002310

المؤلفون: 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

وصف الملف: text

Relation: https://eprints.whiterose.ac.uk/132314/1/rr5152.pdf; Keegan, Ronan M., McNicholas, Stuart J, Thomas, Jens M H et al. (7 more authors) (2018) Recent developments in MrBUMP : better search-model preparation, graphical interaction with search models, and solution improvement and assessment. Acta crystallographica. Section D, Structural biology. pp. 167-182. ISSN 2059-7983

الاتاحة: https://eprints.whiterose.ac.uk/132314/
https://eprints.whiterose.ac.uk/132314/1/rr5152.pdf
https://doi.org/10.1107/S2059798318003455