Conference Agenda

Overview and details of the sessions of this conference. Please select a date or location to show only sessions at that day or location. Please select a single session for detailed view (with abstracts and downloads if available).

 
 
Session Overview
Date: Wednesday, 15/Nov/2023
9:00am - 10:15amCZE1: ELIXIR Czech Republic 1
Location: Chamber Hall
Session Chair: Jiri Damborsky
 
9:00am - 9:15am

Welcome

Jiří Vondrášek

Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences



9:15am - 9:35am

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



9:35am - 9:55am

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

David Hoksza, Hamza Gamouh, Marian Novotný

Charles University, Czech Republic



9:55am - 10:15am

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

 
10:15am - 10:45amCB0: Coffee break
Location: Forum Hall Foyer 3
10:45am - 12:00pmCZE2: ELIXIR Czech Republic 2
Location: Chamber Hall
Session Chair: Radka Svobodová
 
10:45am - 11:05am

Dynamics from Alphafold - Elastic network approach

Vojtech Spiwok

University of Chemistry and Technology, Prague, Czech Republic



11:05am - 11:25am

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

David Bednar1,2, Milos Musil1,2,3, Rayyan Tariq Khan1,2, Jan Stourac1,2, Andrej Jezik1,3, Jana Horackova1, Simeon Borko1,2,3, Petr Kabourek1,2, Jiri Damborsky1,2

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



11:25am - 11:45am

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



11:45am - 12:00pm

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

 
12:00pm - 1:00pmL1: Lunch and get together of the Czech and International sections
Location: Forum Hall Foyer 3
1:00pm - 1:30pmIntro: Introductory session
Location: Chamber Hall
Session Chair: Bohdan Schneider
 
1:00pm - 1:10pm

Purpose and highlights of the conference

Christine Orengo

University College London, United Kingdom



1:10pm - 1:20pm

ELIXIR welcome

Elixir Rep I

Elixir



1:20pm - 1:50pm

Welcome and organizational notes

Bohdan Schneider

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

 
1:30pm - 3:30pmS1: Activity 1 - To develop the infrastructure for FAIR structural and functional annotations
Location: Chamber Hall
Session Chair: Sameer Velankar
 
1:30pm - 1:45pm

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

External Resource:
Video Link


1:45pm - 2:15pm

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

External Resource:
Video Link


2:15pm - 2:30pm

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

External Resource:
Video Link


2:30pm - 2:45pm

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

External Resource:
Video Link


2:45pm - 3:00pm

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

External Resource:
Video Link


3:00pm - 3:15pm

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

External Resource:
Video Link


3:15pm - 3:30pm

Developing Training Materials for Structural Biology

Paulyna Magana

EMBL-EBI, United Kingdom

External Resource:
Video Link
 
3:30pm - 4:00pmCB1: Coffee break
Location: Forum Hall Foyer 3
4:00pm - 6:00pmS2: Activity 2 - To create open resources for sharing, integrating and benchmarking software tools for modelling the proteome in 3D
Location: Chamber Hall
Session Chair: Shoshana Wodak
 
4:00pm - 4:30pm

An atlas of protein homo-oligomerization across domains of life

Hugo Schweke

Weizmann Institute of Science, Israel

External Resource:
Video Link


4:30pm - 5:00pm

Datasets and models for modeling of antibody-antigen complexes

Dina Schneidman

The Hebrew University of Jerusalem, Israel

External Resource:
Video Link


5:00pm - 5:15pm

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

Emmanuel Levy

Elixir Activity II community

External Resource:
Video Link


5:15pm - 5:30pm

Explaining Conformational Diversity in Protein Families through Molecular Motions

Valentin Lombard1, Sergei Grudinin2, Elodie Laine1,3

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

External Resource:
Video Link


5:30pm - 5:45pm

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

External Resource:
Video Link


5:45pm - 6:00pm

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

External Resource:
Video Link
 
6:00pm - 9:00pmPosters: Posters
Location: Forum Hall Foyer 3
 

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 Álvarez1,2, 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 Svobodová1,2

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 Bushuiev1,4, Anatolii Filkin1, Petr Kouba1,2, Marketa Gabrielova1, Jiri Sedlar1, Tomas Pluskal4, Jiri Damborsky2,3, Stanislav Mazurenko2,3, 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 Svobodová1,3, Karel Berka4, David Sehnal1,3

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 Hegedűs1,3

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 Rooman1,2, Fabrizio Pucci1,2

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 Dobson1,2, 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 Szulc1,3

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. Rodrigues1,2, Antoine Daina3,4, Marta A.S. Perez3,4, Vincent Zoete3,4, 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 Hegedus1,2

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 Kouba1,2, Sérgio M. Marques2,3, Joan Planas-Iglesias2,3, Jiří Damborský2,3, Stanislav Mazurenko2,3, Josef Šivic1, David Bednář2,3, 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 Svobodová2,3, 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 Ludwiczak2,3, Andrei Lupas1, Stanislaw Dunin-Horkawicz1,2

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 Durairaj1,2, Andrew M. Waterhouse1,2, Toomas Mets3,4, Tetiana Brodiazhenko3, Minhal Abdullah3,4, Gabriel Studer1,2, Gerardo Tauriello1,2, Mehmet Akdel5, Antonina Andreeva6, Alex Bateman6, Tanel Tenson3, Vasili Hauryliuk3,4,7,8, Torsten Schwede1,2, Joana Pereira1,2

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 Svobodová1,2

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. Salo1,2, Outi Lampela2, Andre Juffer2, Johanna Myllyharju1,2, Rik K. Wierenga1, M. Kristian Koski1,2

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 Rosinec1,2,3, Tomas Svoboda1,2,3, Tomas Racek1,2,3, Josef Handl1, Jozef Sabo2,3, Ales Krenek3, Radka Svobodova1,2

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 Rybarczyk1,2, 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 Vávra2,3, Tomáš Raček4,5, Václav Bazgier1, David Sehnal4,5, Jiří Damborský2,3, Radka Svobodová4,5, David Bednář2,3, 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 Tauriello1,2, Gabriel Studer1,2, Stefan Bienert1,2, Andrew Waterhouse1,2, Torsten Schwede1,2

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 Beining1,2

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 Antczak1,2, Marta Szachniuk1,2

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

 
Date: Thursday, 16/Nov/2023
9:00am - 9:30amS3: Activity 4 - To develop tools to Describe, Analyse, Annotate, and Predict Nucleic Acid Structures
Location: Chamber Hall
Session Chair: Christine Orengo

ELIXIR program 2024-2028

9:30am - 11:30amS4: Activity 4 - To develop tools to Describe, Analyse, Annotate, and Predict Nucleic Acid Structures
Location: Chamber Hall
Session Chair: Bohdan Schneider
 
9:30am - 10:00am

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

External Resource:
Video Link


10:00am - 10:30am

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

Blake Sweeney

EMBL-EBI, United Kingdom

External Resource:
Video Link


10:30am - 10:45am

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

Marta Szachniuk1,2, Maciej Antczak1,2, Mariusz Popenda2, Joanna Sarzynska2, Tomasz Zok1

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

External Resource:
Video Link


10:45am - 11:00am

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

External Resource:
Video Link


11:00am - 11:15am

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

Clément Bernard1, Sahar Ghannay2, Guillaume Postic1, Fariza Tahi1

1IBISC, France; 2LISN, CNRS, France

External Resource:
Video Link


11:15am - 11:30am

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

External Resource:
Video Link
 
11:30am - 12:00pmCB2: Coffee break
Location: Forum Hall Foyer 3
12:00pm - 1:00pmS5: Activity 2, 5 - Additional talks
Location: Chamber Hall
Session Chair: Lynne Regan
Session Chair: Bohdan Schneider
 
12:00pm - 12:30pm

Protein Quaternary Structures in Solution are a Mixture of Multiple forms

Gideon Schreiber

Weizmann Institute of Science, Israel

External Resource:
Video Link


12:30pm - 1:00pm

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

Arne Skerra

Technical University of Munich, Germany

External Resource:
Video Link
 
1:00pm - 2:00pmL2: Lunch
Location: Forum Hall Foyer 3
2:00pm - 3:30pmS6a: Activity 5 - To establish a Biostudies database of protein engineering results
Location: Chamber Hall
Session Chair: Lynne Regan
 
2:00pm - 2:30pm

Novel Strategies and Web-based Tools for Protein Engineering

Jiri Damborsky

Masaryk University and ICRC-FNUSA, Czech Republic

External Resource:
Video Link


2:30pm - 3:00pm

Novel immunotherapeutic drugs through computational protein design

Clara Tabea Schoeder

Leipzig University, Faculty of Medicine, Germany

External Resource:
Video Link


3:00pm - 3:15pm

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

Outi Tuulikki Lampela1, Tiila-Riikka Kiema1, Takayuki Ohnuma2,3, Tamo Fukamizo3, Rikkert Wierenga4, André Juffer1,4

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

External Resource:
Video Link


3:15pm - 3:30pm

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

Serena Rosignoli, Alessandro Paiardini

Sapienza, Italy

External Resource:
Video Link
 
3:30pm - 4:00pmCB3: Coffee break
Location: Forum Hall Foyer 3
4:00pm - 4:45pmS6b: Activity 5 - To establish a Biostudies database of protein engineering results
Location: Chamber Hall
Session Chair: Lynne Regan
 
4:00pm - 4:15pm

Design of novel peptides targeted to human primary amine oxidase

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

Åbo Akademi university, Finland

External Resource:
Video Link


4:15pm - 4:30pm

Assessing the performance of protein regression models

Wouter Boomsma

University of Copenhagen, Denmark

External Resource:
Video Link


4:30pm - 4:45pm

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

External Resource:
Video Link
 
4:45pm - 6:00pmDiscussion: Elixir Platform Discussion
Location: Chamber Hall
Session Chair: Bohdan Schneider

Elixir Platform Discussions.

Chairs: Sameer Velankar, Shoshana Wodak, Vincent Zoete, Bohdan Schneider, Lynne Regan

Video Link
Date: Friday, 17/Nov/2023
9:00am - 11:00amS7: Activity 3 - To develop models for protein-ligand interactions
Location: Chamber Hall
Session Chair: Vincent Zoete
 
9:00am - 9:15am

Introduction and status of the ligand-protein activity

Vincent Zoete

SIB Swiss Institute of Bioinformatics, Switzerland

External Resource:
Video Link


9:15am - 9:45am

AlphaFill: enriching AlphaFold models with ligands and cofactors

Robbie P. Joosten

Netherlands Cancer Institute, Netherlands, The

External Resource:
Video Link


9:45am - 10:15am

A Bottom-Up Approach to Screening Massive Virtual Collections

Xavier Barril1,2,3

1University of Barcelona; 2ICREA; 3Gain Therapeutics

External Resource:
Video Link


10:15am - 10:30am

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

External Resource:
Video Link


10:30am - 10:45am

Automated benchmarking of protein-ligand complex prediction

Janani Durairaj1,2, Michele Leemann1,2, Ander Sagasta1,2, Louis Ollivier1,2, Peter Skrinjar1,2, Arthur Goetzee1,2, Leila Alexander1,2, Xavier Robin1,2, Torsten Schwede1,2

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

External Resource:
Video Link


10:45am - 11:00am

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

External Resource:
Video Link
 
11:00am - 11:30amCB4: Coffee break
Location: Forum Hall Foyer 3
11:30am - 12:30pmS8: Final Session
Location: Chamber Hall
Session Chair: Bohdan Schneider

Keynote by Michael Sternberg

Discussion and concluding remarks

Chairs: Shoshana Wodak, Vincent Zoete, Bohdan Schneider, Lynne Regan, Mihaly Varadi, Geraldo Tauriello

 
11:30am - 12:30pm

Structure-based modelling of missense variants in the AlphaFold era

Michael Sternberg

Imperial College London, United Kingdom

External Resource:
Video Link
 
12:30pm - 1:00pmDiscussion2: Elixir Platform Discussion
Location: Chamber Hall
Session Chair: Bohdan Schneider

Elixir Platform Discussions.

Chairs: Sameer Velankar, Shoshana Wodak, Vincent Zoete, Bohdan Schneider, Lynne Regan

Video Link
1:00pm - 2:00pmL3: Lunch
Location: Forum Hall Foyer 3

 
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