From sermarcue at gmail.com Wed Mar 6 09:00:00 2024 From: sermarcue at gmail.com (Sergio Martinez Cuesta) Date: Wed, 6 Mar 2024 08:00:00 +0000 Subject: [SocBiN] Postdoctoral research position at the Barts Cancer Institute - Queen Mary University London Message-ID: Hi all, Are you an enthusiastic PhD interested in developing bioinformatics approaches to understand the role of transposable elements in cancer? Ozgen Deniz 's team at the Barts Cancer Institute (Queen Mary University of London) has a postdoctoral opening. Check it out and apply! https://www.jobs.ac.uk/job/DFN649/postdoctoral-research-assistant Application deadline *20th March* Thanks, Sergio --------------------------- We are looking for a computational postdoctoral research assistant to join our group at the Barts Cancer Institute, London. The appointed PDRA will be integrated into a multidisciplinary team and will collaborate with bioinformaticians, experimentalists and clinicians and develop/apply transposable elements-centered bioinformatic pipelines for transcriptomic and epigenomic data sets. The post is funded by the Cancer Research UK, full time (35 hours per week) and fixed term appointment for 30 months with potential extension. The application deadline is 20th March. For more information and questions, see the job advertisement attached and contact us (o.deniz at qmul.ac.uk). -------------- next part -------------- An HTML attachment was scrubbed... URL: From arne.elofsson at gmail.com Wed Mar 6 10:57:48 2024 From: arne.elofsson at gmail.com (Arne Elofsson) Date: Wed, 6 Mar 2024 10:57:48 +0100 Subject: [SocBiN] =?utf-8?q?Fwd=3A_Professor_or_Associate_Professor_=28Lev?= =?utf-8?q?el_2=29_in_Biochemistry=2C_=C3=85bo_Akademi_University?= =?utf-8?q?=2C_Turku=2C_Finland?= In-Reply-To: <513fc7bf03d540ed8d414b5751b28687@abo.fi> References: <323ed2d1040241a1b7fa245fd99a7ee7@abo.fi> <035a478edb0c442b99432d5b064243b4@abo.fi> <2ffdf447171e40cf9ca9cf832700472c@abo.fi> <513fc7bf03d540ed8d414b5751b28687@abo.fi> Message-ID: From: Tiina Salminen Date: Wed, Mar 6, 2024 at 10:42 AM Subject: Professor or Associate Professor (Level 2) in Biochemistry, Åbo Akademi University, Turku, Finland To: Arne Elofsson Hej, Jag är inte säker om min epost via 3D-Bioinfo skickades vidare så mailar nu direkt till dig. Jag skulle vara väldigt tacksam om du kan skicka informationen om den utannonserade tjänsten (nedan) vidare via dina informationskanaler. Förvaltningsspråket vid Åbo Akademi är primärt svenska, undervisningsspråken svenska och engelska. Tack på förhand. mvh, Tiina ------------------------------ Dear all, Åbo Akademi University (Turku, Finland) invites applications for the position as *Professor or Associate Professor (Level 2) in Biochemistry* at the Faculty of Science and Engineering (FNT), starting 1 December 2024 or by separate agreement. The closing date for applications is on *2.4.2024 at 12:00 (Finnish local time)*. *Detailed information about the position, the qualification and evaluation criteria and the recruitment process are found in the appointment plan and the details how to apply in the call text * *.* Best regards, Tiina ********************************************** Tiina A. Salminen, Professor Head of Subject Cluster for Biochemistry and Cell Biology Structural Bioinformatics Laboratory and InFLAMES Research Flagship Center Biochemistry, Faculty of Science and Engineering Abo Akademi University Tykistökatu 6A FI-20520 Turku Finland +358 40 515 0201 ------------------------------ -------------- next part -------------- An HTML attachment was scrubbed... URL: From lionel.guy at imbim.uu.se Wed Mar 6 11:07:51 2024 From: lionel.guy at imbim.uu.se (Lionel Guy) Date: Wed, 6 Mar 2024 10:07:51 +0000 Subject: [SocBiN] PhD student position in evolutionary microbiology at Uppsala University Message-ID: <98E4349B-6EDC-4E7C-9893-EDA91F75B65D@imbim.uu.se> A PhD student position in evolutionary microbiology, with focus on the evolution of intracellular bacteria, is now available at Uppsala University, Sweden. The position is fully funded for four years. Start date: Summer/autumn 2024. Deadline to apply: 8 April 2024. Please find all the details and instructions on how to apply at: https://uu.varbi.com/en/what:job/jobID:708285/ The Department of Medical Biochemistry and Microbiology (IMBIM) at Uppsala University provides a broad international environment for research and teaching. Research at IMBIM) broadly spans the areas of biochemistry, cell and molecular biology, tumour biology, comparative genetics, functional genomics, immunology, bacteriology, and virology. The research is essentially of fundamental nature, but with relevance and application in health and disease in both animals and humans. More info: https://www.imbim.uu.se/research-areas/. We are looking for a highly motivated PhD student to be involved in the project “A two-billion-years history of infections: evolution of host-adaptation in early Gammaproteobacteria”, funded by the Swedish Research Board. The project is led by Lionel Guy, and the PhD student will be located at the Biomedical Centre, Uppsala, Sweden. Project description The ability to feed on other organisms through phagocytosis is a crucial step in the evolution of eukaryotes, a prerequisite for food webs, multicellularity and, arguably, the acquisition of mitochondria. It also paved the way for intracellular parasitism, as some bacteria avoided digestion by their hosts and multiplied in the nutrient-rich cytoplasm. Here, we focus on the Deep-branching Intracellular Gammaproteobacteria (DIG), a large group of related bacteria (e.g. Legionella and Francisella) with a wide variety of host-adaptation strategies. We hypothesize that the last common ancestor of DIG, appeared during eukaryogenesis, 2 Ga ago, and was among the first bacteria to infect eukaryotes. In this project, the PhD student will gather a solid set of DIG genomes, reconstruct their evolutionary history, assess their metabolic potential, and identify their host-adaptation genes. They will screen genomes for horizontal gene transfers from early eukaryotes or Asgard archaea. Through a better understanding of the relationships between the first eukaryotes and their early invaders, the gained results will shed light on eukaryogenesis, particularly the role of phagocytosis. Duties The main duties of PhD students are to devote themselves to their research studies, which includes participating in research projects and third cycle courses. The work duties can also include teaching and other departmental duties (not more than 20 % of full time). Requirements To meet the entry requirements for doctoral studies, you must - hold a Master’s (second-cycle) degree in bioinformatics, molecular biology, microbiology, microbial ecology or similar field, or - have completed at least 240 credits in higher education, with at least 60 credits at Master’s level including an independent project worth at least 15 credits, or - have acquired substantially equivalent knowledge in some other way. - Documented coding skills in Python or R - Experience in using and/or developing methods in metagenomics and molecular evolution - Background understanding of, and interest in, microbial evolution - Proficiency in spoken and written English; Ability to conceive, execute, and complete research projects independently Creativity and good group-working skills Additional qualifications - Experience in creating pipelines for use with high performance computing clusters - Competence in large dataset handling The requirements listed above need to be met before the employment starts, but not necessarily by the application deadline. Lionel Guy lionel.guy at imbim.uu.se -- Lionel Guy Department for Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden phone: +46 18 471 4246; mobile +46 73 976 0618; postal address: Box 582, SE-751 23 Uppsala; visiting address: BMC D7:308b, Husargatan 3, SE-752 37 Uppsala lionel.guy at imbim.uu.se -------------- next part -------------- A non-text attachment was scrubbed... Name: smime.p7s Type: application/pkcs7-signature Size: 4654 bytes Desc: not available URL: From sonja.lorenz at mpinat.mpg.de Wed Mar 6 11:15:36 2024 From: sonja.lorenz at mpinat.mpg.de (Sonja Lorenz) Date: Wed, 6 Mar 2024 11:15:36 +0100 Subject: [SocBiN] PhD and Postdoc positions @ the Max Planck Institute in Goettingen, Germany In-Reply-To: <98E4349B-6EDC-4E7C-9893-EDA91F75B65D@imbim.uu.se> References: <98E4349B-6EDC-4E7C-9893-EDA91F75B65D@imbim.uu.se> Message-ID: <4F566FBA-6D95-476C-9A27-3D1FAC2B1B5E@mpinat.mpg.de> Dear colleagues, there are PhD and postdoc positions available in my laboratory at the Max Planck Institute for Multidisciplinary Sciences in Goettingen/Germany. I would be very grateful if you could share the ad and link below with suitable candidates. Link to the job offer: https://www.mpinat.mpg.de/4634381/11-24 https://www.mpinat.mpg.de/4634381/11-24 Many thanks and best wishes, Sonja Lorenz =========================================== The Max Planck Institute for Multidisciplinary Sciences is a leading international research institute of exceptional scientific breadth. With more than 40 research groups and some 1,000 employees from over 50 nations, it is the largest institute of the Max Planck Society. The research group Ubiquitin Signaling Specificity (Dr. Sonja Lorenz) invites applications for the position as PhD student or Postdoc (f/m/d) – Specificity mechanisms of ubiquitin ligase complexes – Our laboratory aims to understand how the posttranslational modifier ubiquitin regulates myriad aspects of eukaryotic physiology. A major key lies in the action of ubiquitin ligases, a highly diversified enzyme class that recognizes specific substrates for ubiquitination and determines the types of modifications they are decorated with. The immense potential of ubiquitin ligases for therapeutic applications has been illustrated by the clinical efficacy of immunomodulatory drugs in the treatment of hematological malignancies and recent advances of Protacs/molecular glues. Yet, efficient targeting of ubiquitin ligases in the clinic is still hampered by our limited understanding of their structural mechanisms and integration into cellular pathways. We offer PhD or Postdoc positions to explore structure-function relationships in ubiquitin ligases. Building on strong preliminary data, available projects focus on (i) the isolation/ biochemical reconstitution of ubiquitin ligases complexes with substrates and regulators for cryo-EM analyses; (ii) the cell-based identification of ubiquitin ligase complexes and functional analyses; (iii) solution NMR analyses of the regulation and conformational dynamics of ubiquitination enzymes. Our projects typically combine several of the above-mentioned techniques and can be tailored to the particular interests of the successful candidate. For an example of our ongoing work, please see: https://www.nature.com/articles/s41594-023-01203-4 PhD candidates should hold/soon expect a MSc or equivalent degree in a relevant area of the life sciences. Initial experience in one or more of the following techniques is desired: protein biochemistry, mammalian cell biology, or any aspect of structural biology. Postdoctoral candidates should have/soon expect a PhD or equivalent degree in a relevant area of the life sciences. A proven track record in either cryo EM or solution NMR, including experience in protein purification/isolation of protein complexes. The successful candidates for either position should be curiosity-driven, creative, and passionate about science. A high degree of self-motivation and independence is important, as well as the ability to communicate well within an international, multidisciplinary team. We offer · competitive research in an inspiring, world-class environment professional training, networking and career-development opportunities; free language courses · on-site health management: free fitness and yoga room, sports groups, beach volleyball league, and courses for a "moving lunch break” a wide range of opportunities to balance work and family life, including an on-campus kindergarten and vacation care spacious on-site cafeteria offering warm meals and a salad bar · initiatives for sustainability and a green environment, including an on-site biotope About us Based at one of Germany’s premier research campuses, our research group has access to leading-edge infrastructure in all areas of cell and structural biology, including cryo-EM. We are an international team, supported by the Max Planck Society, the German Research Foundation, and the EMBO Young Investigator Program. Our working language is English; knowledge of German is not required. The historic city of Göttingen, located in the center of Germany, offers great outdoor and cultural opportunities, a vibrant student scene, and an impressive scientific heritage. Position details The positions should be filled as soon as possible; the exact start date is flexible. PhD students will be funded for three years (with a possibility of extension) and have the opportunity to enroll in one of several PhD programs in collaboration with the University of Göttingen. Fast-track MSc/PhD students are also welcome to apply. Postdoc positions are initially funded for two years with a possibility of extension. Payment and benefits are based on the TVöD (wage agreement for public service personell) guidelines. The Max Planck Society is committed to increasing the number of individuals with disabilities in its workforce and encourages applications from such qualified individuals. The Max Planck Society strives for gender and diversity equality. We welcome applications from all backgrounds. Application Please submit your application including a cover letter (explaining background and motivation), CV, academic transcripts, publication list, and the contact addresses of two preferably references as a single PDF file to the email address below. Review of applications will begin immediately. ausschreibung11-24 at mpinat.mpg.de Max Planck Institute for Multidisciplinary Sciences Research Group Ubiquitin Signaling Specificity Dr. Sonja Lorenz Am Faßberg 11 37077 Göttingen Germany Web: https://www.mpinat.mpg.de/lorenz Twitter: SLorenzLab Information pursuant to Article 13 DS-GVO on the collection and processing of personal data during the application process can be found on our website below the respective job advertisement. -------------- next part -------------- An HTML attachment was scrubbed... URL: From coordinator at rth.dk Thu Mar 7 13:44:43 2024 From: coordinator at rth.dk (Betina Wingreen Jensen) Date: Thu, 7 Mar 2024 13:44:43 +0100 Subject: [SocBiN] (Deadline March 19) Postdoc position in computational CRISPR guide RNA design at University of Copenhagen, Denmark References: <3719d2c0350748999460844143c98d77@sund.ku.dk> <3176c9be4df54c76b53615763885b540@sund.ku.dk> Message-ID: <000001da708d$3a630b00$af292100$@rth.dk> Dear Colleagues, There is still time to apply for this a super exciting 3-year position for a Postdoc in computational CRISPR guide RNA design targeting network modules here at the University of Copenhagen, Denmark, as we have extended the application deadline until March 19, 2024. For more information about the position and on how to apply, please visit the UCPH website: https://candidate.hr-manager.net/ApplicationInit.aspx/?cid=1307 &departmentId=19008&ProjectId=161190&MediaId=5&SkipAdvertisement=false Application deadline: March 19, 2024 Start date is May 15, 2024, or as soon as possible thereafter. Best wishes, Betina Betina Wingreen Jensen Special Advisor/Project Manager University of Copenhagen Department of Veterinary and Animal Sciences Grønnegårdsvej 3 & 7 & Ridebanevej 3 & 9 1870 Frederiksberg C DIR +45 35 33 47 04 MOB +45 21 51 09 32 bwj at sund.ku.dk How we protect personal data -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image001.png Type: image/png Size: 5384 bytes Desc: not available URL: From besenbacher at clin.au.dk Wed Mar 13 23:00:51 2024 From: besenbacher at clin.au.dk (=?utf-8?B?U8O4cmVuIEJlc2VuYmFjaGVy?=) Date: Wed, 13 Mar 2024 22:00:51 +0000 Subject: [SocBiN] Bioinformatics/Data Science Postdoc in Aarhus, Denmark Message-ID: We seek a Bioinformatics/Data Science Postdoc for an exciting project concerning germline mutational processes in humans. Please check out the call if you are interested: https://au.career.emply.com/en/ad/bioinformatics-data-science-postdoc-analysing-mutation-processes-in-the-human-ge/k7eejq Contact me by email if you have questions about the position or the application procedure. Best, Søren Besenbacher, Associate Professor Department of Molecular Medicine (MOMA) Aarhus University From leo.lahti at utu.fi Wed Mar 13 23:56:26 2024 From: leo.lahti at utu.fi (Leo Lahti) Date: Wed, 13 Mar 2024 22:56:26 +0000 Subject: [SocBiN] Nordic Summer School on Computational Microbiome Research Message-ID: Dear recipient, We are excited to announce a new annual training and networking event for microbiome researchers from nordic countries and beyond! This year's program includes the latest trends and methods in metagenomic assembly, data integration and antibiotic resistance mapping, and industry perspectives. The programme also includes participant talks and posters, networking and other social bits. 13-15 Aug, 2024 BioCity, Turku, Finland Lecturers: Antton Alberdi (GLOBE Institute, DK) H. Bjørn Nielsen (Clinical Microbiomics, DK) Anders Andersson (KTH/SciLifeLab, SWE) Oliver Aasmets (University of Tartu, EST) Aura Raulo (Oxford University, UK) Antti Karkman (University of Helsinki, FIN) Katariina Pärnänen (University of Turku, FIN) Organizers: Leo Lahti (University of Turku) Matti Ruuskanen (University of Turku) Tommi Vatanen (University of Helsinki) Attendance fee 300 EUR (includes lunch, coffee, social program, does not include accommodation) Apply at https://sites.utu.fi/microbiomesummerschool/ Applications submitted by April 8 will be prioritized. For more information contact us at microbiome-school at utu.fi From ovidiu.radulescu at umontpellier.fr Thu Mar 14 18:04:50 2024 From: ovidiu.radulescu at umontpellier.fr (Ovidiu Radulescu) Date: Thu, 14 Mar 2024 18:04:50 +0100 Subject: [SocBiN] tenure track position in Montpellier (AI and multiscale modeling in biology and bio-medicine) Message-ID: Dear All, A tenure track position (CPJ) on AI and multiscale modeling in biology and bio-medicine is republished this year. The job is located in my team at the University of Montpellier. In France, CPJ is an independent position, offering an accelerated track to professorship, reduced teaching duties and attractive starting grants. The junior professor is expected to develop autonomous activity. During the tenure track, teaching may be conducted in English. Please spread the word. https://systems-biology-lphi.cnrs.fr/cpj/ Best, Ovidiu Radulescu -- Prof. Ovidiu Radulescu Université de Montpellier ------------------------------------------------------------------- LPHI - UMR 5235 CNRS/UM   Phone: +33-(0)4-6714-9221 Pl. E. Bataillon - Bat. 24      Fax:   +33-(0)4-6714-4286 Université de Montpellier      email: ovidiu.radulescu at umontpellier.fr CP 107 34095 Montpellier Cedex 5 FRANCE From arne.elofsson at gmail.com Mon Mar 18 08:32:07 2024 From: arne.elofsson at gmail.com (Arne Elofsson) Date: Mon, 18 Mar 2024 08:32:07 +0100 Subject: [SocBiN] Fwd: CASP: Call for targets for the 2024 CASP modeling experiment In-Reply-To: <20240317010410.6FF0537C2945@predictioncenter5.genomecenter.ucdavis.edu> References: <20240317010410.6FF0537C2945@predictioncenter5.genomecenter.ucdavis.edu> Message-ID: CASP (Critical Assessment of Structure Prediction) experiments are held every two years. Recent rounds have seen dramatic increases in modeling accuracy, resulting from the introduction of deep learning methods: In 2018, for the first time, the folds of most proteins were correctly computed1; in 2020, the accuracy of many computed protein structures rivaled that of the corresponding experimental ones2; in 2022, there was an enormous increase in the accuracy of protein complexes3. We have seen the beginning of what deep learning methods may achieve in structural biology. In addition to further increases in the accuracy of protein complexes, methods are being developed for RNA structures, organic ligand-protein complexes, and for moving beyond single macromolecular structures to compute conformational ensembles. Accurate computational methods together with experimental data also offer the prospect of probing previously inaccessible biological systems. CASP has expanded its scope to provide critical assessment in all these areas. CASP is only possible with the generous participation of the experimental structural biology community in providing suitable targets: A total of over 1100 targets have been obtained over the previous CASP rounds. We are now requesting targets for the 2024 CASP16 experiment. We need challenge targets in the following areas: Single protein structures: The 2020 and 2022 CASPs showed that, so far, Alphafold2 and methods built around it are by far the most accurate4. But there are limitations, particularly for some proteins where only a shallow sequence alignment is available and for very large proteins (more than 1000 amino acids). The best results also require substantial amounts of computing resources, well beyond that of the AlphaFold2 default settings. Many new methods are continuing to appear and these may remove some of the remaining difficulties. All types of protein targets are needed, but especially those with shallow sequence alignments, without structural templates, and large proteins. Protein complexes: In the 2022 CASP15, advanced deep learning methods were applied to protein complexes for the first time5. The result was a huge improvement in accuracy compared with classical docking approaches. But overall, the results are still not at the level achieved for single proteins. So, in CASP16 we need all sorts of targets in this area so as to determine progress since then. We particularly need complexes where there is no evolutionary information across the protein-protein interfaces, for example, antibody-antigen complexes. (This CASP category is conducted in close collaboration with our colleagues at CAPRI - Critical Assessment of protein interactions6). Nucleic acid structures and complexes: In recognition of the major role nucleic acid structures and complexes play in biology, CASP now includes this class of target. A number of papers claiming successful RNA structure computation using deep learning methods have been published, but those participating in the 2022 CASP RNA category performed less well than classical approaches, and no methods were able to effectively address the two RNA protein-complexes included7. CASP needs a wide variety of RNA, DNA, and complexes as targets to see if this situation has changed. (This CASP category is conducted in close collaboration with RNApuzzles8). Organic ligand-protein complexes: This area is of major importance for computer-aided drug discovery. Earlier, there have been community experiments to assess the accuracy of methods, particularly SAMPL, CSAR, D3R, and a new one, CACHE, has recently started (cache-challenge.org). These challenges have drawn strong international participation from researchers in both academia and industry. Here too, a number of promising deep learning papers have appeared, but in the 2022 CASP15 pilot, classical methods were still superior9. So, we need appropriate targets to see if progress has been made since. Ideally, these should be sets of three-dimensional protein-ligand complexes from drug discovery projects, but single targets would also be appreciated. Additionally, where available, we will assess non-structural quantities such as affinities or affinity rankings and other properties of pharmaceutical interest when these are available (small molecule pKs, and DMPK related properties). Ensembles of macromolecule conformations: It is now widely recognized that proteins and nucleic acids often adopt multiple conformations that can underpin their functions. In these cases, considering only a single protein or RNA conformation may be a significant oversimplification. The 2022 CASP15 included a pilot experiment to assess methods for computing multiple conformations, with encouraging results10, but with limitations imposed by the available experimental data. For 2024, we seek not only cases of multiple experimental three-dimensional structures for the same macromolecule but also other types of data that might be used for assessment of computed conformation ensembles such as cryoEM, NMR, X-ray crystallography, SAXS, and/or cross-link data. Integrative modeling: The more powerful computational methods open up new possibilities for combination with sparse or low-resolution experimental data to investigate previously inaccessible biological structures and machines. CASP is interested in exploring these possibilities and so requests experimentally difficult targets where structure has nevertheless been obtained. In appropriate cases, we expect to be able to collaborate with other experimental groups to provide appropriate data from NMR, cross-linking or SAXS. There are three avenues to contribute a target to CASP: 1. (preferrable) Submit directly to CASP through our web-interface https://predictioncenter.org/casp16/targets_submission_form.cgi (requires a quick registration at https://predictioncenter.org/login.cgi if you do not have an account with us). 2. Email to targets at predictioncenter.org with your target suggestions or to discuss any questions. 3. Submit your structure to the PDB (on-hold) and designate it as a CASP target through PDB’s submission interface. The timeline for the 2024 CASP requires that targets are submitted starting now and until July 1. We would like to hear from you as soon as possible if you may have something suitable or have suggestions about other target sources. In order to maintain rigor, the experimental data for a target must not be publicly available until after computed structures have been collected. For assessment, CASP requires the experimental data by August 15, but the data can remain confidential after that. Target providers are invited to contribute to papers11-15 for a special CASP issue of the journal Proteins. 1. Kryshtafovych A, Schwede T, Topf M, Fidelis K, Moult J. Critical assessment of methods of protein structure prediction (CASP)-Round XIII. Proteins 2019;87(12):1011-1020. 2. Kryshtafovych A, Schwede T, Topf M, Fidelis K, Moult J. Critical assessment of methods of protein structure prediction (CASP)-Round XIV. Proteins 2021;89(12):1607-1617. 3. Kryshtafovych A, Schwede T, Topf M, Fidelis K, Moult J. Critical assessment of methods of protein structure prediction (CASP)-Round XV. Proteins 2023;91(12):1539-1549. 4. Simpkin AJ, Mesdaghi S, Sanchez Rodriguez F, Elliott L, Murphy DL, Kryshtafovych A, Keegan RM, Rigden DJ. Tertiary structure assessment at CASP15. Proteins 2023;91(12):1616-1635. 5. Ozden B, Kryshtafovych A, Karaca E. The impact of AI-based modeling on the accuracy of protein assembly prediction: Insights from CASP15. Proteins 2023;91(12):1636-1657. 6. Lensink MF, Brysbaert G, Raouraoua N, Bates PA, Giulini M, Honorato RV, van Noort C, Teixeira JMC, Bonvin A, Kong R, Shi H, Lu X, Chang S, Liu J, Guo Z, Chen X, Morehead A, Roy RS, Wu T, Giri N, Quadir F, Chen C, Cheng J, Del Carpio CA, Ichiishi E, Rodriguez-Lumbreras LA, Fernandez-Recio J, Harmalkar A, Chu LS, Canner S, Smanta R, Gray JJ, Li H, Lin P, He J, Tao H, Huang SY, Roel-Touris J, Jimenez-Garcia B, Christoffer CW, Jain AJ, Kagaya Y, Kannan H, Nakamura T, Terashi G, Verburgt JC, Zhang Y, Zhang Z, Fujuta H, Sekijima M, Kihara D, Khan O, Kotelnikov S, Ghani U, Padhorny D, Beglov D, Vajda S, Kozakov D, Negi SS, Ricciardelli T, Barradas-Bautista D, Cao Z, Chawla M, Cavallo L, Oliva R, Yin R, Cheung M, Guest JD, Lee J, Pierce BG, Shor B, Cohen T, Halfon M, Schneidman-Duhovny D, Zhu S, Yin R, Sun Y, Shen Y, Maszota-Zieleniak M, Bojarski KK, Lubecka EA, Marcisz M, Danielsson A, Dziadek L, Gaardlos M, Gieldon A, Liwo A, Samsonov SA, Slusarz R, Zieba K, Sieradzan AK, Czaplewski C, Kobayashi S, Miyakawa Y, Kiyota Y, Takeda-Shitaka M, Olechnovic K, Valancauskas L, Dapkunas J, Venclovas C, Wallner B, Yang L, Hou C, He X, Guo S, Jiang S, Ma X, Duan R, Qui L, Xu X, Zou X, Velankar S, Wodak SJ. Impact of AlphaFold on structure prediction of protein complexes: The CASP15-CAPRI experiment. Proteins 2023;91(12):1658-1683. 7. Das R, Kretsch RC, Simpkin AJ, Mulvaney T, Pham P, Rangan R, Bu F, Keegan RM, Topf M, Rigden DJ, Miao Z, Westhof E. Assessment of three-dimensional RNA structure prediction in CASP15. Proteins 2023;91(12):1747-1770. 8. Magnus M, Antczak M, Zok T, Wiedemann J, Lukasiak P, Cao Y, Bujnicki JM, Westhof E, Szachniuk M, Miao Z. RNA-Puzzles toolkit: a computational resource of RNA 3D structure benchmark datasets, structure manipulation, and evaluation tools. Nucleic Acids Res 2020;48(2):576-588. 9. Robin X, Studer G, Durairaj J, Eberhardt J, Schwede T, Walters WP. Assessment of protein-ligand complexes in CASP15. Proteins 2023;91(12):1811-1821. 10. Kryshtafovych A, Montelione GT, Rigden DJ, Mesdaghi S, Karaca E, Moult J. Breaking the conformational ensemble barrier: Ensemble structure modeling challenges in CASP15. Proteins 2023;91(12):1903-1911. 11. Kretsch RC, Andersen ES, Bujnicki JM, Chiu W, Das R, Luo B, Masquida B, McRae EKS, Schroeder GM, Su Z, Wedekind JE, Xu L, Zhang K, Zheludev IN, Moult J, Kryshtafovych A. RNA target highlights in CASP15: Evaluation of predicted models by structure providers. Proteins 2023;91(12):1600-1615. 12. Alexander LT, Durairaj J, Kryshtafovych A, Abriata LA, Bayo Y, Bhabha G, Breyton C, Caulton SG, Chen J, Degroux S, Ekiert DC, Erlandsen BS, Freddolino PL, Gilzer D, Greening C, Grimes JM, Grinter R, Gurusaran M, Hartmann MD, Hitchman CJ, Keown JR, Kropp A, Kursula P, Lovering AL, Lemaitre B, Lia A, Liu S, Logotheti M, Lu S, Markusson S, Miller MD, Minasov G, Niemann HH, Opazo F, Phillips GN, Jr., Davies OR, Rommelaere S, Rosas-Lemus M, Roversi P, Satchell K, Smith N, Wilson MA, Wu KL, Xia X, Xiao H, Zhang W, Zhou ZH, Fidelis K, Topf M, Moult J, Schwede T. Protein target highlights in CASP15: Analysis of models by structure providers. Proteins 2023;91(12):1571-1599. 13. Alexander LT, Lepore R, Kryshtafovych A, Adamopoulos A, Alahuhta M, Arvin AM, Bomble YJ, Bottcher B, Breyton C, Chiarini V, Chinnam NB, Chiu W, Fidelis K, Grinter R, Gupta GD, Hartmann MD, Hayes CS, Heidebrecht T, Ilari A, Joachimiak A, Kim Y, Linares R, Lovering AL, Lunin VV, Lupas AN, Makbul C, Michalska K, Moult J, Mukherjee PK, Nutt WS, Oliver SL, Perrakis A, Stols L, Tainer JA, Topf M, Tsutakawa SE, Valdivia-Delgado M, Schwede T. Target highlights in CASP14: Analysis of models by structure providers. Proteins 2021;89(12):1647-1672. 14. Lepore R, Kryshtafovych A, Alahuhta M, Veraszto HA, Bomble YJ, Bufton JC, Bullock AN, Caba C, Cao H, Davies OR, Desfosses A, Dunne M, Fidelis K, Goulding CW, Gurusaran M, Gutsche I, Harding CJ, Hartmann MD, Hayes CS, Joachimiak A, Leiman PG, Loppnau P, Lovering AL, Lunin VV, Michalska K, Mir-Sanchis I, Mitra AK, Moult J, Phillips GN, Jr., Pinkas DM, Rice PA, Tong Y, Topf M, Walton JD, Schwede T. 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