Welcome

Jiří Vondrášek

Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences

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

Marian Novotny, Christos Feidakis, Radoslav Krivak, David Hoksza

Charles University, Czech Republic

Binding residue prediction with protein language models: Does the structure matter?

David Hoksza, Hamza Gamouh, Marian Novotný

Charles University, Czech Republic

New ways of protein family visualization in AlphaFold era

Radka Svobodová¹, Karel Berka², Ivana Hutařová Vařeková², Tomáš Raček¹, Ondřej Schindler¹

¹CEITEC and NCBR, Masaryk University Brno, Kamenice 5, 625 00 Brno, Czech Republic; ²Department of Physical Chemistry, Faculty of Science, Palacký University, tř. 17. listopadu 12, 771 46 Olomouc, Czech Republic

Dynamics from Alphafold - Elastic network approach

Vojtech Spiwok

University of Chemistry and Technology, Prague, Czech Republic

FireProt and FireProt-ASR – Web Tools for Computational Protein Stabilisation

David Bednar^1,2, Milos Musil^1,2,3, Rayyan Tariq Khan^1,2, Jan Stourac^1,2, Andrej Jezik^1,3, Jana Horackova¹, Simeon Borko^1,2,3, Petr Kabourek^1,2, Jiri Damborsky^1,2

¹Masaryk University, Czech Republic; ²St. Anne´s University Hospital Brno, Czech Republic; ³University of Technology, Brno, Czech Republic

Annotation, validation, refinement, and modeling of nucleic acid structures.

Jiri Cerny, Paulina Bozikova, Barbora Schramlova, Bohdan Schneider

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

Are kuravirus capsid diameters quantized? The first all-atom genome tracing method for double-stranded DNA viruses

Samuel Coulbourn Flores¹, Michal Malý2², Dominik Hrebík³, Pavel Plevka³, Jiří Černý²

¹Swedish University of Agricultural Sciences, Sweden; ²Institute of Biotechnology of the Czech Academy of Sciences; ³Central European Institute of Technology, Brno, Czech Republic

Purpose and highlights of the conference

Christine Orengo

University College London, United Kingdom

ELIXIR welcome

Elixir Rep I

Elixir

Welcome and organizational notes

Bohdan Schneider

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

PDBe-KB in 2023: New data pipelines and improved functionality

Mihaly Varadi, Grisell Diaz Leines, Sri D. Appasamy, Joseph I.J. Ellaway, Roshan I. Kunnakkattu, Preeti Choudhary, Sreenath S. Nair, Stephen Anyango, Sameer Velankar

Protein Data Bank in Europe, EMBL-EBI, Hinxton, United Kingdom

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Computational Enzymology in 3D: Modules and Mechanisms

Janet Thornton, AJM Ribeiro, Ioannis Riziotis, JD Tyzack, Neera Borkakoti, Roman Laskowski

European Bioinformatics Institute (EMBL-EBI), Wellcome > Genome Campus, Cambridge CB10 1SD, UK

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The Evolution of Local Energetic Frustration in Protein Families and Superfamilies

Maria I. Freiberger¹, Victoria Ruiz-Serra², Miriam Poley², Marco Ludaic², Camila Pontes², Miguel Romero², Cesar Ramirez-Sarmiento³, Marcelo Marti¹, Peter Wolynes⁴, R. Gonzalo Parra², Alfonso Valencia²

¹Buenos Aires University, Argentina; ²Barcelona Supercomputing Center, Spain; ³Pontificia Universidad Católica de Chile, Chile; ⁴Pontificia Universidad Católica de Chile, Chile

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Finding structure specific entity types in literature

Melanie Vollmar¹, Santosh Tirunagari², Sameer Velankar¹

¹PDBe, European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Cambridge, UK; ²Europe PMC, European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Cambridge, UK

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FiTMuSiC: Leveraging structural and (co)evolutionary data for protein fitness prediction.

Matsvei Tsishyn, Gabriel Cia Beriain, Pauline Hermans, Jean Marc Kwasigroch, Marianne Rooman, Fabrizio Pucci

Université Libre de Bruxelles, Belgium

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The MOKCa database 2023.

Biniam T Haile¹, Adnan Cinar¹, Chistopher J Richardson², Frances M G Pearl¹

¹University of Sussex, Brighton, United Kingdom; ²The Institute of Cancer Research, London, United Kingdom

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Developing Training Materials for Structural Biology

Paulyna Magana

EMBL-EBI, United Kingdom

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An atlas of protein homo-oligomerization across domains of life

Hugo Schweke

Weizmann Institute of Science, Israel

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Datasets and models for modeling of antibody-antigen complexes

Dina Schneidman

The Hebrew University of Jerusalem, Israel

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Discriminating physiological from non-physiological interfaces in structures of protein complexes: a community-wide study

Emmanuel Levy

Elixir Activity II community

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Explaining Conformational Diversity in Protein Families through Molecular Motions

Valentin Lombard¹, Sergei Grudinin², Elodie Laine^1,3

¹Sorbonne University, France; ²Université Grenoble Alpes, CNRS, France; ³Institut universitaire de France (IUF)

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Systematic identification and characterisation of domain movements in proteins from low-dimensional representations of conformational ensembles

Sergei Grudinin¹, Steven Hayward²

¹LJK CNRS, Grenoble, France; ²University of East Anglia, UK

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FAIR workflow to chart and characterize the conformational landscape of native proteins. A combined work of ELIXIR 3D-BioInfo structural community and the BioExcel Centre of Excellence for Computational Biomolecular Research

Adam Hospital Gasch

IRB Barcelona, Spain

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RNA-Puzzles : Blind Assessments of (Semi)-Automatic 3D RNA Modeling

Eric Westhof¹, Zhichao Miao²

¹Architecture et Réactivité de l'ARN, Université de Strasbourg, Institut de biologie moléculaire et cellulaire du CNRS, 67000 Strasbourg France; ²GMU-GIBH Joint School of Life Sciences, Guangzhou Laboratory, Guangzhou Medical University, Guangzhou, China

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Rfam, RNA 3D structures, and issues facing RNA 3D structure prediction

Blake Sweeney

EMBL-EBI, United Kingdom

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Unraveling the RNA web: detecting and deciphering entanglements in 3D structures

Marta Szachniuk^1,2, Maciej Antczak^1,2, Mariusz Popenda², Joanna Sarzynska², Tomasz Zok¹

¹Poznan University of Technology, Poland; ²Institute of Bioorganic Chemistry PAS, Poland

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Posttranscriptional Modifications in RNA Experimental 3D Structures: Occurrences and Effect on Interbase Hydrogen Bonding

Mohit Chawla¹, Luigi Cavallo¹, Romina Oliva²

¹King Abdullah University of Science and Technology (KAUST), Physical Sciences and Engineering Division, Kaust Catalysis Center, Thuwal 23955-6900, Saudi Arabia; ²Department of Sciences and Technologies, University Parthenope of Naples, Centro Direzionale Isola C4, I-80143 Naples, Italy

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RNAdvisor: Evaluation of RNA 3D structures with metrics and energies

Clément Bernard¹, Sahar Ghannay², Guillaume Postic¹, Fariza Tahi¹

¹IBISC, France; ²LISN, CNRS, France

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Prediction of secondary structure for long non-coding RNAs using a recursive cutting method based on deep learning

Loïc Omnes¹, Eric Angel¹, Pierre Bartet³, François Radvanyi², Fariza Tahi¹

¹Université Paris-Saclay, Univ Evry, France; ²CNRS - Institut Curie, France; ³ADLIN Science, France

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Protein Quaternary Structures in Solution are a Mixture of Multiple forms

Gideon Schreiber

Weizmann Institute of Science, Israel

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Structural plasticity in the loop region of engineered lipocalins with novel ligand specificities – Anticalins

Arne Skerra

Technical University of Munich, Germany

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Novel Strategies and Web-based Tools for Protein Engineering

Jiri Damborsky

Masaryk University and ICRC-FNUSA, Czech Republic

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Novel immunotherapeutic drugs through computational protein design

Clara Tabea Schoeder

Leipzig University, Faculty of Medicine, Germany

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Using molecular dynamics (MD) calculations for the characterization of structural transitions

Outi Tuulikki Lampela¹, Tiila-Riikka Kiema¹, Takayuki Ohnuma^2,3, Tamo Fukamizo³, Rikkert Wierenga⁴, André Juffer^1,4

¹Biocenter Oulu, University Of Oulu, Finland; ²Department of Advanced Bioscience, Kindai University, Japan; ³Agricultural Technology and Innovation Research Institute (ATIRI), Kindai University, Japan; ⁴Faculty of Biochemistry and Molecular Medicine, Univeristy of Oulu, Finland

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From AlphaFold to PyMOL: enabling seamless access to Structural Bioinformatics Tools

Serena Rosignoli, Alessandro Paiardini

Sapienza, Italy

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Design of novel peptides targeted to human primary amine oxidase

Marion, Denise Alix, Gabriela Guédez, Tiina, Annamaria Salminen

Åbo Akademi university, Finland

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Assessing the performance of protein regression models

Wouter Boomsma

University of Copenhagen, Denmark

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Prediction of bacterial interactomes based on genome-wide coevolutionary networks: an updated implementation of the ContextMirror approach

Miguel Fernandez, Camila Pontes, Victoria Ruiz-Serra, Alfonso Valencia

Barcelona Supercomputing Center, Spain

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Introduction and status of the ligand-protein activity

Vincent Zoete

SIB Swiss Institute of Bioinformatics, Switzerland

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AlphaFill: enriching AlphaFold models with ligands and cofactors

Robbie P. Joosten

Netherlands Cancer Institute, Netherlands, The

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A Bottom-Up Approach to Screening Massive Virtual Collections

Xavier Barril^1,2,3

¹University of Barcelona; ²ICREA; ³Gain Therapeutics

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SiteMine: large scale binding site similarity searching in protein databases

Thorben Reim¹, Christiane Ehrt¹, Joel Graef¹, Sebastian Günther², Alke Meents², Matthias Rarey¹

¹Center for Bioinformatics, Universität Hamburg, Bundesstraße 43, 20146 Hamburg, Germany; ²Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron, Notkestraße 85, 22607 Hamburg, Germany

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Automated benchmarking of protein-ligand complex prediction

Janani Durairaj^1,2, Michele Leemann^1,2, Ander Sagasta^1,2, Louis Ollivier^1,2, Peter Skrinjar^1,2, Arthur Goetzee^1,2, Leila Alexander^1,2, Xavier Robin^1,2, Torsten Schwede^1,2

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

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Jumpcount: Exact confidence intervals for free energy difference estimations

Pavel Kříž¹, Jan Beránek², Vojtěch Spiwok²

¹Faculty of Mathematics and Physics, Charles University, Prague, Czech Republic; ²Department of Biochemistry and Microbiology, University of Chemistry and Technology, Prague, Czech Republic

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Structure-based modelling of missense variants in the AlphaFold era

Michael Sternberg

Imperial College London, United Kingdom

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