Marcin J. Skwark, Ph.D. - Publications

2017- Biochemistry University of Cambridge, Cambridge, England, United Kingdom 
protein structure prediction, bioinformatics, drug discovery

27 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2023 Woszczyło M, Pasikowski P, Devaraj S, Kokocińska A, Szumny A, Skwark MJ, Niżański W, Dzięcioł M. Urinary Proteins of Female Domestic Dog () during Ovarian Cycle. Veterinary Sciences. 10. PMID 37104448 DOI: 10.3390/vetsci10040292  0.332
2023 Beguir K, Skwark MJ, Fu Y, Pierrot T, Carranza NL, Laterre A, Kadri I, Korched A, Lowegard AU, Lui BG, Sänger B, Liu Y, Poran A, Muik A, Şahin U. Early computational detection of potential high-risk SARS-CoV-2 variants. Computers in Biology and Medicine. 155: 106618. PMID 36774893 DOI: 10.1016/j.compbiomed.2023.106618  0.331
2023 Woszczyło M, Szumny A, Knap P, Jezierski T, Niżański W, Kokocińska A, Skwark MJ, Dzięcioł M. The influence of manual semen collection in male trained dogs (Canis familiaris), in the presence or absence of a female in estrus, on the concentrations of cortisol, oxytocin, prolactin and testosterone. Plos One. 18: e0278524. PMID 36730259 DOI: 10.1371/journal.pone.0278524  0.191
2022 Boeck L, Burbaud S, Skwark M, Pearson WH, Sangen J, Wuest AW, Marshall EKP, Weimann A, Everall I, Bryant JM, Malhotra S, Bannerman BP, Kierdorf K, Blundell TL, Dionne MS, et al. Mycobacterium abscessus pathogenesis identified by phenogenomic analyses. Nature Microbiology. 7: 1431-1441. PMID 36008617 DOI: 10.1038/s41564-022-01204-x  0.729
2022 Saleh A, Noguchi Y, Aramayo R, Ivanova ME, Stevens KM, Montoya A, Sunidhi S, Carranza NL, Skwark MJ, Speck C. The structural basis of Cdc7-Dbf4 kinase dependent targeting and phosphorylation of the MCM2-7 double hexamer. Nature Communications. 13: 2915. PMID 35614055 DOI: 10.1038/s41467-022-30576-1  0.26
2022 Borza CM, Bolas G, Zhang X, Browning Monroe MB, Zhang MZ, Meiler J, Skwark MJ, Harris RC, Lapierre LA, Goldenring JR, Hook M, Rivera J, Brown KL, Leitinger B, Tyska MJ, et al. The Collagen Receptor Discoidin Domain Receptor 1b Enhances Integrin β1-Mediated Cell Migration by Interacting With Talin and Promoting Rac1 Activation. Frontiers in Cell and Developmental Biology. 10: 836797. PMID 35309920 DOI: 10.3389/fcell.2022.836797  0.456
2020 Vedithi SC, Malhotra S, Skwark MJ, Munir A, Acebrón-García-De-Eulate M, Waman VP, Alsulami A, Ascher DB, Blundell TL. HARP: a database of structural impacts of systematic missense mutations in drug targets of . Computational and Structural Biotechnology Journal. 18: 3692-3704. PMID 33304465 DOI: 10.1016/j.csbj.2020.11.013  0.712
2020 Vedithi SC, Rodrigues CHM, Portelli S, Skwark MJ, Das M, Ascher DB, Blundell TL, Malhotra S. Computational saturation mutagenesis to predict structural consequences of systematic mutations in the beta subunit of RNA polymerase in . Computational and Structural Biotechnology Journal. 18: 271-286. PMID 32042379 DOI: 10.1016/J.Csbj.2020.01.002  0.737
2019 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, et al. Genome3D: integrating a collaborative data pipeline to expand the depth and breadth of consensus protein structure annotation. Nucleic Acids Research. PMID 31733063 DOI: 10.1093/Nar/Gkz967  0.774
2019 Skwark MJ, Torres PHM, Copoiu L, Bannerman B, Floto RA, Blundell TL. Mabellini: a genome-wide database for understanding the structural proteome and evaluating prospective antimicrobial targets of the emerging pathogen Mycobacterium abscessus. Database : the Journal of Biological Databases and Curation. 2019. PMID 31681953 DOI: 10.1093/Database/Baz113  0.627
2019 Waman VP, Vedithi SC, Thomas SE, Bannerman BP, Munir A, Skwark MJ, Malhotra S, Blundell TL. Mycobacterial genomics and structural bioinformatics: opportunities and challenges in drug discovery. Emerging Microbes & Infections. 8: 109-118. PMID 30866765 DOI: 10.1080/22221751.2018.1561158  0.661
2018 Boeck L, Skwark M, Pearson W, Burbaud S, Sangen J, Malhotra S, Bryant J, Blundell TL, Dionne M, Parkhill J, Floto A. Late Breaking Abstract - Multidimensional genomic mapping reveals the pathophysiology of Mycobacterium abscessus European Respiratory Journal. DOI: 10.1183/13993003.Congress-2018.Pa5450  0.363
2017 Teixeira PL, Mendenhall JL, Heinze S, Weiner B, Skwark MJ, Meiler J. Membrane protein contact and structure prediction using co-evolution in conjunction with machine learning. Plos One. 12: e0177866. PMID 28542325 DOI: 10.1371/Journal.Pone.0177866  0.626
2017 Michel M, Skwark MJ, Menéndez Hurtado D, Ekeberg M, Elofsson A. Predicting accurate contacts in thousands of Pfam domain families using PconsC3. Bioinformatics (Oxford, England). PMID 28535189 DOI: 10.1093/Bioinformatics/Btx332  0.635
2017 Skwark MJ, Croucher NJ, Puranen S, Chewapreecha C, Pesonen M, Xu YY, Turner P, Harris SR, Beres SB, Musser JM, Parkhill J, Bentley SD, Aurell E, Corander J. Interacting networks of resistance, virulence and core machinery genes identified by genome-wide epistasis analysis. Plos Genetics. 13: e1006508. PMID 28207813 DOI: 10.1371/Journal.Pgen.1006508  0.63
2016 Borza CM, Su Y, Tran TL, Yu L, Steyns N, Temple KJ, Skwark MJ, Meiler J, Lindsley CW, Hicks BR, Leitinger B, Zent R, Pozzi A. Discoidin domain receptor 1 kinase activity is required for regulating collagen IV synthesis. Matrix Biology : Journal of the International Society For Matrix Biology. PMID 27915093 DOI: 10.1016/J.Matbio.2016.11.009  0.488
2014 Skwark MJ, Raimondi D, Michel M, Elofsson A. Improved contact predictions using the recognition of protein like contact patterns. Plos Computational Biology. 10: e1003889. PMID 25375897 DOI: 10.1371/Journal.Pcbi.1003889  0.667
2014 Feinauer C, Skwark MJ, Pagnani A, Aurell E. Improving contact prediction along three dimensions. Plos Computational Biology. 10: e1003847. PMID 25299132 DOI: 10.1371/Journal.Pcbi.1003847  0.663
2014 Michel M, Hayat S, Skwark MJ, Sander C, Marks DS, Elofsson A. PconsFold: improved contact predictions improve protein models. Bioinformatics (Oxford, England). 30: i482-8. PMID 25161237 DOI: 10.1093/Bioinformatics/Btu458  0.657
2014 Ge C, Gõmez-Llobregat J, Skwark MJ, Ruysschaert JM, Wieslander A, Lindén M. Membrane remodeling capacity of a vesicle-inducing glycosyltransferase Febs Journal. 281: 3667-3684. PMID 24961908 DOI: 10.1111/Febs.12889  0.368
2014 Feinauer C, Skwark MJ, Pagnani A, Aurell E. Improving Contact Prediction along Three Dimensions Plos Computational Biology. 10. DOI: 10.1371/journal.pcbi.1003847  0.575
2013 Skwark MJ, Elofsson A. PconsD: ultra rapid, accurate model quality assessment for protein structure prediction. Bioinformatics (Oxford, England). 29: 1817-8. PMID 23677942 DOI: 10.1093/Bioinformatics/Btt272  0.633
2013 Skwark MJ, Abdel-Rehim A, Elofsson A. PconsC: combination of direct information methods and alignments improves contact prediction. Bioinformatics (Oxford, England). 29: 1815-6. PMID 23658418 DOI: 10.1093/Bioinformatics/Btt259  0.652
2013 Bendz M, Skwark M, Nilsson D, Granholm V, Cristobal S, Käll L, Elofsson A. Membrane protein shaving with thermolysin can be used to evaluate topology predictors. Proteomics. 13: 1467-80. PMID 23512833 DOI: 10.1002/Pmic.201200517  0.616
2011 Larsson P, Skwark MJ, Wallner B, Elofsson A. Improved predictions by using multiple templates. Bioinformatics (Oxford, England). 27: 426-7. PMID 21149277 DOI: 10.1093/Bioinformatics/Btq664  0.749
2009 Larsson P, Skwark MJ, Wallner B, Elofsson A. Assessment of global and local model quality in CASP8 using Pcons and ProQ. Proteins. 77: 167-72. PMID 19544566 DOI: 10.1002/Prot.22476  0.725
2008 Viklund H, Bernsel A, Skwark M, Elofsson A. SPOCTOPUS: a combined predictor of signal peptides and membrane protein topology. Bioinformatics (Oxford, England). 24: 2928-9. PMID 18945683 DOI: 10.1093/Bioinformatics/Btn550  0.695
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