Scientific Program

Invited Speakers 

Prof. Dr. Ingemar André; Biochemistry & Structural Biology
Lund University, Lund/Sweden ingemar.andre@biochemistry.lu.se

Prof. Dr. Sinisa Bjelic
; Centre for Biomaterials Chemistry Linnaeus University, Kalmar/Sweden  sinisa.bjelic@lnu.se

 

Schedule

Scientific Program

	Sunday 04/Sep	Monday 05/Sep	Tuesday 06/Sep	Wednesday 07/Sep	Thursday 08/Sep	Friday 09/Sep	Saturday 10/Sep
09h00-10h00		Lecture	Lecture	Holliday	Lecture	Lecture	Lecture
10h00-10h30		Break	Break		Break	Break	Break
10h30-12h00		Lecture	Lecture		Lecture	Lecture	Lecture
12h00-13h30		Lunch	Lunch		Lunch	Lunch	Lunch
13h30-16h00		Practical	Practical		Practical	Practical
16h00-16h30	Registration	Break	Break		Break	Break
16h30-18h00	Opening	Practical	Practical		Practical	Practical
18h00-20h00	Dinner	Dinner	Dinner
20h00-21h00	Oral section	Oral section	Oral section

 

Monday - Introduction to Rosetta

Lectures:

·      Introduction

·      Motivation: what can you do with Rosetta? What can you not do?

·      Fundamental principles behind Rosetta. 

·      Stability of proteins (Anfinsens principle → lowest energy), sampling.

·      How are proteins represented in Rosetta. 

·      Centroid and fullatom, hydrogens. 

·      Kinematics (torsion based simulations), Rigid body relations between subunits etc.

Practical:

·      Setting up Rosetta on your computers 

·      Tutorial Rosetta applications. 

·      Running a Rosetta application. 

·      Something simple to get everyone going, like scoring. 

·      Looking at the logs and output.

·      Summary of the exercise

 

Tuesday - Fundamentals of Rosetta and Structure prediction

Lectures:

·      Introduction to Energy functions and energy terms. 

·      Degrees of freedom in Rosetta. 

·      Torsions, rotamers, rigid body. 

·      Constraints

·      Going through a structure prediction protocol

Practical:

·      Running a Rosetta application in structure prediction. 

·      Docking/loop modeling

·      Analyzing results of structure prediction. 

·      When is it correct? 

·      Clustering.

·      Energy funnels. 

·      Score vs rmsd.

·      Summary of the exercise

 

Thursday - Writing your own protocols

Lectures:

·      Components of Rosetta: minimization, packer, symmetry.

·      Rosetta interfaces. 

·      Foldit, Pyrosetta, XML.

·      Rosetta scripts.

Practical:

·      Write simple scripts.

·      More scripts or free project to explore for participants.

·      Summary of the exercise

 

Friday - Introduction to protein design with Rosetta

Lectures:

·      Protein design: What are the applications?

·      Protein design principles. 

·      Sequence design, rotamers.

·      Protein design with Rosetta in practice. 

·      How to build a simple protocol. 

Practical:

·      Protein design tutorial.

·      Summary of the exercise

 

Saturday - Design of function

Lectures:

 

Oral Presentation

Sunday (17-18h)	Monday (17-18h)	Tuesday (17-18h)
Ayyaz Mahmood	Florencia Klein Rocha	Maíra de Arruda Lima
Carlos H. B. da Cruz	Gabriela C. de Araujo	Marcelo Depólo Polêto
Gabriel C. A. da Hora	Karina B. dos Santos	Marjorie C. L. C. Freire
Gregório K. Rocha	Keila C. Cunha e Silva	Tatiana C. Stabelini
Laercio Pol Fachin	Larissa G. Maciel	Viviane Correa Santos
Monika A. Coronado	Leandro R. Franco	Catarina M. C. S. de Araújo
Raphael Trevizani	Yagoub Ali I. Adam	Jose Avelino da Costa Jr
Anna Laddach	Angy Liseth D. Macias	Manoela P. de M. Lima
Diego Elias Honda	Arthur P. Camargo	Matheus V. F. Ferraz
Roberto Salinas	Denys E. Silva Santos	Aline Sanches Perez
	Diego E. Barreto Gomes	Aleff Ferreira Francisco