BRFAA - Biomedical Research Foundation Academy Of Athens
Biomedical Research Foundation Academy Of AthensAcademy Of Athens

Calendar

Academic Year 2021-2022

"September 2, 2.30pm, Sébastien Hoyas, Université de Mons, Belgium, "Characterization and Exploitation of Peptoid Secondary Structures: A Synergistic Experimental and Computational Approach"

September 16,2pm, Jon, "Proton mediated enzyme communication and catalysis".

September 20, 3pm, Melina, "Ανάλυση κοιλοτήτων πρόσδεσης της ογκοπρωτεΐνης KRAS-4B με Μοριακές Δυναμικές προσομοιώσεις"

September 30, 3pm, Eleftheria, "Μοριακές Δυναμικές προσομοιώσεις του διμερισμού της ογκοπρωτεΐνης KRAS-4B"

October 7, 3pm, Group gathering, start of the semester

​October 14, 3pm, Zoi, IS2, "Theoretical Study of Cyanotoxin Degradation:  Background and Preliminary studies"

October 21, 2pm, Panagiotis Koukos, Utrecht University,  "Perspectives on biomolecular simulation: From MD to Docking"

November  15, 2pm, Alexis, "Investigating allosteric networks in proteins using computational methods"

November 18-19, 3-8pm, "Online Conference of the European Chemical Society, Theoretical and Computational Division"

December 1, 3 pm, Panos "Shape-restrained modelling of protein-small molecule complexes with HADDOCK."

December 3, 10.30 am, Sofia, "Adaptive Sampling Simulations and Markov State Modeling"

December 13, 10.30 am, Danai, "Understanding how kinase domain mutations of PI3Kα alter lipid kinase activity using Molecular Dynamics simulations"

December 17, 12 pm, ​Michalis

​Christmas Break

January 18, 3 pm, Danai, zoom meeting, "Allostery in Membrane Proteins"

January 26, 3 pm, Isidora, zoom meeting, Investigation of BMAA and its carbamate adducts as potential inhibitors of
the glutamate receptor AMPA using MD/FEP calculations

February 3, 4 pm, Danai, zoom, "Allostery in Membrane Proteins"

February 15, 2-5pm, ΙΣ2, Final presentations by students of "Molecular Modeling of Biomolecules"  2021-2022 Class.

February 17, 5 pm, Danai, zoom, "Investigating the protein-membrane interface"

February 23, 2.30 pm, Danai "Investigating the protein-membrane interface"

February 24, 6pm, 10th EFMC-YSN MedChemBioOnline: What Can the Medicinal Chemists Learn from Data Sciences?

March 3, 4pm, Danai, "Investigating the protein-membrane interface in peripheral membrane proteins using molecular simulations"

March 10, 4 pm, Alexis PhD thesis mock exam

​March 15, 4 pm, Celia, literature review on project

March 31, 4 pm, Klea, literature review on project

April 14, 4pm Bruno, MSc thesis project presentation

Easter Break

Academic Year 2020-2021

September 25, 5 pm, Zoom, Katerina Barbidi and Katerina Basdeki, Presentation of internship projects

October 2, 3 pm, Zoom, Zoi Diamanti, "Στατιστική Μηχανική Μελέτη της Νευροτοξίνης β-Ν-Μεθυλάμινο-L-αλανίνη (BMAA) και Καρβαμιδικών Ενώσεων της σε Υδατικό Διάλυμα με την Μέθοδο Μοριακής Δυναμικής Προσομοίωσης"

October 19,  10 am, teleconference room, Ioannis Andreadelis, "Studying the dimerization of  KRas-4B on the plasma membrane using molecular simulations"

November 5,  3 pm, zoom meeting, Alexis Chatzigoulas, "Prediction of protein membrane binding interfaces using machine learning"

November 11-13, Free Energy meeting, 6.30 - 9.30pm, please register

November 19,  3 pm, zoom meeting, Michalis Papadourakis, PhD Thesis presentation, "Molecular Dynamics based methods for calculating binding free energies and selectivity of pharmaceutical target inhibitors"

November 27,  3 pm, zoom meeting, Isidora Diakogiannaki, "BMAA and its carbamate adducts as potential inhibitors of glutamate receptors."

December 16, 6pm, zoom meeting (please register): "Molecular Simulations in the Time of COVID19 and Beyond,
​Prof. Rommie Amaro

December 17,  3 pm, Prof. Michael Levitt: "50 years of force field for Bio-Design: From empirical to knowledge-based, to quantum mechanical to machine learning". 1st International BioDesign conference.

Christmas Break

January 14, 3 pm, zoom meeting, Sofia Kiriakidi,
PhD mock exam, «Applications of theoretical and biophysical studies on rational drug design»

January 26, 2.30pm, zoom meeting, Final Exam of Computer Modeling of Biomolecules

February 4, 11.30am, Dr. Richard Henchman (University of Manchester), "Entropy and analysis of molecular simulations". Register here:  https://www.ccpbiosim.ac.uk/entropy2021. Recording available here.

February 11, 3pm, zoom meeting, Zoi Diamanti, Theoretical study of cyanotoxin degradation for the purification of water resources

February 15-19, ​7th Virtual Winter School for Computational Chemistry, register here: https://winterschool.cc/

February 25, 2pm, Alexis, "Predicting protein dynamics from evolutionarily conserved pathways using Graph Neural Networks"

March 4, 2pm, Eleni Chousa, "Part 1: Transport properties of polymeric systems based on poly (ethylene glycol)" and "Part 2: Dynamics of dense suspensions of mechanosensitive microorganisms".

March 11, 3 pm, Dr. Eleni Michael, University of Cyprus, "High-Throughput Computational Protein Design: Development and Applications".

March 18, 3pm, Isidora, "Studying the stability of glutamate, BMAA and its adducts on the glutamate receptor AMPA using MD simulations."

March 22,  10pm (Athens), Professor Peter Tieleman, University of Calgary (Canada): "Insights In Lipid-Protein Interactions from Computer Simulations".

March 24, 11:00-11.45am (Athens time) Dr. Elisa Fadda "Functional role of the glycan shield in the activation of the SARS-CoV-2 S protein" , EuroHPC Summit Week 2021, register here.

March 29-31, 4th Conference on Multiscale Modelling of Condensed Phase and Biological Systems - CCPBioSim & CCP5

April 1, 3pm, Danae Kotzampasi, University of Crete, Computational studies for protein function and for the discovery of novel potent protein modulators

​April 8, 3pm, Melina, "An overview of binding pocket analysis of the oncoprotein KRAS-4B in model cell membranes and perspectives on time-dependent binding pocket analysis studied with MD simulations"

April 15, 3pm, Eleftheria, "A literature review on Coarse-grained MD simulations to study the dimerization of the oncoprotein KRAS-4B in model cell membranes: "

April 22-24, Workshop on Computer Simulations and Theory of Macromolecules.

Easter break

May 13, 3pm, zoom meeting, Zoi Diamanti, "Literature review on the theoretical study of cyanotoxin degradation for the purification of water resources"

May 20, 2pm, zoom meeting, Themis Aivaliotis, "Investigating the structure and dynamics of Myc inhibitors bound on the intrinsically disordered oncoprotein Myc"

May 27, 6pm, Δρ. Ευαγγελία Χρυσίνα, «Ξετυλίγοντας το νήμα της πρωτεϊνικής δομής»

June 10, 6pm, Kαθ. Θωμάς Μαυρομούστακος, “Χρήσιμες Γλωσσικές Επισημάνσεις κατά τη Συγγραφή Μεταπτυχιακών και
Διδακτορικών Εργασιών»

June 15-17, 6pm-9pm, Workshop on Free Energy Methods in Drug Design

June 22, 6pm, zoom meeting, Isidora's mock exam, "Στατιστική Μηχανική Μελέτη μέσω Μοριακής Δυναμικής Προσομοίωσης της δράσης της β Ν μεθυλάμινο L αλανίνης και των καρβαμιδικών παραγώγων της ως αναστολείς του γλουταμινικού υποδοχέα ΑΜΡΑ."

June 24, 10.30am, Themis' mock exam, "Αξιολόγηση πιθανών αναστολέων του ογκογονιδίου c-Myc με προσομοιώσεις Μοριακής Δυναμικής"

June 25, Isidora's exam, "Στατιστική Μηχανική Μελέτη μέσω Μοριακής Δυναμικής Προσομοίωσης της δράσης της β Ν μεθυλάμινο L αλανίνης και των καρβαμιδικών παραγώγων της ως αναστολείς του γλουταμινικού υποδοχέα ΑΜΡΑ."

June 28, 10am, Themis diploma thesis exam, "Αξιολόγηση πιθανών αναστολέων του ογκογονιδίου c-Myc με προσομοιώσεις Μοριακής Δυναμικής​"

July 1, 11am, Kαθ. Θωμάς Μαυρομούστακος, Τμήμα Χημείας, "Χρήσιμες Γλωσσικές Επισημάνσεις κατά τη Συγγραφή Μεταπτυχιακών και Διδακτορικών Εργασιών»

Summer Break - end of the academic year



Academic Year 2019-2020

September 10, 10am IS2, Dora, "Investigating the structure and dynamics of the intrinsically disordered oncoprotein Myc"

September 26, 3pm BRFAA Amphitheater, Stefan, GSPD Seminar, "Ιnvestigating the dynamics and dimerization of oncoprotein KRas-4B through molecular simulations."

October 1, 10am IS2, Dimitris, mock exam, "Using Free Energy Perturbation calculations as a predictive tool in lead optimization"

October 15, 10am IS2, Christos, "Simulating the protein dimerization process using coarse-grained MD simulations"

October 29, 12pm IS2, Themis Lazaridis, "Computational Studies of Protein-Membrane interactions"

November 1, 10am IS2, Alexis, "Prediction of protein membrane binding interfaces using machine learning"

November 11, 11am IS2, Christophe Chipot, "Taming rugged free energy landscapes using an average force"

November 19, 10am IS2, Anastasia, "Studying the structure and dynamics of the oncoprotein KRas-4B on the plasma membrane using molecular simulations".

December 3, 12pm  IS2, Katerina, "Relative Binding Free Energy calculations for the optimization of the inhibitor CK-666 of the protein complex Arp2/3"

Christmas Break

January 21, 10am IS1, Dimitra Panou (Department of Informatics, UoA), DeepFoldit - A Deep Reinforcement Learning Neural Network Folding Proteins

January 23, 10am IS2, Ioannis Andreadelis (Department of Chemistry, UoA), NMR spectroscopy and molecular dynamics simulations for the study of cyclodextrin complexes with bioactive compounds.

January 28, 10am IS2, Katerina, "Free energy perturbation calculations as a Lead Optimization Method: The case of Arp2/3"

January 29, Final Exam of Computer Modeling of Biomolecules, 10am - 1pm, teleconference room

February 3, Human Brain Project Open Day

February 6, GSPD Seminar, 2.15pm, BRFAA Amphitheater, Anastasia, "Targeting IL33 as an anti-inflammatory agent with computer-aided drug design"

February 6, 3.30-6.30pm BRFAA Amphitheater, HBP CDP6 Mini Symposium: "Computational Drug Design",

February 11, 10am IS2 Shafi Khan, "Sequential ligand and structure-based virtual screening approach for the identification of potential G protein-coupled estrogen receptor-1 (GPER-1) modulators"

February 20, 10am IS2 Christos"Simulating the protein dimerization process using coarse-grained MD simulations"

February 25, 3pm IS2, Anastasia, "Studying the structure and dynamics of the oncoprotein KRas-4B on the plasma membrane using molecular simulations".

March 10-11, GRNET course on Machine Learning in HPC 

March 17, 10am IS2, Giannis Nastos, "Creating functionalized nanoparticles for simulation"

March 31, 10am IS2, Alexis, "Prediction of protein membrane binding interfaces using machine learning"

April 7, 10am IS2, Ioannis, "KRAS signaling in health and disease. Opportunities for drug discovery"

Easter Break

June 4, 4pm IS2, Giannis Nastos, mock exam, "A web-based tool for the creation of functionalized nanoparticles"

June 25, 4pm IS2, Sofia Kiriakidi, "Exploring the role of the lipid bilayer in the structure and function of membrane proteins and associated drugs"

July 9, 4pm IS2, Giannis Vaxevanakis, W-DIAMOnD: Finding gene pathways associated with diseases and implementation to protein allosteric pathways.

July 27, 4pm, IS2, Christos Lamprakis, "Evaluating Coarse-Grained Molecular Dynamics simulations for studying protein dimerization in aqueous and membrane environments"



Academic Year 2018 - 2019

October 12, IS2, 6pm - mock exam Cleopatra: Developing a real time gene database for an Android application

October 19, 9.15am ΙΣ2 - MSc thesis Exam, Cleopatra: Developing a real time gene database for an Android application

October 25, 1-3pm, ΙΣ1 - Elena: Free Energy Perturbation (FEP) / MD calculations applied to lead optimization: The case of Arp2/3

November 12 - Chris Chipot, 12pm, amphitheater: "The Dangerous Liaisons between Detergents and Membrane Proteins" and "Frontiers in free-energy calculations of biological systems"

November 20 - Alexis, 4-6pm, ΙΣ1: Investigating Allostery in Enzymes using Computational Methods

December 7 - Dora, 6.30pm, ΙΣ1: Computational Study of the Tacticity Effect on the Conformational Properties of Polypropylene and Poly(ethylene-propylene) Copolymers

December 10, Leandro, 5pm, ΙΣ1: Design, synthesis and biological evaluation of antivirals against chikungunya virus

December 18, Anastasia 4-6pm, ΙΣ1  (IL33)

Christmas break

February 18, Dora 5-7pm, ΙΣ2 - Structure and dynamics of the oncoprotein Myc and development of novel anti-Myc inhibitors

January 29, Michalis, 6.15-8pm, ΙΣ1 - (TBA)

February 4-5, PRACE Workshop, GRNET

February 6, Leandro, 530pm IS2, Lead optimization of antivirals against chikungunya virus

February 12, Empowering Women in Chemistry: A Global Networking Event, University of Athens, University of Peiraus, check the programme in the links here. 9am - 4pm

February 20, Final Exam of Computer Modeling of Biomolecules, 9am - 2pm, teleconference room

February 26, Dimitris, 10am IS2, Relative Binding Free Energy calculations for the optimization of the inhibitor CK-666 of the protein complex Arp2/3.

February 27, repeat exam of Computer Modeling of Biomolecules, 1030am - 1130am, teleconference room

February 27, Dimitris Skaltsas, lecture hall of the Department of Informatics and Telecommunications, 14:00. Leveraging big data and AI to assess probability of success in drug development"

March 8, Michalis Tsakos,  1-3pm IS2, Cellular target identification and mode-of-action studies of bioactive secondary metabolites

March 19, Dimitris, 10am IS2, Relative Binding Free Energy calculations for the optimization of the inhibitor CK-666 of the protein complex Arp2/3.

March 22,  Alexis, 10am IS2, Drugging peripheral membrane proteins at the protein-membrane interface

March 26, Anastasia, 10am IS2 Investigating the structure and dynamics of IL-33 as an anti-inflammatory target using MD simulations

April 9, Georgia, 10am IS2, "Biology of RXRα and the effects of the S427F mutation"

April 16, Dora, 10am, IS2 "Investigating the structure and dynamics of the oncoprotein Myc and discovery of novel Myc inhibitors"

April 22, 10 am, Stefan Doerr, IS2, "Applications of machine learning in molecular simulations"

April 23, 11am, NTUA, School of Chemical Engineering, Dimitris:
"Relative Binding Free Energy Calculations as a tool in lead optimization for drug design."

​April 23, 12pm, Anastasia: "Targeting IL33 as an anti-inflammatory agent with computer-aided drug design"

Easter Break

June 7, 2pm, IS1, Konstantinos Vogiatzis, University of Tennessee, "Combining Machine Learning with Quantum Chemistry for Chemical Applications"

June 12, Christos, 12 pm, IS2: "Unraveling the protein-lipid interplay. Challenges towards accurate coarse grained force field system description"

June 24, Anastasia, 4 pm, NTUA Chem Eng department, mock exam: "Targeting IL33 as an anti-inflammatory agent with computer-aided drug design"

June 28, Anastasia, 12.45 pm, NTUA Chem Eng department, Room32, FINAL EXAM: "Targeting IL33 as an anti-inflammatory agent with computer-aided drug design"

June 28, Georgia, 3.30 pm, Γ2 mock exam: Investigation of the S427F mutation effects on the RXRα structure and dynamics

July 2, Georgia, 10 am, IS2 EXAM: Investigation of the S427F mutation effects on the RXRα structure and dynamics

July 3, 9am - 3pm, Symposium on "Computational Methods in drug design", BRFAA amphiteater

July 23, Presentation by iGEM Team 2018,  3 pm, IS1 "Toehold Switch Enabled Viral Detection via Routine Glucose Monitoring Technology."

August 2, Polydeukis Diamantis, EPFL, IS1, 2pm, "From Redox Chemistry to Conformational Dynamics: Theoretical Investigation of Chemical and Biological Systems".

August 28 - Rebecca Lait, 10am, IS1, "Using HPC to investigate the structure and dynamics of a KRAS oncogenic mutant"

August 28 - Antonio Miranda, 11am, IS1,  "HPC application for candidate drug optimization using free energy perturbation calculations"

Academic Year 2017 - 2018

September 20: Γ1 2pm, Maria: Comparison of Glide and Autodock for Pose Prediction and Glide and Autodock Vina for Virtual Screening

September 28, IΣ2, 1pm: Michalis & Lefteris - thesis mock exam "Modeling magnetic nanoparticles coated with polyvinyl alcohol and polyarabic acid"

October 3, IΣ2, 3pm: Michalis & Lefteris - thesis mock exam "Modeling magnetic nanoparticles coated with polyvinyl alcohol and polyarabic acid"

October 24: IΣ2, 3pm, Anna Kapela - Design and Synthesis of Targeted Inhibitors of PI3Kα as Candidate anti- Cancer Drugs

November 20:  Γ1 (1pm): Thomas Heinemann - Systematic coarse-graining procedures for molecular systems

December 11 (11:00, ΙΣ1): Matina - An automated workflow for performing free energy perturbation calculations for lead optimization

December 21 (12:30, Γ2): Alexandros - Free energy perturbation calculations for lead optimization: Comparison between FEP+ and FEP/NAMD

​Christmas break

January 15 - Cleopatra - Developing databases for biological applications in Android

January 30 - Alexis, TBA - Thesis Mock Exam

February 1, Alexis, 1pm - Thesis Exam "A web-based crystallographic tool for the construction of nanoparticles"

March 1 -  10:30am-1:00pm (Γ1): Presentation of the final Projects of the MSc course: "Molecular Modeling of Biomolecules"

March 5 - Aggeliki Ntorla (ΙΣ1) 11 am- "Functional characterization of missense mutations in the gene Acetyl-CoA carboxylase beta (ACC2/ACACB) found in a familial case of obesity"

March 12, Manolis Christoforou (ΙΣ1) 10am - Investigating the bioactive conformation of Angiotensin II using MD simulations and Markov State Modeling

March 23 - Phaeton Brotzakis (IS2) , 17.30 - Fast and accurate calculation of the affinity and binding mechanism of Benzamidine in Trypsin using VAC-MetaDynamics" 

Easter Break

May 7 - Christina, 2pm, IΣ1 - Insights into the mechanism of the PI3Kα E545K activating mutation using unbiased and enhanced sampling MD simulations

May 22 - Alexandros, 1pm, ΙΣ1 - Free energy perturbation calculations for lead optimization: Comparison between FEP+, FEP/NAMD, and FEP/GROMACS on Arp2/3 complex inhibitors

May 29 -  Manolis Christoforou, 10am, IΣ1, thesis mock exam - Investigating the bioactive conformation of Angiotensin II using MD simulations and Markov State Modeling

June 1 -  Manolis Christoforou, 9am, thesis exam, Department of Informatics - Investigating the bioactive conformation of Angiotensin II using MD simulations and Markov State Modeling

June 8 - Cleopatra, 2pm, IΣ2 - Developing databases for biological applications in Android

June 15 - Matina, 10am, ΙΣ1 - An automated workflow for performing free energy perturbation calculations for lead optimization

June 30 - Matina, 3pm, IS2 - MOCK exam - An automated workflow for performing free energy perturbation calculations for lead optimization

July 9 - Matina, 1pm, IS2 - MOCK exam - An automated workflow for performing free energy perturbation calculations for lead optimization

July 11 - Matina, 10am, IS2 - EXAM - An automated workflow for performing free energy perturbation calculations for lead optimization

​July 20 - Irene, 3pm, IS2, Design and development of anti-Myc inhibitors

August 3 - Petteri Vainikka, 1pm, IS2, Introduction in High throughput Virtual Screening to discover novel drug candidates

August 3 - Pedro Santos, 2pm, IS2, Introduction into Investigating the effect of the oncogenic mutation E545K of the PI3Kα protein with enhanced sampling MD simulations

August 28 - Petteri Vainikka, 10am, IS2, Final Report on High throughput Virtual Screening to discover novel drug candidates

August 28 - Pedro Santos, 11am, IS2, Final Report on Investigating the effect of the oncogenic mutation E545K of the PI3Kα protein with enhanced sampling MD simulations

August 31 - George, An automated workflow for performing free energy perturbation calculations for lead optimization

End of the Academic Year 2017-2018



​Academic Year 2016 - 2017

Seminars take place in the ground floor seminar room, Wednesdays 15:00 - 17:00

September 26: Zoe (SLURM conference - Technopolis Gkazi) Computer-aided drug design for novel anti-cancer agents

October 6 (Thursday, 4pm, IS2) - Youli: "Validating the Free Energy Perturbation and Replica Exchange with Solute Tempering method for lead optimization"

October 7 -9: Joint International Conference of the Hellenic Crystallographic Association & the Hellenic Society for Computational Biology and Bioinformatics 

October 31 - Christina: "Optimization of Arp2/3 complex inhibitors using Free Energy Perturbation (FEP) calculations and organic synthesis & the D3R challenge"

​November 22 - Anaxagoras (seminar room Γ2): "Development of data mining tools for identifying structural determinats that dictate protein-ligand interactions"

December 1 - Sofia & Christina: "The D3R challenge: the case of FXR"

December 15 (11:00 Γ1)- Giannis: "Metal-Organic Frameworks as drug delivery systems: The case of IRMOF-74-III and gemcitabine studied by a multiscale simulations"

December 19 (12.30 Γ1) - Konstantina: "Development of a crystal morphology tool & application to modeling of nanoparticles as drug delivery systems"

December 20 (12:30 IΣ2) - Konstantina: Master's thesis exam.

​Christmas break

Seminars take place in the ground floor seminar room, Wednesdays 15:00 - 17:00

January 11 - Phaedon Brotzakis: Elucidating the mechanism and role of solvent for beta-lactoglobulin dimerization by using transition path sampling

January 25 - Journal Club

February 10 (13:00 ΙΣ2)- Journal Club

February 17 (13:00 ΙΣ2) - Christina - Diploma thesis mock exam: "Υπολογιστικός σχεδιασμός και σύνθεση αναστολέων του πρωτεϊνικού συμπλέγματος Arp2/3"

February 20 (17:30 Γ1) - Christina - Repeat Diploma thesis mock exam: "Υπολογιστικός σχεδιασμός και σύνθεση αναστολέων του πρωτεϊνικού συμπλέγματος Arp2/3"

February 22 - 11:00-2:00 (Teleconference room): Presentation of the final Projects of the MSc course: "Molecular Modeling of Biomolecules"​

February 24 - (14:30 Department of Chemical Engineering, NTUA) - Christina: Thesis Exam

March 8 (15:30 - 17:00) - Dora - Introduction into the theory of Free Energy Perturbation calculations and recent methodological advances. Structure-activity relationships of the CK666 inhibitor of the Arp2/3 complex.

Seminars take place in the ground floor seminar room, Tuesdays 13:30 - 15:30

March 17 - Michalis & Lefteris: "Introduction in Modeling magnetic nanoparticles coated with polyvinyl alcohol and polyarabic acid"

March 24 (13:00 - 15:00) -  Giannis Tyraksis - Optimization of Arp2/3 complex inhibitor CK-869 using Free Energy Perturbation (FEP) calculations.

March 27 - D3R Challenge webinar (7pm-10 pm, teleconference room): Free Energy Perturbation calculations to predict relative binding affinities for FXR ligands

March 29 - April 2: Athens Science Festival

Easter Break

April 21 - Sophia Hirakis, UCSD, USA: Computational microscopy: insights into cardiac function at multiple scales using computational biophysics

May 2 - Panos Kakoulidis, Pasteur Institute: "Development of a pipeline for secondary and tertiary structural analysis of human miRNA targeting"

May 16 - Vasilis Georgilas, Chem Eng Dept, NTUA - "Molecular Simulation of Cavitation in Polymer networks"

May 30 - Christina: "Computer-aided drug design for binding pose and affinity predictions in the D3R Challenge 2"

​June 9 (16:00) - Michalis & Lefteris: "Modeling magnetic nanoparticles coated with polyvinyl alcohol and polyarabic acid"

June 19 (3pm, IΣ2)-  Alexis: "A web based crystallographic tool for the construction of nanoparticles"

July 4 - (3pm, ΙΣ2) Journal Club

July 11 - (3pm, ΙΣ2) Giannis Tyraskis - Optimization of Arp2/3 complex inhibitor CK-869 using Free Energy Perturbation (FEP) calculations

July 21 - (12.30pm, ΙΣ2) Nephele Agrafiotis - How to estimate convergence in Molecular Dynamics trajectories

Summer Break

 

2015 - 2016 Academic Year

Seminars take place in the ground floor seminar room, Mondays 10:15 - 12:00

September 28 - Giannis Μελέτη της μοριακής βάσης του τρόπου δράσης του ανταγωνιστή του ΑΤ1 υποδοχέα, λοζαρτάνη και του μεταβολίτη του ΕΧΡ3174 με τη χρήση προσομοιώσεων Μοριακής Δυναμικής
October 9 - 11 10th Conference of the Hellenic Society for Computational Biology and Bioinformatics (HSCBB15)
October 26 - Dora Optimization of Arp2/3 inhibitors using FEP calculations, synthesis, and in vitro assays
November 23 - Ioanna Effect of trans arachidonic acid on a model liposomal membrane investigated by Molecular Dynamics simulations
November 30 - Hari Interactions of Angiotensin II with water and water/ethanol mixtures studied with MD simulations and Markov state models
December 7 - Evi Self-assembly of anionic nanoparticles in fluid membranes using MD simulations
December 22 Arp2/3 Greece-Turkey closing project meeting
  Christmas Break
January 25 - Konstantina Modeling and simulations of functionalized magnetic nanoparticles as drug delivery systems
February 10, 11:00-2:00 (Teleconference room) Presentation of the final Projects of the MSc course: "Molecular Modeling of Biomolecules"
February 22 - Ioanna Effect of trans arachidonic acid on a model liposomal membrane investigated by Molecular Dynamics simulations
March 1 - Ioanna "Ανάλυση λιποσωμικών μεμβρανών μέσω βιοφυσικών τεχνικών (AFM και DLS) και προσομοιώσεων Μοριακής Δυναμικής". Master's thesis presentation, Αίθουσα 027 Συνεδριάσεων στο ισόγειο του κτήριου φυσικής της Σ.Ε.Μ.Φ.Ε. στο Εθνικό Μετσόβιο Πολυτεχνείο.
March 7 - Giannis "Investigating the effect of RXRa S427F mutant on RAR-RXRa heterodimers and RXRa homotetramers"
March 28 - Christina TBA
April 5 - Marianna Kotzabasaki (Univ of Crete) "Metal-Organic Frameworks as Efficient Materials for Drug Delivery"
  Easter Break
ΤΒΑ - Marilena Discovery of Novel Myc Inhibitors guided by Structure- and Ligand-based Screening

 

 


2014 - 2015 Academic Year

Seminars take place in the ground floor seminar room, Mondays 10:15 - 12:00

 

October 8 (15:00, Teleconference room) - George
 
Mechanistic and inhibition studies of the Arp2/3 complex, a key regulator of the actin cytoskeleton
October 10-12
 
9th Conference of the Hellenic Society for Computational Biology and Bioinformatics
October 24 (16:30) - Eva
 
"Interactions of Strongly and Weakly Bound Water Molecules to Protein Binding Sites and Propensity for Replacements"
November 10 - Spyros
 
"Simulations of Arp2/3 Complex. Part I: CA Activator, Part II: CK666 Inhibitor"
November 13-15 1st International Conference: From Drug Discovery to Drug Delivery
December 1 - George "Investigation of the activation mechanism of the Arp2/3 complex using standard and steered MD simulations."
 
December 8 (15:00 - 17:00)- Hari "Insights into the mechanism of overactivation of E545K PI3Kalpha mutant using un-biased and steered molecular dynamics simulations."
 
December 18 (12:00 - 15:00 - Αιθουσα Γ1)- Marilena
 
Computational Resources for Drug Discovery (review of the EMBL-EBI workshop)

 
 Christmas Break
January 14, 11:00-2:00 (Teleconference room)
 
Presentation of the final Projects of the MSc course: "Molecular Modeling of Biomolecules"
January 23, 13:00 - 15:00 - Αιθουσα Γ1 - Evi
 
"Investigation of the molecular basis of action of the AT1 antagonist losartan and its metabolite EXP3174 using a coarse-grained and all-atom molecular dynamics simulations"
February 9 - Marilena
 
Design and development of anti-Myc inhibitors
March 2 Discussion of working paper
 
March 17-18 Arp2/3 Greece-Turkey meeting
 
  See the schedule of the meeting here
 

 
Easter Break

 


2013 - 2014 Academic Year

Seminars take place in the THIRD floor seminar room, Fridays 10:15 - 12:00

October 10
 
Visit in Scienomics http://scienomics.com/ (NCSR Demokritos)
October 24
 
George: "The Molecular Basis of Action of the AT1 Antagonist Losartan"
November 12 (12-2pm)
 
Ross Walker: "Lights, Computer, Action: Accelerated Molecular Dynamics, from Enzyme Activation to Membrane Dynamics"
November 21 - Evi
 
"Free Energy Calculations of Aminoadamantane Blockers of Influenza A/M2TM Pore"
November 29
(1 - 3pm)

 
Hari: "The effect of oncogenic mutation E545K on the conformation of PI3Ka"
December 12 - George
 
"Progress toward inhibition and mechanistic studies of the Arp2/3 complex"
  Christmas break
January 23 Lecture in NTUA by Dr. Spyros Vicatos - "Coarse - Grained Models for biological simulations, formulation and applications"
February 14 (Friday, 13:00-15:00 exceptionally) - Spyros Vicatos
 
 Simplified Models for the studies of proteins, applications and recent advances."
March 7th - Evi & Zoe
 
Discussion of working paper (Nanoparticle:membrane interactions)
March 14 - Arp2/3 Meeting
 
Talks by George Patargias, Zoe Cournia, Yavuz Ergun
March 28 - Evi & Zoe
 
Discussion of working paper (H1047R PI3Ka mechanism of over-activation)
April 14 - Marilena - (12pm - 2pm - IS2)
 
The Myc oncoprotein as a cancer drug target: Literature review and proposed studies for drug design

 

Easter Break
May 9 - Harri
 
ΠΕΙΡΑΜΑΤΙΚΗ ΚΑΙ ΥΠΟΛΟΓΙΣΤΙΚΗ ΜΕΛΕΤΗ ΤΗΣ ΑΛΛΗΛΕΠΙΔΡΑΣΗΣ ΑΜΙΝΟΑΔΑΜΑΝΤΑΝΙΚΩΝ ΠΡΟΣΔΕΤΩΝ ΜΕ ΤΟΝ ΔΙΑΜΕΜΒΡΑΝΙΚΟ ΠΟΡΟ ΤΟΥ ΙΟΝΤΙΚΟΥ ΔΙΑΥΛΟΥ ΤΗΣ ΠΡΩΤΕΪΝΗΣ ΤΟΥ IOY ΤΗΣ INFLUENZA A/M2
 
May 12 - 11:30 - Harris
 
Master's defense - School of Pharmacy, Room ΑΦΧ
May 16 - Evi Research Seminar: Molecular dynamics simulations of the wild-type and H1047R mutant PI3K?: Insights to the design of mutant specific inhibitors.
 
May 23 - Hari
 
Study of the E545K PI3Ka mutation
May 27 (15:30 - 17:00 Library) - Zoe & Evi
 
Discussion of working paper
June 5 (16:30 - 18:00 Γ1 seminar room)- George
 
Research Seminar: MD simulations of the Arp2/3 complex with bound VCA and actin
June 16
 
Discussion of Chapter 11 (free energy methods)
June 23 - (16:00-17:00, Library)
 
Discussion of working paper
July 7 - (13:30 - 15:00, teleconference room) Eva
 
Master thesis presentation "DISCOVERY OF POTENT NURR1 ACTIVATORS USING COMPUTER-AIDED DRUG DESIGN FOR THE TREATMENT OF PARKINSON'S DISEASE"
July 11 Eva's Master thesis presentation (Department of Chemical Engineering, U Patras)
 
July 18 - Hari Study of the E545K PI3Ka mutation Part II
 

 
Summer Break

 

 


2012 - 2013 Academic Year

Sept. 25 TUESDAY at 11am exceptionally - Thomas:
 
"Elucidating the oncogenic mechanism of the H1047R PI3Kalpha mutant kinase through molecular dynamics simulations"
Oct. 8 – Eva: “NURR1 as a target to treat Parkinson's disease: Literature Review and Proposed Studies”
 
Oct. 22 – George at 10:15 exceptionally: “Inhibition and mechanistic studies of the Arp2/3 complex through docking and MD simulations.”
 
Nov. 6 Cancelled
 
Nov. 20 (TUESDAY) – Evi:
 
"The effect of cholesterol in membrane phase transitions and NP translocation"
Dec. 4 (TUESDAY) – Harris "Interaction of aminoadamantine derivatives with the influenza A virus M2 channel through docking and FEP calculations"
 
Dec. 17 Ming Han

Seminars take place in the ground floor seminar room, Mondays 10:15 - 12:00

Jan. 28 George: Journal Club
 
Feb. 18 Eva: Journal Club
 
Mar. 4 Evi: Journal Club
 
Mar. 18 Harris: Journal Club
 
Apr. 1 Ming: Journal Club
 
Apr. 15 George: TBA
 
 
 
Easter Break
May 13 Evi: TBA
 
May 27 Harris: Master's thesis presentation
 
June 10 Eva: Master's thesis presentation
 
June 24 Ming: TBA
 
 
 
Summer Break

2011 - 2012 Academic Year

Nov 7-11 EIE Workshop
 
Nov 28: George Molecular modeling studies of viral ion channels
 
December 12: Evi “Interaction of aminoadamantine derivatives with the influenza A virus M2 channel through docking and FEP calculations.
 
  Christmas Break
 
Jan. 16:  Thomas: “The c-Myc oncoprotein as a cancer drug target: molecular modeling and inhibition studies.”
 
Jan. 30: George Journal Club
 
Feb. 13: Evi Journal Club
 
March 5: Thomas Journal Club
 
March 16
(11:15am): Evi

 
“Virtual Screening and in vitro studies targeting the mutant PI3Ka protein."
April 10 No group meeting
 
April 23: Harris "Synthesis of heterocyclic compounds containing thiazole and thiazolidine ring."
 
May 7: George “Inhibition studies of the Arp2/3 complex.”
 
May 18: George “Inhibition studies of the Arp2/3 complex.” (Friday)
 
May 21: Thomas “MD simulations of the WT and mutant PI3Ka protein: Insights into the mechanism of oncogenesis.”
 
June 1: Evi Journal Club (Friday)
 
June 18: Thomas Journal Club
 
July 2: George Journal Club
 
July 16: Eva: "Molecular Dynamics Simulations of Palmitic Acid"
 
  Summer Break

 


2010 - 2011 Academic Year

Dec. 2 - Zoe: "Molecular Modeling and Drug Design: An Overview"
 
Dec. 9 - Evi: "Insights into the mechanism of oncogenesis of the mutated PI3Kα: Literature Review and Proposed Studies"
 
Dec. 16 - Thomas: "Molecular Mechanics of ATP-binding cassette efflux transporters"
 
Dec. 20 - Dimitra: "Microscopic, dynamical and transport properties of cytochrome c oxidase studied with MD simulations: Literature Review and Proposed Studies"
 
  Christmas break
 
Jan. 13, 15:00 talk in “Optimization Techniques for Protein Docking”, Speaker: Yannis Paschalidis, EKPA - Pliroforiki
 
Jan. 14 - Zoe: "Force Field parameterization and Molecular Dynamics Simulations principles"
 
Jan. 20 – lab workshop: “Molecular Dynamics simulations and Normal Mode Analysis of BPTI in vacuum with CHARMM”. This workshop will last a full day and will introduce MD/NMA techniques, script editor “vi”, and the plotting program “xmgrace”.
 
Jan. 23 talk in “Electron Microscopy basics by Prof. Catherine Venien-Bryan (CNRS-University of Paris) at EIE, 14:00
 
Jan. 26 (9:20 - 14:45) Translational Workshop at IIBEAA.
 
Jan. 27 NO Group Seminar - please try to attend the two structural talks and the translational workshop this week.
 
Jan. 28 talk in “Single particle microscopy and electron crystallography” by Prof. Catherine Venien-Bryan (CNRS-University of Paris) at EIE, 12:00
 
Feb. 3 Evi: "Molecular Dynamics simulations of peptide-membrane interactions: Insights into membrane translocation mechanisms of cell-penetrating peptides.
 
Feb. 10 – Feb. 24 No seminar
 
Mar. 3 - Thomas: "Repositioning HIV protease inhibitors to target human kinome: a chemical systems biology approach"
 
Mar. 10 No seminar
 
Mar. 17 - Zoe: "Optimization of a NURR1/RXRalpha agonist as a means to treat Parkinson’s Disease"
 
Mar. 24 - Evi: "Interaction of aminoadamantine derivatives with the influenza A virus M2 channel through docking and FEP calculations"
 
Mar. 31 No seminar
 
Apr. 7 – Giannis: “Energetic and toxicophore filtering of docking poses to improve lead identification”
 
Apr. 14 - Thomas: "TBA: literature review an proposed studies"