Corso Bioinformatica 2019 - uniroma1.it...Applications should be sent by e-mail to...
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Dottorato di Ricerca in Biochimica Scuola di Dottorato in Biologia e Medicina Molecolare Corso di Bioinformatica Teorico-Pratico 7° Edizione “ BIOINFORMATICS:THEORY AND APPLICATIONS FROM GENOMES TO DRUGS” 7° Edition • CFU: 3 (20 hours of theoretical-practical lectures, plus one specialized seminar) Teachers Dr. Veronica Morea Institute of Molecular Biology and Pathology (IBPM) CNR, Rome [email protected] Prof. Alessandro Paiardini Department of Biochemical Sciences “A. Rossi Fanelli” Sapienza University of Rome [email protected] Dr. Allegra Via Institute of Molecular Biology and Pathology (IBPM) CNR, Rome [email protected] Dr. Viviana Caputo Department of Experimental Medicine Sapienza University of Rome [email protected] Dr. Loredana Le Pera Institute of Molecular Biomembranes Bioenergetics and Biotechnology (IBIOM) and Institute of Molecular Biology and Pathology (IBPM) CNR, Rome. [email protected] Dr. Teresa Colombo Institute of Molecular Biology and Pathology (IBPM) CNR, Rome [email protected] Dottorato di Ricerca in Biochimica
Transcript of Corso Bioinformatica 2019 - uniroma1.it...Applications should be sent by e-mail to...
DottoratodiRicercainBiochimicaScuoladiDottoratoinBiologiaeMedicinaMolecolareCorsodiBioinformaticaTeorico-Pratico7°Edizione
“BIOINFORMATICS:THEORYANDAPPLICATIONSFROMGENOMESTODRUGS”
7°Edition
• CFU:3(20hoursoftheoretical-practicallectures,plusonespecializedseminar) Teachers
Dr.VeronicaMoreaInstituteofMolecularBiologyandPathology(IBPM)CNR,Romeveronica.morea@uniroma1.itProf.AlessandroPaiardiniDepartmentofBiochemicalSciences“A.RossiFanelli”SapienzaUniversityofRomealessandro.paiardini@uniroma1.itDr.AllegraViaInstituteofMolecularBiologyandPathology(IBPM)CNR,Romeallegra.via@uniroma1.itDr.VivianaCaputoDepartmentofExperimentalMedicineSapienzaUniversityofRomeviviana.caputo@uniroma1.itDr.LoredanaLePeraInstituteofMolecularBiomembranesBioenergeticsandBiotechnology(IBIOM)andInstituteofMolecularBiologyandPathology(IBPM)CNR,Rome.
Dr.TeresaColomboInstituteofMolecularBiologyandPathology(IBPM)CNR,[email protected]
Dottorato di Ricercain Biochimica
Location
Computer Room C1 of the Department of Biochemical Sciences “A. Rossi Fanelli”, SapienzaUniversityofRome(seemap,buildingn.CU010,2ndfloor)
Calendar
FromJune10thtoJuly17th:everyMondayandWednesday,from2:30to4:30pmStartinglecture:June10th2019at2:30p.m.
ApplicationGuidelines
Thecourseisaddressedto2ndyearstudentsoftheBeMMPh.D.Schoolandcanhostamaximum of 30 students. Applications should be sent by e-mail [email protected], not later than June 5th 2019. Please, indicate“BioinformaticsCourse”asthee-mailobject,andyourSurnameandName,aswellasthetitleofyourPh.D.course,inthetextbody.Studentselectionwillbebasedontimeofarrivalofthe application. Selected students will be notified by e-mail, and should guarantee theirattendance.Certificatesofparticipationwillbeissuedtostudentswhohaveacquiredatleast2/3ofthetotallectures.
AimoftheCourse
- Participants will learn the principles of gene/protein evolution, which constitute thetheoreticalbasisoffundamentalapproachestothestudyofproteinsandnucleicacids.
- Participantswill bepresentedwith a rangeofBioinformatics techniquesmost commonlyemployedinthecomputationalstudyofproteinsandnucleicacids;abouthalfofthecourseisdedicatedtothepracticaluseofthesetechniques.
- Inparticularparticipantswillacquirebasicknowledgeonhowtoanalyseproteinandnucleicacid sequences and protein structures, predict three-dimensional protein structures, andrationallydesignsmallmoleculedrugs
- Bytheendofthecourse,participantswillbeabletorationallyuse,andinterpretresultsof,standard methods presented in the course; importantly, they will gain a deeperunderstandingofwhatbiologicalproblemscanbebesttackledbycomputationalmethods.
- Finally,participantswillbeprovidedwithfundamentalknowledgeandmaterialforfurtherpersonalstudies.
Detailedprogram1.MolecularEvolution:WhyisitImportant?
• Homologyvs.sequence,structureandfunctionsimilarity• Relationshipbetweenproteinsequenceidentityandsimilarityinstructureand/orfunction
2.TheWorldWideWeb:AninfiniteSourceofPrecious(andRubbish)Information
• Separate thewheat fromthechaff: reliable resources (NucleicAcidsResearch;NCBI;EBI;UniProt;ExPASy;PDB;GO)
3.ProteinSequenceAnalysis:Whatcanittellus?
• Knowledgebases(UniProt,NCBIGene):function,interactions,intracellularcompartment
• Sequencecomparisonanddatabasesearch:pairwisevs.profile-basedmethods(Blast;Psi-Blast);%sequenceidentityandE-value;sequencesimilarity;insertionsanddeletions
• Multiplesequencealignmentsandphylogenetictrees4.Sequence-basedPredictions
• domains:buildingblocksoflargeproteins• globularvs.disorderedproteins(domains);membraneornotmembrane;signalpeptides;
secondarystructures• modificationspost-translation:phosphorylation,glycosylation,ubiquitination;• handy tools from ExPasy: amino acid composition; isoelectric point; molecular weight;
hydrophobicity;cleavagesites;one-lettertothree-lettersandback;motifidentification5.ProteinStructurePrediction:AreWeSolvingtheFoldingProblem?
• protein3Dstructurescanbevisualizedinavarietyofways(PyMol)• proteinstructurescanbecompared(CE)• proteinstructurescan(often)bepredicted:
o HomologyModelling(Modeller,PyMod)o FoldRecognition(Phyre;PsiPred)o “Denovo”predictions(Rosetta/Robetta)
6.InteractingwithProteinStructures
• Dockingsmallmoleculestoproteinfunctionalsites• Pharmacophorescreeningandrationaldrugdesign
7.Abig,bigworld:anoverviewof“Omic”disciplinesand“high-throughput”data
• Genomicsandtranscriptomics• Epigenomics
8.NGSandExomeSequencing
• Advancedapproachestostudythemolecularbasisofmendeliandisease
