Scientific Program
Scientific Program
At 7am a mini-van will leave the Jangadeiro Hotel to the Aggeu Magalhães Institute (FIOCRUZ) where the classes will take palce.
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7:00 |
Sunday 05/May
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Monday 06/May Transport to FIOCRUZ |
Tuesday 07/May Transport to FIOCRUZ |
Wednesday 08/May Transport to FIOCRUZ |
Thursday 09/May Transport to FIOCRUZ |
Friday 10/May Transport to FIOCRUZ |
Saturday 11/May
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08:00 - 10:00 |
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Introduction |
Practical |
Practical |
Practical |
Practical |
Discussion |
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10:00 - 10:30 |
Break |
Break |
Break |
Break |
Break |
Break |
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10:30 - 12:00 |
Lecture |
Lecture |
Lecture |
Lecture |
Lecture |
Discussion |
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12:00 - 13:30 |
Lunch |
Lunch |
Lunch |
Lunch |
Lunch |
Closing |
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13:30 - 15:30 |
Practical |
Practical |
Practical |
Practical |
Practical |
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15:30 - 16:00 |
Registration |
Break |
Break |
Break |
Break |
Break |
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16:00 - 17:00 |
Oral Section |
Oral Section |
Oral Section |
Oral Section |
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17:00 |
transport to the hotel |
transport to the hotel |
transport to the hotel |
transport to the hotel |
transport to the hotel |
All the classes will be in the Aggeu Magalhães Instituto (FIOCRUZ) at
Av. Moraes Rego, s/n, Campus da UFPE - Cidade Universitária - Recife/PE.
Invited Speakers
Prof. Dr. Ingemar André (ingemar.andre@biochemistry.lu.se ) Biochemistry & Structural Biology, Lund University, Lund/Sweden Webpage: https://www.andrelab.org
Prof. Dr. Sinisa Bjelic (sinisa.bjelic@lnu.se)
Department of Chemistry and Biomedical Sciences, Linnaeus University, Kalmar/Sweden Webpage: http://protein.technology
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
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
Oral Section:
| 1 | Carlos André dos Santos Silva | Investigation of genetic and molecular bases of CABMV resistant/susceptible cowpea genotypes through molecular docking | |
| 2 | Danilo Fernandes Coêlho | In silico design of a new high-affinity antigen for HIV-1 2F5 antibodies | |
| 3 | Diana Andreia Pereira Lousa | Optimizing the efficiency of enzymes in the shikimate pathway | |
| 4 | Felipe Trajtenberg | Integrative biology to unravel the flagellar motility apparatus of Leptospira | |
| 5 | Flavia Pirola Rosselli | Emission Redshift in DCM2-Doped Alq3: a Non-Linear Stark-Effect Mode | |
| 6 | Jéssica Cristiane Magalhães Ierich | Computational insights on the biorecognition process of myelin oligodendrocyte glycoprotein by antibodies in demyelinating and neurodegenerative diseases | |
| 7 | Luiz Felipe Gomes Rebello Ferreira | GriDoMol: Integrating a computational grid and Rosetta framework for reverse vaccinology studies |
Tuesday - Writing your own Rosetta protocol with RosettaScripts
Practical:
• Setting up a protein–protein docking run
Lectures:
• Introduction to RosettaScripts framework
• RosettaScripts XML-files and scripting
• Movers and Taskoperations
• Making your own protocol
Practical:
• Writing a RosettaScript input file
• Running RosettaScripts to analyze docking results
Oral Section:
| 1 | Marx Oliveira de Lima | In silico prospection of plant antimicrobial peptides in transcriptomic data | |
| 2 | Pablo Ricardo Arantes | Structural and conformational characterization of Nek1 protein and new pyrimidine inhibitors with therapeutic potential in the treatment of glioblastoma | |
| 3 | Antonio Fernando da Purificação Júnior | Computational Design of Neutralizing Aptamer Bind Epitopes on CHIKV E2 protein | |
| 4 | Felipe Akihiro Melo Otsuka | Improvement of the homodimer interface energy of a β-glycosidase | |
| 5 | Fernando Bruno da Silva | CpHMD-SBM Simulations to Study the Protein G Stability at Different pHs and Salt Concentrations | |
| 6 | Khayth Marronny Rabelo Nagata | In silico study of the interaction between the Purine Nucleoside Phosphorylase of Plasmodium falciparum with Beta-Caryophylene |
Wednesday – Protein design: From structure to interface design
Practical:
• Continued from Tuesday.
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:
• De novo design of structural fold
• Protein–protein interface design
Oral Section:
| 1 | Larissa Gonçalves Maciel | The enzyme 3-hydroxykynurenine transaminase from Aedes aegypti as target for 1,2,4-oxadiazoles | |
| 2 | Mario Andres Rodrigues Pineda | Fast time scale backbone dynamics the sodium-calcium exchanger (CALX) CBD2 domain | |
| 3 | Maximilia Frazão de Souza Degenhardt | DYNAMICS AND STRUCTURE REFINEMENT OF A TWO-DOMAIN PROTEIN USING SAXS | |
| 4 | Mira Raya Paula de Lima | ||
| 5 | Peter Park | Flip to Enter: Initial Steps of BP-100/Membrane Interaction | |
| 6 | Emerson Moreira |
Thursday – Folding proteins by including the knowledge from sequences
Practical:
• Continued from Wednesday
Lecture:
• Protein folding with covariational constraints
• Generating your own sequence constraints
• Clustering your results
Practical:
• Use of constraint in folding
Oral Section:
| 1 | Matheus Vitor Ferreira Ferraz | Rational Design of a High Affinity Nanobody Binding ZIKV NS1 Protein Aiming at Serological Differential Diagnostic | |
| 2 | Wenny Camilla dos Santos Adan | Assessing VHHs Structural Dynamics and its Influence on their Binding Affinity to Antigens | |
| 3 | Higor Vinícius Dias Rosa | Septin heterocomplex structure reveals the molecular determinants at G-interface | |
| 4 | Madson Allan de Luna Aragão | Structural Prediction of the eIF4E and eIF4G on the Leish-eIF4F Complex | |
| 5 | Manuela Correia Dionísio | Structural genomics of Xanthomonas citri subsp. malvacearum | |
| 6 | Vinicius Firmino dos Santos | Computational simulations of PDMAEMA for the transport of nucleic acids |
Friday – Tutorial rampage: Immerse yourself in your favorite Rosetta topic
A whole day practical to gain in depth knowledge of your favorite Rosetta application. Alternatively, work on to finish any of the previous tutorials.
Available tutorials:
• Calculating free energy differences (∆∆G) upon residue mutation
• Generating unnatural amino acids
• And many more …