3D protein structures: what sequences cannot tell you

Preliminary programme

  • 09:30-10:00 Arrival and coffee
  • 10:00-10:05 Welcome word

Session I:

  • 10:05-10:50 Keynote I.Vlad Cojocaru, Hubrecht Insitute: “Molecular simulations of DNA recognition by transcription factors”
  • 10:50-11:10 Jan Huertas, MPI for Molecular Biomedicine, Germany: “Sequence-dependent nucleosome dynamics: Implications for transcription factor binding”
  • 11:10-11:30 Carlos Ramírez, University of Groningen: “In silicoenzyme design of omega-transaminases”

SessionII:

  • 11:30-12:15 Keynote II. Marc Baaden, Institut de Biologie Physico-Chimique: “3D protein structures in virtual molecular reality - insights from immersive visual exploration and touching molecules in motion”
  • 12:15-12:35 Andrea Basciu, Università di Cagliari, Italy: “Druggable protein conformations from enhanced-sampling of pocket volume and shape”

Lunch and posters

  • 12:35-14:00 Lunch, poster session, and VR demo

SessionIII:

  • 14:00-14:45 Keynote III. Chris Oostenbrink, Institute of Molecular Modeling and Simulation, BOKU Vienna, Austria: “Binding molecules in free-energy calculations”
  • 14:45-15:05 Janani Durairaj, Wageningen University & Research:“Structure-based Prediction of Sesquiterpene Synthase Product Specificity”
  • 15:05-15:25Jan Walther Perthold, Institute of Molecular Modeling and Simulation, BOKU Vienna, Austria: “Automated Free Energy Calculation for Drug Design: Accelerated Enveloping Distribution Sampling”

Coffee break

  • 15:25-16:00 Coffee break

SessionIV:

  • 16:00-16:20 Bogac Ercig, Sanquin: “From autoantibodies to therapeutics: en route to novel treatment for immune TTP”
  • 16:20-17:05 Keynote IV. Peter Peters, Maastricht University: “Beauty and Benefits of cryo-EM; our new endeavors in vitrification of proteins and cells”
  • 17:05 Closure & Poster/Presentation prize

 

Registration

Attendance is free of charge but registration is required.

Organized with the support of:

               

3D Protein Structures: what sequences cannot tell you

November 16th 2018

Venue: Boothzaal, University Library De Uithof, Utrecht 

The Netherlands Society on Biomolecular Modelling (NSBM) is an independent society that brings people together in The Netherlands and beyond, that work on three dimensional structures of biomolecules and biomolecular simulations. This is a first announcement of our Fall meeting to which you are cordially invited. During the meeting, the floor will be given to students, PhD students, post-docs and a number of invited guest speakers who study protein structure and/or structural bioinformatics or related topics.

 Location and dates

Deadlines

  • Registration deadline for posters or to be considered for a short talk: November 5th
  • Registration deadline (including lunch): November 9th

Application procedure

  • Participants should send an email to register (required but free registration) to: This email address is being protected from spambots. You need JavaScript enabled to view it.
  • Submission of an abstract is required if you want to present a poster.
  • Indicate in your email if you want to be selected for a short oral presentation.

Note: The maximum number of participants is limited to 75! So please register on time.

Lead contact

  • Dr. Gerry Nicolaes – This email address is being protected from spambots. You need JavaScript enabled to view it.

http://www.3dstructure-function.nl/nsbm-fall-meeting/

 

Confirmed speakers are:

o   Dr. Vlad Cojocaru (Hubrecht Institute) - "Molecular simulations of DNA recognition by transcription factors"

o   Dr. Marc Baaden (Institut de Biologie Physico-Chimique) - " 3D protein structures in virtual molecular reality"

o   Dr. Chris Oostenbrink (Institute of Molecular Modeling and Simulation, BOKU Vienna) -  “Binding molecules in free-energy calculations”

o   Prof. Peter Peters (Maastricht University) - “Beauty and Benefits of cryo-EM; our new endeavors in vitrification of proteins and cells

Abstract submission is still open and we have several free slots in the sessions for students, PhD students and post-docs

 

Costs

Attendance is free of charge but registration is required.

Lunch and coffee will be provided thanks to the financial support of the Nijmegen Centre for Molecular and Biomolecular Informatics.

 

Fall meeting

eScience Solutions and Opportunities in the Netherlands

November 29th 2017

 

Venue: Boothzaal, University Library De Uithof, Utrecht

 

The Netherlands Society on Biomolecular Modelling (NSBM) is an independent society that brings people together in The Netherlands that work on three dimensional structures of biomolecules and biomolecular simulations. Generally twice per year, meetings are hosted by the NSBM that are open to anyone interested, regardless of the affiliation, from within or outside the Netherlands. The NSBM cordially invites you to participate in its 2017 fall meeting in Utrecht. During the meeting, the floor will be given to PhD students and post-docs who study protein structure and/or structural bioinformatics or related topics.

Location and dates

Deadlines

  • Registration deadline to be considered for a short talk: November 17th
  • Registration deadline (including lunch): November 22nd

Application procedure

  • Participants should send an email to register (required but free registration) to: This email address is being protected from spambots. You need JavaScript enabled to view it.
  • Submission of an abstract is required if you want to present a poster.
  • Indicate in your email if you want be selected for a short oral presentation.

Note: The maximum number of participants is limited to 75! So please register on time.

 

Lead contact

  • Gerry Nicolaes – This email address is being protected from spambots. You need JavaScript enabled to view it.

http://www.3dstructure-function.nl/nsbm-fall-meeting/

 

Preliminary Programme

  • 09:30-10:00 Arrival and coffee
  • 10:00-10:10 Welcome word
  • 10:10-11:00 Keynote I

o Prof. Jürgen Pleiss, Institut für Technische Biochemie (ITB), Stuttgart University (D)
o Data-integrated simulation of enzymes

  • 11:00-11:20 Short talk selected from abstracts
  • 11:20-11:40 Short talk selected from abstracts
  • 11:40-12:10 Lecture

o Tom van den Bergh, Bio-Prodict, Nijmegen (NL)
PDB-wide data integration with 3DM

12:10-12:30 Lecture

  • o Short talk selected from abstracts
  • 12:30-14:00 Lunch and poster session
  • 14:00-14:50 Keynote II:

o Prof. Chris Ulens, KU Leuven (B)
o Allosteric modulation of ligand-gated ion channels

  • 14:50-15:10 Short talk selected from abstracts
  • 15:10-15:30 Short talk selected from abstracts
  • 15:30-16:00 Coffee break
  • 16:00-16:50 Keynote III:

o Dr. Chris de Graaf, VU Computational Medicinal Chemistry group, Amsterdam (NL)
o 3D-e-Chem: Structural cheminformatics tools for navigating protein-ligand interaction space

 

16:50 Closure

 

3D Protein Structures: what sequences cannot tell you

November 16th 2018

Venue: Boothzaal, University Library De Uithof, Utrecht

The Netherlands Society on Biomolecular Modelling (NSBM) is an independent society that brings people together in The Netherlands and beyond, that work on three dimensional structures of biomolecules and biomolecular simulations. This is a first announcement of our Fall meeting to which you are cordially invited. During the meeting, the floor will be given to students, PhD students, post-docs and a number of invited guest speakers who study protein structure and/or structural bioinformatics or related topics.

Location and dates

Deadlines

  • Registration deadline for posters or to be considered for a short talk: November 5th
  • Registration deadline (including lunch): November 9th

Application procedure

  • Participants should send an email to register (required but free registration) to: This email address is being protected from spambots. You need JavaScript enabled to view it.
  • Submission of an abstract is required if you want to present a poster.
  • Indicate in your email if you want to be selected for a short oral presentation.

Note: The maximum number of participants is limited to 75! So please register on time.

Lead contact

  • Dr. Gerry Nicolaes – This email address is being protected from spambots. You need JavaScript enabled to view it.

http://www.3dstructure-function.nl/nsbm-fall-meeting/

 

A programme will be published as soon as possible

 

Costs

Attendance is free of charge but registration is required.

Lunch and coffee will be provided thanks to the financial support of the Nijmegen Centre for Molecular and Biomolecular Informatics.

 

Please reserve November 29 in your calendars for the 2017 Fall meeting of NSBM, which will be held in Utrecht like last year. The meeting agenda is still in preparation.