Isolation and functional analysis of phage‐displayed antibody fragments targeting the staphylococcal superantigen‐like proteins

Ida Alanko¹, Rebecca Sandberg¹, Eeva‐Christine Brockmann², Carla J. C. de Haas³, Jos A. G. van Strijp³, Urpo Lamminmäki², Outi M. H. Salo-Ahen¹

¹Faculty of Sciences and Engineering, Pharmaceutical Sciences Laboratory (Pharmacy) & Structural Bioinformatics Laboratory (Biochemistry) Turku, Åbo Akademi University, Turku, Finland; ²Department of Life Technologies, University of Turku, Turku, Finland; ³Department of Medical Microbiology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands

Detailed analysis of a thermostable protein-DNA complex: the case of Sac7d as a prototype for protein-DNA interaction

Elena Álvarez^1,2, Stéphane Téletchéa¹, Simon Huet², Bernard Offmann¹

¹Nantes Université, US2B, CNRS, UMR6286 & Affilogic F-44000 Nantes, France; ²Affilogic SAS, F-44000 Nantes, France

Method for analysis of protein-DNA interactions using probability density maps

Daniel Berdár, Bohdan Schneider, Lada Biedermannová

Institute of Biotechnology, Czech Academy of Science, Czech Republic

Prediction of DNA hydration based on data mining of crystallographic structures

Lada Biedermannová, Bohdan Schneider

Institute of Biotechnology, Czech Republic

Conformational study of small carbon rings in ligands

Gabriela Bučeková¹, Viktoriia Doshchenko¹, Radka Svobodová^1,2

¹National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 753/5, 625 00 Brno, Czech Republic; ²CEITEC - Central European Institute of Technology, Masaryk University, Kamenice 753/5, 625 00 Brno, Czech Republic

Predicting the effects of mutations on protein-protein interactions via self-supervised machine learning

Anton Bushuiev¹, Roman Bushuiev^1,4, Anatolii Filkin¹, Petr Kouba^1,2, Marketa Gabrielova¹, Jiri Sedlar¹, Tomas Pluskal⁴, Jiri Damborsky^2,3, Stanislav Mazurenko^2,3, Josef Sivic¹

¹Czech Institute of Informatics, Robotics and Cybernetics, Czech Technical University in Prague; ²Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University; ³International Clinical Research Center, St. Anne's University Hospital Brno; ⁴Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences

Mol*VS Visualization and Interpretation of Cell Imaging Data alongside Macromolecular Structure Data and Biological Annotations

Aliaksei Chareshneu¹, Adam Midlik¹, Alessio Cantara¹, Crina-Maria Ionescu¹, Alexander Rose², Vladimír Horský¹, Radka Svobodová^1,3, Karel Berka⁴, David Sehnal^1,3

¹National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, 602 00, Czech Republic; ²Mol* Consortium - San Diego, CA, USA; ³CEITEC - Central European Institute of Technology, Masaryk University, Brno, 625 00, Czech Republic; ⁴Department of Physical Chemistry, Faculty of Science, Palacký University Olomouc, Olomouc, 779 00, Czech Republic

Application and analysis of protein language models for predicting membrane interacting peptide regions

Máté Csepi¹, Gábor Erdős², Zsuzsanna Dosztányi², Tamás Hegedűs^1,3

¹Semmelweis University, Hungary; ²Eötvös Loránd University, Hungary; ³Eötvös Loránd Research Network, Hungary

SpikePro: a webserver to predict the fitness of SARS-CoV-2 variants

Gabriel Cia Beriain¹, Jean Kwasigroch¹, Marianne Rooman^1,2, Fabrizio Pucci^1,2

¹Computational Biology and Bioinformatics, Université Libre de Bruxelles, Brussels, Belgium; ²Interuniversity Institute of Bioinformatics in Brussels, Brussels, Belgium

Extension of the SUGRES coarse-grained model of polysaccharides to heparin

Annemarie Danielsson, Sergey A. Samsonov, Adam Liwo, Adam K. Sieradzan

Department of Theoretical Chemistry, Faculty of Chemistry, University of Gdansk, Poland

Mapping and characterization of the human missense variation universe using AlphaFold 3D models

Elbert I. Timothy, Suhail A. Islam, Gordon Hanna, Michael J.E. Sternberg, Alessia David

Imperial College London, United Kingdom

Computational resources for analyzing transmembrane protein structures, and topology

Laszlo Dobson^1,2, Gabor Tusnady¹

¹Research Centre for Natural Sciences, Magyar Tudosok Korutja, 1117-Budapest, Hungary; ²European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117-Heidelberg, Germany

On modelling signalling amyloid motifs

Witold Dyrka¹, Jakub Gałązka¹, Marlena Gąsior-Głogowska¹, Krzysztof Pysz¹, Monika Szefczyk², Natalia Szulc^1,3

¹Katedra Inżynierii Biomedycznej, Wydział Podstawowych Problemów Techniki, Politechnika Wrocławska, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland; ²Katedra Chemii Bioorganicznej, Wydział Chemiczny, Politechnika Wrocławska, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland; ³Katedra Fizyki i Biofizyki, Wydział Biotechnologii i Nauk o Żywności, Uniwersytet Przyrodniczy we Wrocławiu, Norwida 25, 50-375 Wrocław, Poland

AHoJ DB: A PDB-wide assignment of apo & holo relationships based on individual protein-ligand interactions

Christos Feidakis¹, Radoslav Krivak², David Hoksza², Marian Novotny¹

¹Charles University, Faculty of Science, Department of Cell Biology, Czech Republic; ²Charles University, Faculty of Science, Department of Software Engineering, Czech Republic

Toward a database of genetically encoded non-canonical amino acids

Carolina F. Rodrigues^1,2, Antoine Daina^3,4, Marta A.S. Perez^3,4, Vincent Zoete^3,4, Bohdan Schneider¹, Gustavo Fuertes¹

¹Institute of Biotechnology of the Czech Academy of Sciences, Czech Republic; ²Instituto Politécnico de Setúbal, Escola Superior de Tecnologia de Barreiro, Portugal; ³University of Lausanne, Switzerland; ⁴SIB Swiss Institute of Bioinformatics Lausanne, Switzerland

Valinomycin interactions with water

Jindřich Hašek¹, Michal Dušek², Ivana Císařová³, Jiří Dybal⁴, Tereza Skálová¹, Jarmila Dušková¹, Jan Dohnálek¹

¹Institute of Biotechnology, Academy of Sciences of the CR, Czech Republic; ²Institute of Physics, Academy of Sciences, Cukrovarnická 2, Praha, Czech Republic; ³Faculty of Science, Charles University, Hlavova 2030, Praha, Czech Republic; ⁴Institute of Macromol.Chemistry, Academy of Sciences, Heyrovského nám.2, Praha, Czech Republic

AlphaMissense performance on transmembrane proteins

Hedvig Tordai¹, Tamas Hegedus^1,2

¹Semmelweis University, Hungary; ²HUN-REN-SU Biophysical Virology Research Group

Large-scale application of ProteinMPNN to design conformation-specific GPCR agonists

Hannes Junker

Leipzig University, Germany

Determining Structural Characteristics of Native and de novo Proteins for Improved Protein Design Algorithms

Johannes Andreas Klier

Leipzig University, Germany

Assessing the Effects of Mutations and Corrector Molecules on APOE Dynamics via Comparative Markov State Analysis

Jakub Kopko¹, Petr Kouba^1,2, Sérgio M. Marques^2,3, Joan Planas-Iglesias^2,3, Jiří Damborský^2,3, Stanislav Mazurenko^2,3, Josef Šivic¹, David Bednář^2,3, Jiří Sedlář¹

¹Czech Institute of Informatics, Robotics and Cybernetics, Czech Technical University in Prague, Jugoslávských partyzánů 1580/3, 160 00 Prague, Czech Republic; ²Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic; ³International Clinical Research Center, St. Anne's University Hospital Brno, Pekařská 53, 656 91 Brno, Czech Republic

E-pRSA: protein language models improve the prediction of residue solvent accessibility from sequence

Matteo Manfredi, Castrense Savojardo, Pier Luigi Martelli, Rita Casadio

University of Bologna, Italy

Proteome secondary structures generated by AlphaFold

Ivana Hutařová Vařeková¹, Dominik Martinat¹, Radka Svobodová^2,3, Karel Berka¹

¹Department of Physical Chemistry, Faculty of Science, Palacký University Olomouc, tř. 17. listopadu 12, 77146 Olomouc, Czech Republic; ²CEITEC – Central European Institute of Technology, Masaryk University Brno, Kamenice 5, 625 00 Brno, Czech Republic; ³National Centre for Biomolecular Research, Faculty of Science, Masaryk University Brno, Kamenice 5, 625 00 Brno, Czech Republic

Old folds can learn new tricks: Alphafold-driven insights on coiled-coil structure

Mikel Martinez Goikoetxea¹, Rafal Madaj², Jan Ludwiczak^2,3, Andrei Lupas¹, Stanislaw Dunin-Horkawicz^1,2

¹Max Planck Institute for Biology, Tuebingen, Germany; ²Institute of Evolutionary Biology, Faculty of Biology, Biological and Chemical Research Centre, University of Warsaw, Warsaw, Poland; ³Prescient Design, Genentech Research & Early Development, Roche Group, Basel, Switzerland

The Protein Universe Atlas

Janani Durairaj^1,2, Andrew M. Waterhouse^1,2, Toomas Mets^3,4, Tetiana Brodiazhenko³, Minhal Abdullah^3,4, Gabriel Studer^1,2, Gerardo Tauriello^1,2, Mehmet Akdel⁵, Antonina Andreeva⁶, Alex Bateman⁶, Tanel Tenson³, Vasili Hauryliuk^3,4,7,8, Torsten Schwede^1,2, Joana Pereira^1,2

¹Biozentrum, University of Basel, Basel, Switzerland; ²SIB Swiss Institute of Bioinformatics, University of Basel, Basel, Switzerland; ³Institute of Technology, University of Tartu, Tartu, Estonia; ⁴Department of Experimental Medical Science, Lund University, Lund, Sweden; ⁵VantAI, New York, USA; ⁶European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, United Kingdom; ⁷Science for Life Laboratory, Lund, Sweden; ⁸Virus Centre, Lund University, Lund, Sweden

Exploring the relationship between structural quality and journal impact factor

Jana Porubská¹, Veronika Horská¹, Vladimír Horský¹, Radka Svobodová^1,2

¹National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 753/5, 625 00 Brno, Czech Republic; ²CEITEC – Central European Institute of Technology, Masaryk University, Kamenice 753/5, 625 00 Brno, Czech Republic

Towards finding high affinity binders of the PSB domain of human collagen prolyl 4-hydroxylase

M. Mubinur Rahman¹, Hongmin Tu², Bukunmi Adediran¹, Sudarshan Murthy¹, Antti M. Salo^1,2, Outi Lampela², Andre Juffer², Johanna Myllyharju^1,2, Rik K. Wierenga¹, M. Kristian Koski^1,2

¹Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland; ²Biocenter Oulu, University of Oulu, Oulu, Finland

Onedata4Sci: Life-science experimental datasets management system

Adrian Rosinec^1,2,3, Tomas Svoboda^1,2,3, Tomas Racek^1,2,3, Josef Handl¹, Jozef Sabo^2,3, Ales Krenek³, Radka Svobodova^1,2

¹National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 753/5, Brno, 625 00, Czech Republic; ²CEITEC - Central European Institute of Technology, Kamenice 753/5, Brno, 625 00, Czech Republic; ³Institute of Computer Science, Masaryk University, Sumavská 416/15, Brno, 602 00, Czech Republic

The analysis of the Impact of Substitutions within EXO-Motifs on Hsa-MiR-1246 Intercellular Transfer in Breast Cancer Cells

Agnieszka Rybarczyk^1,2, Tomasz P. Lehmann³, Ewa Iwańczyk-Skalska³, Wojciech Juzwa⁴, Kamil Kopciuch¹, Paweł P. Jagodziński³

¹Institute of Computing Science, Poznan University of Technology, Poland; ²Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland; ³Department of Biochemistry and Molecular Biology, Poznan University of Medical Sciences, Poznan, Poland; ⁴Department of Biotechnology and Food Microbiology, Poznan University of Life Sciences, Poznan, Poland

The hijacker of host immune system: Structural analysis of Klebsiella immune evasin A

Mia Åstrand¹, Tobias Eriksberg¹, Joana Sá-Pessoa², José A. Bengoechea², Christine Touma¹, Tiina A. Salminen¹

¹1Structural Bioinformatics Laboratory and InFLAMES Research Flagship Center, Biochemistry, Faculty of Science and Engineering, Åbo Akademi University, Turku, Finland; ²2Wellcome-Wolfson Institute for Experimental Medicine, School of Medicine, Dentistry and Biomedical Sciences, Queen's University Belfast, Belfast, UK

ChannelsDB 2.0: A Comprehensive Database of Protein Tunnels and Pores in AlphaFold Era

Anna Špačková¹, Ondřej Vávra^2,3, Tomáš Raček^4,5, Václav Bazgier¹, David Sehnal^4,5, Jiří Damborský^2,3, Radka Svobodová^4,5, David Bednář^2,3, Karel Berka¹

¹Department of Physical Chemistry, Faculty of Science, Palacký University, tř. 17. listopadu 12, 771 46 Olomouc, Czech Republic; ²Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic; ³International Clinical Research Center, St. Anne’s University Hospital Brno, Pekařská 53, 656 91 Brno, Czech Republic; ⁴CEITEC – Central European Institute of Technology, Masaryk University Brno, Kamenice 5, 625 00 Brno, Czech Republic; ⁵National Centre for Biomolecular Research, Faculty of Science, Kamenice 5, 625 00 Brno, Czech Republic

C-RCPred: a multi-objective algorithm for interactive secondary structure prediction of RNA complexes integrating user knowledge and SHAPE data

Mandy Ibéné, Audrey Legendre, Guillaume Postic, Eric Angel, Fariza Tahi

Université Paris-Saclay / Univ. Evry, France

Reusing and accessing computed structure models with SWISS-MODEL and ModelArchive

Gerardo Tauriello^1,2, Gabriel Studer^1,2, Stefan Bienert^1,2, Andrew Waterhouse^1,2, Torsten Schwede^1,2

¹Biozentrum, University of Basel, Basel, Switzerland; ²SIB Swiss Institute of Bioinformatics, University of Basel, Basel, Switzerland

Protein folding enhanced by Adversarial Autoencoders

Guglielmo Tedeschi¹, Vladimír Višňovský², Aleš Křenek², Vojtech Spiwok¹

¹Department of Biochemistry and Microbiology - University of Chemistry and Technology, Prague; ²Department of Machine Learning and Data Processing - Faculty of Informatics - Masaryk University, Brno

LIGYSIS: a pipeline and web application for the analysis of ligand binding sites

Javier S. Utgés, Stuart A. MacGowan, Geoffrey J. Barton

University of Dundee, United Kingdom

Defining conformational states and their variability

Jose Gavalda Garcia, David Bickel, Joel Roca Martinez, Wim Vranken

Interuniversity Institut of Bioinformatics in Brussels, Vrije Universiteit Brussel, Belgium

Computational design of a cyclic peptide for inhibition of CD59 using hotspot extension in Rosetta

Max Beining^1,2

¹Institute for Drug Discovery, Leipzig University Faculty of Medicine, Leipzig, Germany; ²School of Embedded Composite Artificial Intelligence (SECAI), Cooperation of University Leipzig and TU Dresden

3D-Bioinfo nucleic acid activity - a progress report

Bohdan Schneider

Institute of Biotechnology of the Czech Academy of Sciences, Czech Republic

Validation of nucleic acid valence geometry at dnatco.datmos.org

Jiří Černý, Paulína Božíková, Barbora Schramlová, Bohdan Schneider, Lada Biedermannová, Michal Malý

Institute of Biotechnology of the Czech Academy of Sciences, Czech Republic

Reference-free ranking method for RNA 3D models

Tomasz Zok¹, Jan Pielesiak¹, Maciej Antczak^1,2, Marta Szachniuk^1,2

¹Poznan University of Technology, Poland; ²Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poland