Bioinformatics (Schwede)

Molodenskiy, Dmitry et al. (2024) ‘AlphaPulldown2 - A General Pipeline for High-Throughput Structural Modeling’, bioRxiv [Preprint]. Cold Spring Harbor Laboratory. Available at: https://doi.org/10.1101/2024.11.28.625873.

Hillenbrand, Caroline A. et al. (2024) ‘BK Polyomavirus (BKPyV) Serotype-Specific Antibody Responses in Blood Donors and Kidney Transplant Recipients with and without new-onset BKPyV-DNAemia: A Swiss Transplant Cohort Study’, American Journal of Transplantation, p. Online ahead of print. Available at: https://doi.org/10.1016/j.ajt.2024.11.019.

Weissbach, Fabian H. et al. (2024) ‘Single-cell RNA-sequencing of BK polyomavirus replication in primary human renal proximal tubular epithelial cells identifies specific transcriptome signatures and a novel mitochondrial stress pattern’, Journal of Virology, 98(12). Available at: https://doi.org/10.1128/jvi.01382-24.

Dörig, Christian et al. (2024) ‘Global profiling of protein complex dynamics with an experimental library of protein interaction markers’, Nature Biotechnology, p. Online ahead of print. Available at: https://doi.org/10.1038/s41587-024-02432-8.

Pertseva, Margarita et al. (2024) ‘TCR clustering by contrastive learning on antigen specificity’, Briefings in Bioinformatics, 25(5). Available at: https://doi.org/10.1093/bib/bbae375.

Durairaj, Janani et al. (2024) ‘PLINDER: The protein-ligand interactions dataset and evaluation resource’, bioRxiv [Preprint]. Cold Spring Harbor Laboratory. Available at: https://doi.org/10.1101/2024.07.17.603955.

Palermo, G. et al. (2024) ‘LIGATE - LIgand Generator and portable drug discovery platform AT Exascale’, in 20th ACM International Conference on Computing Frontiers. New York, NY, USA: ACM (20th ACM International Conference on Computing Frontiers), pp. 107–109. Available at: https://doi.org/10.1145/3637543.3656335.

Eberhardt, Jérôme et al. (2024) ‘Combining Bayesian optimization with sequence- or structure-based strategies for optimization of peptide-binding protein’, ChemRxiv [Preprint]. American Chemical Society (ACS). Available at: https://doi.org/10.26434/chemrxiv-2023-b7l81-v2.

Pantolini, Lorenzo et al. (2024) ‘Embedding-based alignment: combining protein language models with dynamic programming alignment to detect structural similarities in the twilight-zone’, Bioinformatics, 40(1). Available at: https://doi.org/10.1093/bioinformatics/btad786.

Durairaj, Janani et al. (2024) ‘Structural implications of BK polyomavirus sequence variations in the major viral capsid protein Vp1 and large T-antigen: a computational study’, mSphere, p. Online ahead of print. Available at: https://doi.org/10.1128/msphere.00799-23.

Vallat, Brinda et al. (2024) ‘IHMCIF: An Extension of the PDBx/mmCIF Data Standard for Integrative Structure Determination Methods: IHMCIF Data Standard for Integrative Structures’, Journal of Molecular Biology, 436(17). Available at: https://doi.org/10.1016/j.jmb.2024.168546.

Waterhouse, Andrew et al. (2024) ‘The Structure Assessment Web Server: for Proteins, Complexes and More’, Nucleic Acids Research, p. Online ahead of print. Available at: https://doi.org/10.1093/nar/gkae270.

Durairaj, Janani et al. (2023) ‘Structural implications of BK polyomavirus sequence variations in the major viral capsid protein Vp1 and large T-antigen: a computational study’. bioRxiv. Available at: https://doi.org/10.1101/2023.12.21.572635.

Studer, G., Tauriello, G. and Schwede, T. (2023) ‘Assessment of the assessment—All about complexes’, Proteins: Structure, Function and Bioinformatics, 91(12), pp. 1850–1860. Available at: https://doi.org/10.1002/prot.26612.

Kryshtafovych, A. et al. (2023) ‘Critical assessment of methods of protein structure prediction (CASP)—Round XV’, Proteins: Structure, Function, and Bioinformatics, 91(12), pp. 1539–1549. Available at: https://doi.org/10.1002/prot.26617.

Eberhardt, Jérôme, Lill, Markus and Schwede, Torsten (2023) ‘Combining Bayesian optimization with sequence- or structure-based strategies for optimization of peptide-binding protein’, ChemRxiv [Preprint]. American Chemical Society (ACS). Available at: https://doi.org/10.26434/chemrxiv-2023-b7l81.

Robin, X. et al. (2023) ‘Automated benchmarking of combined protein structure and ligand conformation prediction’. Authorea. Available at: https://doi.org/10.22541/au.168382988.85108031/v1.

Li, C. et al. (2023) ‘Maize resistance to witchweed through changes in strigolactone biosynthesis’, Science, 379(6627), pp. 94–99. Available at: https://doi.org/10.1126/science.abq4775.

Alexander, Leila T et al. (2023) ‘Protein target highlights in CASP15: Analysis of models by structure providers.’, Proteins, 91(12), pp. 1571–1599. Available at: https://doi.org/10.1002/prot.26545.

Durairaj, Janani et al. (2023) ‘From Genomes to Variant Interpretations Through Protein Structures’, pp. 41–50. Available at: https://doi.org/10.1007/978-3-031-30691-4_6.

Durairaj, Janani, de Ridder, Dick and van Dijk, Aalt D.J. (2023) ‘Beyond sequence: Structure-based machine learning’, Computational and Structural Biotechnology Journal, 21, pp. 630–643. Available at: https://doi.org/10.1016/j.csbj.2022.12.039.

Durairaj, Janani et al. (2023) ‘Uncovering new families and folds in the natural protein universe’, Nature, 622(7983), pp. 646–653. Available at: https://doi.org/10.1038/s41586-023-06622-3.

Kryshtafovych, Andriy et al. (2023) ‘New prediction categories in CASP15.’, Proteins, 91(12), pp. 1550–1557. Available at: https://doi.org/10.1002/prot.26515.

Leemann, Michèle et al. (2023) ‘Automated benchmarking of combined protein structure and ligand conformation prediction’, Proteins: Structure, Function and Bioinformatics, 91, pp. 1912–1924. Available at: https://doi.org/10.1002/prot.26605.

Marone, Romina et al. (2023) ‘Epitope-engineered human hematopoietic stem cells are shielded from CD123-targeted immunotherapy’, Journal of Experimental Medicine, 220(12). Available at: https://doi.org/10.1084/jem.20231235.

Mullowney, Michael W. et al. (2023) ‘Artificial intelligence for natural product drug discovery’, Nature Reviews Drug Discovery, 22, pp. 895–916. Available at: https://doi.org/10.1038/s41573-023-00774-7.

Palermo, G. et al. (2023) ‘Tunable and Portable Extreme-Scale Drug Discovery Platform at Exascale: the LIGATE Approach’, pp. 272–278. Available at: https://doi.org/10.1145/3587135.3592172.

Robin, Xavier et al. (2023) ‘Assessment of protein–ligand complexes in CASP15’, Proteins: Structure, Function and Bioinformatics, 91, pp. 1811–1821. Available at: https://doi.org/10.1002/prot.26601.

Schweke, Hugo et al. (2023) ‘Discriminating physiological from non-physiological interfaces in structures of protein complexes: A community-wide study’, Proteomics, 23(17), p. e2200323. Available at: https://doi.org/10.1002/pmic.202200323.

Topitsch, Annika, Schwede, Torsten and Pereira, Joana (2023) ‘Outer membrane β-barrel structure prediction through the lens of AlphaFold2.’, Proteins, 92(1), pp. 3–14. Available at: https://doi.org/10.1002/prot.26552.

Vallat, Brinda et al. (2023) ‘ModelCIF: An extension of PDBx/mmCIF data representation for computed structure models’, Journal of Molecular Biology, 435(14), p. 168021. Available at: https://doi.org/10.1016/j.jmb.2023.168021.

Akdel, Mehmet et al. (2022) ‘A structural biology community assessment of AlphaFold2 applications’, Nature Structural and Molecular Biology, 29(11), pp. 1056–1067. Available at: https://doi.org/10.1038/s41594-022-00849-w.

Alt, Silke et al. (2022) ‘INCATE: a partnership to boost the antibiotic pipeline’, Nature Reviews. Drug Discovery, 21(9), pp. 621–622. Available at: https://doi.org/10.1038/d41573-022-00138-7.

Landmann, Emmanuelle et al. (2022) ‘Engineered Single Amino Acid Substitutions Protect Hematopoietic Stem and Progenitor Cells from CD123 Targeted Immunotherapy’, Blood, 140(Supplement 1), pp. 5724–5725. Available at: https://doi.org/10.1182/blood-2022-163815.

Topitsch, Annika, Schwede, Torsten and Pereira, Joana (2022) ‘Outer membrane β-barrel structure prediction through the lens of AlphaFold2’. bioRxiv. Available at: https://doi.org/10.1101/2022.10.09.511469.

Varadi, Mihaly et al. (2022) ‘3D-Beacons: decreasing the gap between protein sequences and structures through a federated network of protein structure data resources’, GigaScience, 11, p. giac118. Available at: https://doi.org/10.1093/gigascience/giac118.

Alexander, Leila T. et al. (2021) ‘Target highlights in CASP14: analysis of models by structure providers’, Proteins: Structure, Function, and Bioinformatics, pp. 1–26. Available at: https://doi.org/10.1002/prot.26247.

Kryshtafovych, Andriy et al. (2021) ‘Critical assessment of methods of protein structure prediction (CASP)-Round XIV’, Proteins: Structure, Function, and Bioinformatics, 89(12), pp. 1607–1617. Available at: https://doi.org/10.1002/prot.26237.

Mari, Alfredo et al. (2021) ‘Global Genomic Analysis of SARS-CoV-2 RNA Dependent RNA Polymerase Evolution and Antiviral Drug Resistance’, Microorganisms, 9(5), p. 1094. Available at: https://doi.org/10.3390/microorganisms9051094.

Pereira, Joana and Schwede, Torsten (2021) ‘Interactomes in the era of deep learning’, Science, 374(6573), pp. 1319–1320. Available at: https://doi.org/10.1126/science.abm8295.

Rehm, Heidi L. et al. (2021) ‘GA4GH: International policies and standards for data sharing across genomic research and healthcare’, Cell Genomics, 1(2), p. 100029. Available at: https://doi.org/10.1016/j.xgen.2021.100029.

Robin, Xavier et al. (2021) ‘Continuous Automated Model Evaluation (CAMEO)-Perspectives on the future of fully automated evaluation of structure prediction methods’, Proteins: Structure, Function, and Bioinformatics, 89(12), pp. 1977–1986. Available at: https://doi.org/10.1002/prot.26213.

Studer, Gabriel et al. (2021) ‘ProMod3-A versatile homology modelling toolbox’, PLoS Computational Biology, 17(1), p. e1008667. Available at: https://doi.org/10.1371/journal.pcbi.1008667.

Bignucolo, Olivier and Bernèche, Simon (2020) ‘The Voltage-Dependent Deactivation of the KvAP Channel Involves the Breakage of Its S4 Helix’, Frontiers in molecular biosciences, 7, p. 162. Available at: https://doi.org/10.3389/fmolb.2020.00162.

Coman Schmid, Diana et al. (2020) ‘SPHN - The BioMedIT Network: A Secure IT Platform for Research with Sensitive Human Data’, Studies in health technology and informatics, 270, pp. 1170–1174. Available at: https://doi.org/10.3233/shti200348.

Gervasoni, Silvia et al. (2020) ‘A Comprehensive Mapping of the Druggable Cavities within the SARS-CoV-2 Therapeutically Relevant Proteins by Combining Pocket and Docking Searches as Implemented in Pockets 2.0’, International journal of molecular sciences, 21(14), p. 5152. Available at: https://doi.org/10.3390/ijms21145152.

Righetto, Ricardo D. et al. (2020) ‘High-resolution cryo-EM structure of urease from the pathogen Yersinia enterocolitica’, Nature Communications, 11(1), p. 5101. Available at: https://doi.org/10.1038/s41467-020-18870-2.

Righetto, Ricardo D. et al. (2020) ‘Author Correction: High-resolution cryo-EM structure of urease from the pathogen Yersinia enterocolitica’, Nature Communications, 11(1), p. 5873. Available at: https://doi.org/10.1038/s41467-020-19845-z.

Berman, Helen M. et al. (2019) ‘Federating Structural Models and Data: Outcomes from A Workshop on Archiving Integrative Structures’, Structure (London, England : 1993), 27(12), pp. 1745–1759. Available at: https://doi.org/10.1016/j.str.2019.11.002.

Cheng, Jianlin et al. (2019) ‘Estimation of model accuracy in CASP13’, Proteins, 87(12), pp. 1361–1377. Available at: https://doi.org/10.1002/prot.25767.

Delezie, Julien et al. (2019) ‘BDNF is a mediator of glycolytic fiber-type specification in mouse skeletal muscle’, Proceedings of the National Academy of Sciences (PNAS), 116(32), pp. 16111–16120. Available at: https://doi.org/10.1073/pnas.1900544116.

Haas, Juergen et al. (2019) ‘Introducing ‘best single template’ models as reference baseline for the Continuous Automated Model Evaluation (CAMEO)’, Proteins, 87(12), pp. 1378–1387. Available at: https://doi.org/10.1002/prot.25815.

Kryshtafovych, Andriy et al. (2019) ‘Critical assessment of methods of protein structure prediction (CASP)-Round XIII’, Proteins, 87(12), pp. 1011–1020. Available at: https://doi.org/10.1002/prot.25823.

Lepore, Rosalba et al. (2019) ‘Target highlights in CASP13: Experimental target structures through the eyes of their authors’, Proteins: Structure, Function, and Bioinformatics, 87(12), pp. 1037–1057. Available at: https://doi.org/10.1002/prot.25805.

Studer, Gabriel et al. (2019) ‘QMEANDisCo - Distance Constraints Applied on Model Quality Estimation’, Bioinformatics, 36(6), pp. 1765–1771. Available at: https://doi.org/10.1093/bioinformatics/btz828.

Studer, Gabriel et al. (2019) ‘Modeling of Protein Tertiary and Quaternary Structures Based on Evolutionary Information’, Methods in Molecular Biology, 1851, pp. 301–316. Available at: https://doi.org/10.1007/978-1-4939-8736-8_17.

Haas, Jürgen et al. (2018) ‘Continuous Automated Model Evaluation (CAMEO) Complementing the Critical Assessment of Structure Prediction in CASP12’, Proteins, 86 Suppl 1, pp. 387–398. Available at: https://doi.org/10.1002/prot.25431.

Kryshtafovych, Andriy et al. (2018) ‘Target highlights from the first post-PSI CASP experiment (CASP12, May-August 2016)’, Proteins: Structure, Function, and Bioinformatics, 86 Suppl 1(1), pp. 27–50. Available at: https://doi.org/10.1002/prot.25392.

Kryshtafovych, Andriy et al. (2018) ‘Evaluation of the template-based modeling in CASP12’, Proteins, 86 Suppl 1, pp. 321–334. Available at: https://doi.org/10.1002/prot.25425.

Lafita, Aleix et al. (2018) ‘Assessment of protein assembly prediction in CASP12’, Proteins: Structure, Function, and Bioinformatics, 86 Suppl 1(1), pp. 247–256. Available at: https://doi.org/10.1002/prot.25408.

Moult, John et al. (2018) ‘A tribute to Anna Tramontano (1957-2017)’, Proteins: Structure, Function, and Bioinformatics, 86(1), pp. 5–6. Available at: https://doi.org/10.1002/prot.25406.

Moult, John et al. (2018) ‘Critical assessment of methods of protein structure prediction (CASP) - Round XII’, Proteins: Structure, Function, and Bioinformatics, 86 Suppl 1(1), pp. 7–15. Available at: https://doi.org/10.1002/prot.25415.

Waterhouse, Andrew et al. (2018) ‘SWISS-MODEL: homology modelling of protein structures and complexes’, Nucleic acids research, 46(W1), pp. W296–W303. Available at: https://doi.org/10.1093/nar/gky427.

Capella-Gutierrez, Salvador et al. (2017) ‘Lessons Learned: Recommendations for Establishing Critical Periodic Scientific Benchmarking’, bioRxiv [Preprint]. Cold Spring Harbor Laboratory. Available at: https://doi.org/10.1101/181677.

Bertoni, Martino et al. (2017) ‘Modeling protein quaternary structure of homo- and hetero-oligomers beyond binary interactions by homology’, Scientific Reports, 7(1), p. 10480. Available at: https://doi.org/10.1038/s41598-017-09654-8.

Bienert, Stefan et al. (2017) ‘The SWISS-MODEL Repository - new features and functionality’, Nucleic Acids Research, 45(D1), pp. D313–D319. Available at: https://doi.org/10.1093/nar/gkw1132.

Bozadjieva, Nadejda et al. (2017) ‘Loss of mTORC1 signaling alters pancreatic α cell mass and impairs glucagon secretion’, The Journal of Clinical Investigation, 127(12), pp. 4379–4393. Available at: https://doi.org/10.1172/jci90004.

Burley, Stephen K. et al. (2017) ‘PDB-Dev: a Prototype System for Depositing Integrative/Hybrid Structural Models’, Structure, 25(9), pp. 1317–1318. Available at: https://doi.org/10.1016/j.str.2017.08.001.

Daina, Antoine et al. (2017) ‘Drug Design Workshop: A Web-Based Educational Tool To Introduce Computer-Aided Drug Design to the General Public’, Journal of Chemical Education, 94(3), pp. 335–344. Available at: https://doi.org/10.1021/acs.jchemed.6b00596.

Glusman, Gustavo et al. (2017) ‘Mapping genetic variations to three-dimensional protein structures to enhance variant interpretation: a proposed framework’, Genome medicine, 9(1), p. 113. Available at: https://doi.org/10.1186/s13073-017-0509-y.

Heck, Angela et al. (2017) ‘Exome sequencing of healthy phenotypic extremes links TROVE2 to emotional memory and PTSD’, Nature Human Behaviour, 1, p. 0081. Available at: https://doi.org/10.1038/s41562-017-0081.

Heer, Florian T. et al. (2017) ‘Mechanism of activation at the selectivity filter of the KcsA K(+) channel’, eLife, 6, p. e25844. Available at: https://doi.org/10.7554/elife.25844.

Johner, Niklaus B. and Berneche, Simon (2017) ‘Effect of Membrane Composition on Ion Conduction in a Voltage-Gated Potassium Channel’, Biophysical Journal. Cell Press, 112(3, Supplement 1). Available at: https://doi.org/10.1016/j.bpj.2016.11.2930.

Kryshtafovych, Andriy et al. (2017) ‘Assessment of model accuracy estimations in CASP12’, Proteins, 86 Suppl 1(S1), pp. 345–360. Available at: https://doi.org/10.1002/prot.25371.

Romano, Valentina, de Beer, Tjaart A. P. and Schwede, Torsten (2017) ‘A computational protocol to evaluate the effects of protein mutants in the kinase gatekeeper position on the binding of ATP substrate analogues’, BMC Research Notes, 10(1), p. 104. Available at: https://doi.org/10.1186/s13104-017-2428-9.

Sprecher, Kathrin S. et al. (2017) ‘Cohesive Properties of the Caulobacter crescentus Holdfast Adhesin Are Regulated by a Novel c-di-GMP Effector Protein’, mBio, 8(2), pp. e00294–17. Available at: https://doi.org/10.1128/mbio.00294-17.

Starek, Greg et al. (2017) ‘Gating energetics of a voltage-dependent K(+) channel pore domain’, Journal of Computational Chemistry, 38(16), pp. 1472–1478. Available at: https://doi.org/10.1002/jcc.24742.

Thornton, Janet M., Valencia, Alfonso and Schwede, Torsten (2017) ‘Anna Tramontano 1957-2017’, Nature Structural and Molecular Biology, 24(5), pp. 431–432. Available at: https://doi.org/10.1038/nsmb.3410.

Trewhella, Jill et al. (2017) ‘2017 publication guidelines for structural modelling of small-angle scattering data from biomolecules in solution: an update’, Acta Crystallographica Section D, 73(Pt 9), pp. 710–728. Available at: https://doi.org/10.1107/s2059798317011597.

Vullo, Sabrina et al. (2017) ‘Conformational dynamics and role of the acidic pocket in ASIC pH-dependent gating’, Proceedings of the National Academy of Sciences of the United States of America, 114(14), pp. 3768–3773. Available at: https://doi.org/10.1073/pnas.1620560114.

Xu, Yanyan, Seelig, Anna and Bernèche, Simon (2017) ‘Unidirectional Transport Mechanism in an ATP Dependent Exporter’, ACS Central Science, 3(3), pp. 250–258. Available at: https://doi.org/10.1021/acscentsci.7b00068.

Xu, Yanyan et al. (2017) ‘Molecular Mechanism of Cl-/H+ Coupling in a CLC Antiporter’, Biophysical Journal. Cell Press, 112(3, Supplement 1). Available at: https://doi.org/10.1016/j.bpj.2016.11.1819.

Dubey, Badri N. et al. (2016) ‘Cyclic di-GMP mediates a histidine kinase/phosphatase switch by noncovalent domain cross-linking’, Science Advances, 2(9), p. e1600823. Available at: https://doi.org/10.1126/sciadv.1600823.

Kryshtafovych, Andriy et al. (2016) ‘Methods of model accuracy estimation can help selecting the best models from decoy sets: assessment of model accuracy estimations in CASP11’, Proteins: Structure, Function, and Bioinformatics, 84 Suppl 1(1), pp. 349–69. Available at: https://doi.org/10.1002/prot.24919.

Kryshtafovych, Andriy et al. (2016) ‘Some of the most interesting CASP11 targets through the eyes of their authors’, Proteins: Structure, Function, and Bioinformatics, 84(Suppl 1), pp. 34–50. Available at: https://doi.org/10.1002/prot.24942.

Moult, John et al. (2016) ‘Critical assessment of methods of protein structure prediction: Progress and new directions in round XI’, Proteins: Structure, Function, and Bioinformatics, 84 Suppl 1(1), pp. 4–14. Available at: https://doi.org/10.1002/prot.25064.

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Gallo Cassarino, Tiziano, Bordoli, Lorenza and Schwede, Torsten (2014) ‘Assessment of ligand binding site predictions in CASP10.’, Proteins, 82 Suppl 2(S2), pp. 154–63. Available at: https://doi.org/10.1002/prot.24495.

Haas, Jürgen and Schwede, Torsten (2014) ‘Unabhängige Validierung von Methoden zur Proteinstrukturvorhersage’, Biospektrum, 20(2), pp. 236–237. Available at: https://doi.org/10.1007/s12268-014-0432-3.

Kryshtafovych, Andriy et al. (2014) ‘Assessment of the assessment : evaluation of the model quality estimates in CASP10’, Proteins, 82 Suppl 2(S2), pp. 112–26. Available at: https://doi.org/10.1002/prot.24347.

Kryshtafovych, Andriy et al. (2014) ‘Challenging the state-of-the-art in protein structure prediction : highlights of experimental target structures for the 10(th) Critical Assessment of Techniques for Protein Structure Prediction Experiment CASP10’, Proteins, 82(S2), pp. 26–42. Available at: https://doi.org/10.1002/prot.24489.

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