On the occasion of the 25th Anniversary of SWISS-MODEL, this symposium will provide an overview of recent progress in the Computational Structural Biology field and highlight the key challenges for the coming years. SWISS-MODEL was the first fully automated Web-based server for protein structure modelling. A major driver behind its development has been to mask the complexity associated with protein modelling behind an intuitive user interface, thereby broadening the uses and applications of protein models. Today SWISS-MODEL processes over 1 million model requests per year and is one of the most widely used structure modelling servers worldwide.
The symposium will feature a full day of lectures and presentations by international experts. Leaders in their field will present their perspective on how break-through developments in computational structural biology have contributed to our understanding of biological processes and diseases. The event will be open for anybody interested in structural biology and computational methods in this area. We particularly encourage the participation of students and junior scientists, who will have the opportunity to exchange ideas with international leaders in the field, and expand their collaborative network.
Swiss Institute of Bioinformatics & Biozentrum, University of Basel, CH
Founder of SWISS-MODEL
PMI, Neuchâtel Area, CH
We invite scientists and professionals working in the fields of life sciences to propose oral presentations about successful research projects, where SWISS-MODEL has been used and the models contributed to scientific outcome of the study. The presenting author of selected abstracts will be invited to give a talk at the SWISS-MODEL 25 Years Symposium, and will receive free registration to the Symposium, travel and accommodation.
Abstracts should describe published results of research projects in which SWISS-MODEL has been used and the models contributed to the scientific outcome of this study. Submissions are accepted online via the [ EasyChair ] system. The abstract should have the following overall structure:
Title: The intended title for the conference presentation. (The title will be published online on the Symposium website).
Authors: Please list all authors who contributed to this work.
Scientific Abstract: Please summarize the main questions which were addressed in this work, the approach taken, and the results of this study. Please specify in which way structural modelling has contributed to the results (max 1 page; the scientific abstract will be published online in the Symposium program).
Reference: Please provide a reference to a peer reviewed scientific publication of the presented results in the form of a link to PubMed or by uploading a single PDF file of the paper (published or in press).
Highlights: Please briefly describe why this work would make a great symposium presentation. (This information is only for the selection process – will not be published).
Presenter: Please indicate who of co-authors will give the presentation, and provide a brief summary of her/his scientific experience. (This information is only for the selection process – will not be published).
The program committee will select abstracts to be presented at the meeting considering relevance, interest, and value of the topic to symposium attendees, impact of the work on life sciences, and the likelihood that the work will make an interesting conference presentation illustrating the role of structure prediction for the specific application.
There is no fee to submit an abstract. All abstracts must be submitted via [ EasyChair ] by September 22nd 2018. By submitting an abstract, all submitting authors confirm the following statements: (1) I have read, understand, and agree to the rules and guidelines; (2) the presenting author is submitting this abstract with the intent of attending the SWISS-MODEL 25 Years Symposium; and (3) I confirm that each co-author has been informed of this abstract submission and has agreed to all information as it was submitted.
Note: Authors who submit abstracts are not automatically registered for the meeting. Please register on the symposium website.
After you submit your abstract, you will receive an immediate on-screen confirmation of receipt by the [ EasyChair ] system as well as a confirmation by email. If you do not receive a confirmation of receipt, then your abstract was not successfully submitted and it will not be reviewed or programmed by the SWISS-MODEL 25 Years Symposium Program Committee.
To make changes to an abstract (including author changes) before the submission deadline, return to the abstract submission site and log into your [EasyChair] account. Abstract revisions changes will not be possible after the submission deadline.
Complete abstracts received by the submission deadline will be reviewed by members of the Program Committee. Authors of accepted abstracts will be notified latest by 25th of September to confirm their participation to the meeting.
To withdraw an abstract before the submission deadline, return to the submission site and log into your [EasyChair] account. After acceptance and confirmation by the presenting author, abstracts are published on the SWISS-MODEL 25 Years Symposium website and cannot be withdrawn (even at the request of the author and/or principal investigator).
The presenting author of selected abstracts will be invited to present at the SWISS-MODEL 25 Years Symposium, and will receive free registration to the Symposium, hotel (max. two nights) and travel will be reimbursed (train or airplane economy class, according to expense rules of the SNF Swiss National Science Foundation).
Note: Authors who submit abstracts are not automatically registered for the meeting. Please register on the symposium website, and make your own arrangements for travel and accommodation.
Symposium on Computational Structural Biology - 25 years of SWISS-MODEL
8:00 – 18:00: Registration and information desk open 8:45 – 9:00: Welcome and announcements 9:00 – 10:30: Scientific presentations 10:30 – 11:00: Coffee break 11:00 – 12:30: Scientific presentations 12:30 – 14:00: Lunch break 14:00 – 16:15: scientific presentations 16:15 – 16:45: coffee break 16:45 – 18:15: scientific presentations 18:30 - : Celebration party
Computational Enzymology – Enzymes in the PDB
We seek to understand how enzymes work, how they evolve to perform new functions and how we might learn to design new enzymes and new metabolic pathways. We are using computational approaches to address these questions, developing new data resources and novel algorithms/protocols, based in part on structures in the Protein Databank (PDB) and models.
Since we are trying to get an overview of enzyme evolution, we analyse many enzyme families and attempt to relate their function to structure. One of the challenges in this work is how to find the most relevant structure in the PDB and, if not available, make a reasonable model of the protein including relevant ligands. There are currently over 50,000 known enzyme structures, so analyzing each one by hand is impossible.
In this talk I will describe our efforts to develop tools and databases to improve the annotation of ligands in enzymes and to generate appropriate models. I will focus on coenzymes, cognate substrates/products and their binding sites. This is part of the FunPDBe project, led by PDBeurope, which aims to improve functional annotations for PDB entries.
A brief history of CASP: ideas, successes, failures, and surprises
CASP (Critical Assessment of Structure Prediction) was founded about the same time as SWISS-MODEL. Its goal is to determine the state of the art in modeling protein structure from amino acid sequence, and so advance the field. Community experiments are conducted every two years, with participants submitting models that are evaluated by independent assessors. Participants do not know the experimental structures of the target proteins, and assessors are blinded to participant identity, bolstering rigor and objectivity. During the quarter century of these experiments, the field of protein structure modeling has been transformed from an arcane academic pursuit into a widely accepted tool for obtaining structure. How did this come about? In this talk I’ll address that question from a CASP perspective, considering how the ideas underlying modeling methods have evolved, which methods succeeded, which failed, and why. Notably, both successes and failures have often been surprising.
Application of protein structure prediction and protein complex structure prediction to G-protein-coupled receptors
We have been developing computational tools that can be utilized for atomic-level understanding of protein structure and function. They include methods for template-based protein structure prediction, protein loop and terminus structure prediction, protein model structure refinement, template-based protein complex structure prediction and refinement, template-based ligand binding site prediction, protein-protein docking, protein-peptide docking, and protein-ligand docking. All these methods involve optimization of hybrid energy functions designed to describe both local and global structures of proteins accurately. These methods are available as free webservers or downloadable softwares in http://galaxy.seoklab.org. We have also extended these methods to docking ligand onto predicted GPCR structure by allowing receptor structure relaxation and to GPCR extracellular loop structure prediction by combining with conserved disulfide bond prediction. However, some limitations of these methods have been recognized during application studies such as in community-wide blind prediction experiments. We have also generated candidate model structures for Norrin-Frizzled4 complex as a collaborative effort with experimentalists. Template-based modeling of transmembrane domain of the Frizzled4 receptor, docking of the crystal structure of Norrin-cysteine-rich domain of Frizzled4 to the model structure of transmembrane domain, modeling of the linker region connecting the cysteine-rich domain and the transmembrane domain, and molecular dynamics simulation in the presence of explicit lipid bilayer and water molecules were performed. The models could be used to explain the results of hydrogen-deuterium exchange-mass spectrometry experiment and binding affinity measurement.
Dynamically generating benchmark sets of large heteromeric protein complexes
Multi-protein machines are responsible for most cellular tasks. Unfortunately, the atomic details necessary to understand their function are available for a tiny fraction of them. The computational biology community is developing strategies to model ever-larger molecular machines. However, there is no gold-standard set of three-dimensional (3D) complexes to benchmark the performance of these methodologies and detect their limitations.
In this talk, I present a strategy to dynamically generate non-redundant sets of 3D heteromeric complexes. By changing the values of sequence identity and components overlap between assemblies, we can create sets of representative complexes with known 3D structure (target complexes). Moreover, for each target complex, we identify sets of assemblies, of varying degrees of similarity that can be readily used as input in complex modelling exercises (template subcomplexes). The results of this strategy are made available through a user-friendly web resource available at https://DynBench3D.irbbarcelona.org. We hope that resources like these will help the development and progress assessment of novel methodologies, as docking benchmarks and blind prediction contests did.
As well as the SWISS-MODEL Symposium on Thursday 18th October, you can also register for the 3D Bioinfo Launch Meeting on Friday 19th October.
To attend only one of these events, the cost is 50 CHF. To attend both events the cost is 70 CHF.
The registration fee includes:
Registration closes on 1st October 2018.
Terms and conditions:
Situated in Switzerland at the heart of Europe, Basel is one of the continent’s most convenient locations for major events. Basel is easily accessible from many European cities by plane or high-speed trains. Approximate travel times to the Congress Center:
Train station: Basel Badischer Bahnhof (DB) Train station is in walking distance to the conference site. Or 3 minutes with tram lines 2 or 6, exit at "Messeplatz".
Train station: Basel SBB or SBB/SNCF Ca. 20 minutes by public transport (3.80 CHF/ 3.50 EUR). Take tram line 1 or 2 and exit at "Messeplatz".
Basel EuroAirport (BSL) Ca. 15 minutes by taxi (ca. 40 CHF / 35 EUR); ca. 20 minutes by public transport (3.80 CHF/ 3.50 EUR). When arriving at Basel airport, take the exit to "Switzerland" (not France). For public transport, take bus line 50 to SBB train station and from there tram lines 1 or 2 and exit at "Messeplatz".
Zürich Airport (ZRH) Ca. 90 minutes by train and public transport to the conference site (ca. 45 CHF / 37 EUR). Trains to Basel are leaving from Zürich airport every 30 minutes (either direct or via Zürich main station; train schedules are displayed at the luggage belts. Take the train to either Basel SBB or Basel Badischer Bahnhof.
In Basel you will find more than 4'000 hotel beds. First-class establishments with style and tradition, comfortable middle-class hotels and a choice of friendly small hotels and guest houses to suit the smaller budget.
The hotels in Basel are centrally located. All attractions, museums, restaurants and bars, as well as diverse opportunities for shopping are therefore easy to reach on foot or by public transport. When checking in as a guest at a hotel in Basel, you will receive a Mobility Ticket which gives you free use of public transport during your stay.Online booking services
For information please contact:
SWISS-MODEL 25 Years Symposium c/o Prof. Torsten Schwede, SIB Swiss Institute of Bioinformatics, Biozentrum University of Basel, Klingelbergstrasse 50-70, CH 4056 Basel, Switzerland Email: firstname.lastname@example.org Tel: +41 61 207 15 86
Swiss Institute of Bioinformatics & Biozentrum, University of Basel, CH