In territori ampi come la Sardegna in cui il raggiungimento delle strutture ospedaliere specializzate può richiedere tempi di viaggio incompatibili per la sopravvivenza del paziente diventa fondamentale ampliare il campo di applicazione delle tecnologie informatiche al campo medico. Per soddisfare questa esigenza clinica è nato il progetto REMOTE finanziato dall'Assessorato alla Programmazione della RAS che ha visto coinvolti la Struttura Semplice Dipartimentale di Cardiologia Pediatrica dell'Ospedale Brotzu diretta dal Dottor Tumbarello ed il programma Healthcare Flows del CRS4. REMOTE è finalizzato a permettere allo specialista di effettuare diagnosi a distanza ed in real-time guidando ove necessario l'esecuzione dell'esame effettuato da un operatore specializzato. Durante il seminario verrà illustrato il sistema integrato e le tecnologie utilizzate per la realizzazione dell'infrastruttura basata sul riutilizzo e l'integrazione di tecnologie esistenti ed a basso costo, preferibilmente Open Source.
Si trattano maggiormente gli aspetti implementativi, attraverso l'illustrazione delle scelte progettuali adottate sul campo per far fronte alle sfide del settore, fornendo esempi concreti di implementazione.
The document provides an overview of the Visual Computing group at CRS4. It summarizes that the group conducts research in visual computing, with a focus on acquiring, processing, distributing, rendering and exploring massive 3D models. Some of the key areas of research mentioned include effective acquisition of color and geometry from 3D scans, scalable surface processing techniques, and novel methods for rendering and streaming massive models.
In territori ampi come la Sardegna in cui il raggiungimento delle strutture ospedaliere specializzate può richiedere tempi di viaggio incompatibili per la sopravvivenza del paziente diventa fondamentale ampliare il campo di applicazione delle tecnologie informatiche al campo medico. Per soddisfare questa esigenza clinica è nato il progetto REMOTE finanziato dall'Assessorato alla Programmazione della RAS che ha visto coinvolti la Struttura Semplice Dipartimentale di Cardiologia Pediatrica dell'Ospedale Brotzu diretta dal Dottor Tumbarello ed il programma Healthcare Flows del CRS4. REMOTE è finalizzato a permettere allo specialista di effettuare diagnosi a distanza ed in real-time guidando ove necessario l'esecuzione dell'esame effettuato da un operatore specializzato. Durante il seminario verrà illustrato il sistema integrato e le tecnologie utilizzate per la realizzazione dell'infrastruttura basata sul riutilizzo e l'integrazione di tecnologie esistenti ed a basso costo, preferibilmente Open Source.
Si trattano maggiormente gli aspetti implementativi, attraverso l'illustrazione delle scelte progettuali adottate sul campo per far fronte alle sfide del settore, fornendo esempi concreti di implementazione.
The document provides an overview of the Visual Computing group at CRS4. It summarizes that the group conducts research in visual computing, with a focus on acquiring, processing, distributing, rendering and exploring massive 3D models. Some of the key areas of research mentioned include effective acquisition of color and geometry from 3D scans, scalable surface processing techniques, and novel methods for rendering and streaming massive models.
Cadd and molecular modeling for M.PharmShikha Popali
THE CADD IS FOR THE DRUG DEVELOPMENT THE DIFFERENT STRATEGIES ARE MENTIONED LIKE QSAR MOLECULAR DOCKING, THE DIFFERENT DIMNSIONAL FORMS OF QSAR , THE ADVANCE SAR of it.
The document discusses structure-based drug design (SBDD). It first provides background on drug design and SBDD. It then describes some key aspects of SBDD, including using the 3D structure of the biological target obtained from techniques like X-ray crystallography and NMR spectroscopy. It also discusses ligand-based and receptor-based drug design approaches. The document then outlines the typical steps involved in SBDD, including target selection, ligand selection, target preparation, docking, evaluating results, and discusses some molecular docking techniques and scoring functions used to predict binding.
This document provides an introduction to the process of drug design given by Subhasis Banerjee. It discusses key areas of drug design including target identification and validation, lead finding and optimization, and ligand-based and structure-based drug design. It also describes the application of cheminformatics in drug design for data mining large databases of small molecules and proteins. The goal of drug design is to progress from initial hits identified through screening to optimized lead compounds through iterative chemical modifications and testing.
The document discusses structure-based drug design and molecular docking. It begins with introductions to drug design, drug targets, and structure-based drug design. It then describes molecular docking as a technique to predict how small molecules bind to protein targets by calculating binding affinities. The document outlines the docking process, including generating a protein's molecular surface, matching ligand and protein atoms to determine potential orientations, and scoring docked poses to identify favorable interactions. It also discusses using docking for virtual screening to identify potential drug leads from compound libraries.
This document discusses various topics related to drug discovery through bioinformatics. It begins by describing how genome-wide RNAi screening in the nematode C. elegans can be used to identify genes involved in biological pathways related to diseases like type-2 diabetes. It then discusses topics like structural genomics, target identification and validation, high-throughput screening approaches and facilities, sources for screening libraries, criteria for hit and lead compounds, and computational methods used in hit identification and optimization like pharmacophore modeling and evaluating compounds against the "rule of five". Descriptors that can be used for characterizing compounds are also listed.
This document discusses cheminformatics and its applications. Cheminformatics combines chemistry and computer science to store and analyze chemical data for applications like drug discovery. It encompasses designing, organizing, analyzing and visualizing chemical information. Key topics covered include molecular representations, chemical databases, similarity searching, machine learning methods, and tools for molecular docking and drug discovery.
In spite of extensive effort by industry and academia to develop new drugs, there are still several diseases that are in need of therapeutic agents and have yet to be developed.
10 years the identification rate of disease-associated targets has been higher than the therapeutics identification rate.
Nevertheless, it is apparent that computational tools provide high hopes that many of the diseases under investigation can be brought under control.
Drug Discovery Today: Fighting TB with Technologyrendevilla
This document discusses desktop drug discovery and development using computational methods. It covers rational drug design approaches like computer-aided drug design (CADD), targeting identification and validation, lead discovery and optimization, and preclinical testing using molecular modeling and simulation. Specific examples are provided of structure-based drug design against targets for tuberculosis and the preclinical evaluation of candidate compounds.
Molecular recognition is the specific interaction between two or more complementary molecules through noncovalent bonding such as hydrogen bonding, metal coordination, hydrophobic forces, etc. This process is crucial in biological systems and modern chemical research. Molecular recognition can be static, involving a 1:1 complex between a host and guest molecule, or dynamic, where binding of the first guest induces a conformational change affecting binding of a second guest. Molecular recognition is important in fields like supramolecular chemistry, self-assembly, and host-guest chemistry. It has applications in areas like sensing, molecular motors, and enzyme mimicry.
Bioinformatics role in Pharmaceutical industriesMuzna Kashaf
Bioinformatics plays a key role in the pharmaceutical industry by enabling target identification of diseases, rational drug design, compound refinement, and other processes. It facilitates identifying target diseases and compounds, detecting molecular bases of diseases, designing drugs, refining compounds, and testing drug solubility and effects. Bioinformatics supports various stages of drug development including formulation, crystallization determination, polymer modeling, and testing before human use. Its integration into the pharmaceutical industry supports drug discovery, healthcare advances, and realizing the promises of projects like the Human Genome Project.
The document discusses various topics related to computer-aided drug design (CADD), including:
1) The definitions of drug-likeness, druggability, and the Rule of Five for screening drug-like molecules. The Rule of Five outlines molecular properties important for a drug's absorption and metabolism.
2) Pharmacophore-based and ligand-based virtual screening methods which use the structure of known active ligands to search compound libraries for similar molecules.
3) The role of virtual screening in CADD to select compounds for biological testing from large databases using techniques like structure-based docking and ligand-based similarity searching. Scoring functions are also used to rank compounds.
This document discusses molecular docking and different models used to describe molecular recognition between biomolecules. It begins by defining molecular recognition and docking, and describes early models like the lock-and-key and induced-fit models. It then discusses computational docking methods, including representing molecules, scoring docked poses, and search algorithms to generate poses. Flexibility is an important consideration, and methods to incorporate flexibility of both small molecule ligands and protein receptors are described.
An Introduction to Chemoinformatics for the postgraduate students of AgricultureDevakumar Jain
1. Chemoinformatics is the application of informatics methods to solve chemical problems and encompasses the design, creation, organization, management, retrieval, analysis, dissemination, visualization and use of chemical information.
2. It combines aspects of chemistry and computer science to address challenges such as representing and searching large chemical structure databases, predicting molecular properties, and aiding in drug discovery.
3. Chemoinformatics tools and methods have applications in diverse areas including organic synthesis, analytical chemistry, toxicology prediction, and agrochemical discovery.
This document provides an overview of computer aided drug design (CADD). It discusses how CADD uses computational methods like molecular docking, virtual screening, and quantitative structure-activity relationships (QSAR) to aid in the drug design process. Molecular docking uses software to predict how drug molecules bind to biological targets. QSAR analyzes relationships between chemical structure and biological activity. CADD aims to identify and optimize lead drug compounds in silico to reduce costs and save on experimental trials in drug development.
Bioinformatics is an interdisciplinary field that combines biology, computer science, and information technology. It enables the discovery of new biological insights and unifying principles in biology through the merging of these disciplines. There are three main sub-disciplines: developing algorithms and statistics for analyzing large datasets, analyzing various types of biological data like sequences and structures, and developing tools for accessing and managing information.
PRESENTED BY: HARSHPAL SINGH WAHI, SHIKHA D. POPALI
USEFUL FOR PHARMACY STUDENTS AND ACADEMICS, INDUSTRIALS FOR MOLECULE DEVELOPMENT, MODELING, DRUG DISCOVERY, COMPUTATIONAL TOOLS, MOLECULAR DOCKING ITS TYPES, FACTORS AFFECTING, DIFFERENT STAGES, QSAR ADVANTAGES, NEED
1) Nanomedicine uses nanotechnology to prevent and treat disease by imparting properties like antibacterial and anti-odor functionality to skin products using nanomaterials.
2) Molecular biomimetics marries materials science and molecular biology to develop functional hybrid systems composed of inorganic and protein materials. It uses protein templates designed through genetics, surface proteins to bind synthetic entities, and the ability of proteins to self-assemble into complex structures.
3) Combinatorial biology techniques like phage display and cell-surface display are used to select protein sequences that strongly bind to inorganic surfaces from large random peptide libraries. This allows obtaining inorganic-binding proteins without an a priori knowledge of their sequence.
The document appears to be a list of numbers paired with "30° CRS4" repeated many times. It includes the phrases "Enjoy the reading!" and names Christian Solinas as the President of the Autonomous Region of Sardinia.
More Related Content
Similar to La chemoinformatica: uno strumento computazionale per la chimica farmaceutica
Cadd and molecular modeling for M.PharmShikha Popali
THE CADD IS FOR THE DRUG DEVELOPMENT THE DIFFERENT STRATEGIES ARE MENTIONED LIKE QSAR MOLECULAR DOCKING, THE DIFFERENT DIMNSIONAL FORMS OF QSAR , THE ADVANCE SAR of it.
The document discusses structure-based drug design (SBDD). It first provides background on drug design and SBDD. It then describes some key aspects of SBDD, including using the 3D structure of the biological target obtained from techniques like X-ray crystallography and NMR spectroscopy. It also discusses ligand-based and receptor-based drug design approaches. The document then outlines the typical steps involved in SBDD, including target selection, ligand selection, target preparation, docking, evaluating results, and discusses some molecular docking techniques and scoring functions used to predict binding.
This document provides an introduction to the process of drug design given by Subhasis Banerjee. It discusses key areas of drug design including target identification and validation, lead finding and optimization, and ligand-based and structure-based drug design. It also describes the application of cheminformatics in drug design for data mining large databases of small molecules and proteins. The goal of drug design is to progress from initial hits identified through screening to optimized lead compounds through iterative chemical modifications and testing.
The document discusses structure-based drug design and molecular docking. It begins with introductions to drug design, drug targets, and structure-based drug design. It then describes molecular docking as a technique to predict how small molecules bind to protein targets by calculating binding affinities. The document outlines the docking process, including generating a protein's molecular surface, matching ligand and protein atoms to determine potential orientations, and scoring docked poses to identify favorable interactions. It also discusses using docking for virtual screening to identify potential drug leads from compound libraries.
This document discusses various topics related to drug discovery through bioinformatics. It begins by describing how genome-wide RNAi screening in the nematode C. elegans can be used to identify genes involved in biological pathways related to diseases like type-2 diabetes. It then discusses topics like structural genomics, target identification and validation, high-throughput screening approaches and facilities, sources for screening libraries, criteria for hit and lead compounds, and computational methods used in hit identification and optimization like pharmacophore modeling and evaluating compounds against the "rule of five". Descriptors that can be used for characterizing compounds are also listed.
This document discusses cheminformatics and its applications. Cheminformatics combines chemistry and computer science to store and analyze chemical data for applications like drug discovery. It encompasses designing, organizing, analyzing and visualizing chemical information. Key topics covered include molecular representations, chemical databases, similarity searching, machine learning methods, and tools for molecular docking and drug discovery.
In spite of extensive effort by industry and academia to develop new drugs, there are still several diseases that are in need of therapeutic agents and have yet to be developed.
10 years the identification rate of disease-associated targets has been higher than the therapeutics identification rate.
Nevertheless, it is apparent that computational tools provide high hopes that many of the diseases under investigation can be brought under control.
Drug Discovery Today: Fighting TB with Technologyrendevilla
This document discusses desktop drug discovery and development using computational methods. It covers rational drug design approaches like computer-aided drug design (CADD), targeting identification and validation, lead discovery and optimization, and preclinical testing using molecular modeling and simulation. Specific examples are provided of structure-based drug design against targets for tuberculosis and the preclinical evaluation of candidate compounds.
Molecular recognition is the specific interaction between two or more complementary molecules through noncovalent bonding such as hydrogen bonding, metal coordination, hydrophobic forces, etc. This process is crucial in biological systems and modern chemical research. Molecular recognition can be static, involving a 1:1 complex between a host and guest molecule, or dynamic, where binding of the first guest induces a conformational change affecting binding of a second guest. Molecular recognition is important in fields like supramolecular chemistry, self-assembly, and host-guest chemistry. It has applications in areas like sensing, molecular motors, and enzyme mimicry.
Bioinformatics role in Pharmaceutical industriesMuzna Kashaf
Bioinformatics plays a key role in the pharmaceutical industry by enabling target identification of diseases, rational drug design, compound refinement, and other processes. It facilitates identifying target diseases and compounds, detecting molecular bases of diseases, designing drugs, refining compounds, and testing drug solubility and effects. Bioinformatics supports various stages of drug development including formulation, crystallization determination, polymer modeling, and testing before human use. Its integration into the pharmaceutical industry supports drug discovery, healthcare advances, and realizing the promises of projects like the Human Genome Project.
The document discusses various topics related to computer-aided drug design (CADD), including:
1) The definitions of drug-likeness, druggability, and the Rule of Five for screening drug-like molecules. The Rule of Five outlines molecular properties important for a drug's absorption and metabolism.
2) Pharmacophore-based and ligand-based virtual screening methods which use the structure of known active ligands to search compound libraries for similar molecules.
3) The role of virtual screening in CADD to select compounds for biological testing from large databases using techniques like structure-based docking and ligand-based similarity searching. Scoring functions are also used to rank compounds.
This document discusses molecular docking and different models used to describe molecular recognition between biomolecules. It begins by defining molecular recognition and docking, and describes early models like the lock-and-key and induced-fit models. It then discusses computational docking methods, including representing molecules, scoring docked poses, and search algorithms to generate poses. Flexibility is an important consideration, and methods to incorporate flexibility of both small molecule ligands and protein receptors are described.
An Introduction to Chemoinformatics for the postgraduate students of AgricultureDevakumar Jain
1. Chemoinformatics is the application of informatics methods to solve chemical problems and encompasses the design, creation, organization, management, retrieval, analysis, dissemination, visualization and use of chemical information.
2. It combines aspects of chemistry and computer science to address challenges such as representing and searching large chemical structure databases, predicting molecular properties, and aiding in drug discovery.
3. Chemoinformatics tools and methods have applications in diverse areas including organic synthesis, analytical chemistry, toxicology prediction, and agrochemical discovery.
This document provides an overview of computer aided drug design (CADD). It discusses how CADD uses computational methods like molecular docking, virtual screening, and quantitative structure-activity relationships (QSAR) to aid in the drug design process. Molecular docking uses software to predict how drug molecules bind to biological targets. QSAR analyzes relationships between chemical structure and biological activity. CADD aims to identify and optimize lead drug compounds in silico to reduce costs and save on experimental trials in drug development.
Bioinformatics is an interdisciplinary field that combines biology, computer science, and information technology. It enables the discovery of new biological insights and unifying principles in biology through the merging of these disciplines. There are three main sub-disciplines: developing algorithms and statistics for analyzing large datasets, analyzing various types of biological data like sequences and structures, and developing tools for accessing and managing information.
PRESENTED BY: HARSHPAL SINGH WAHI, SHIKHA D. POPALI
USEFUL FOR PHARMACY STUDENTS AND ACADEMICS, INDUSTRIALS FOR MOLECULE DEVELOPMENT, MODELING, DRUG DISCOVERY, COMPUTATIONAL TOOLS, MOLECULAR DOCKING ITS TYPES, FACTORS AFFECTING, DIFFERENT STAGES, QSAR ADVANTAGES, NEED
1) Nanomedicine uses nanotechnology to prevent and treat disease by imparting properties like antibacterial and anti-odor functionality to skin products using nanomaterials.
2) Molecular biomimetics marries materials science and molecular biology to develop functional hybrid systems composed of inorganic and protein materials. It uses protein templates designed through genetics, surface proteins to bind synthetic entities, and the ability of proteins to self-assemble into complex structures.
3) Combinatorial biology techniques like phage display and cell-surface display are used to select protein sequences that strongly bind to inorganic surfaces from large random peptide libraries. This allows obtaining inorganic-binding proteins without an a priori knowledge of their sequence.
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The document appears to be a list of numbers paired with "30° CRS4" repeated many times. It includes the phrases "Enjoy the reading!" and names Christian Solinas as the President of the Autonomous Region of Sardinia.
Tutti a Iscol@ 2017, presentazione della Linea B2: Laboratori Extracurriculari Didattici Tecnologici.
L'iniziativa è promossa da: Regione Autonoma della Sardegna (Assessorato della Pubblica Istruzione);
Agenzia Regionale Sardegna Ricerche;
CRS4.
Ulteriori informazioni: http://iscola-lineab2.crs4.it/
Sardegna Ricerche
CRS4
Presentazione del progetto "Iscol@ Linea B": laboratori didattici innovativi finalizzati all’apertura al territorio delle Istituzioni scolastiche. Regione Autonoma della Sardegna, Agenzia Sardegna Ricerche, CRS4
I progressi tecnologici raggiunti nel campo delle strategie di sequenziamento degli acidi nucleici ("Next Generation Sequencing", NGS) permettono oramai di ottenere con facilità le informazioni contenute all’interno dell’intero genoma umano. Ma solo una piccola percentuale (stimata a 1,6%) del genoma umano viene tradotto nelle proteine che fanno funzionare il corpo umano. Il sequenziamento esomico ("Whole exome sequencing") si concentra proprio sulle parti del genoma che codificano le proteine ("i geni") perché la ricerca di varianti in tali regioni permette di trovare le modificazioni funzionali delle proteine che sono associate a malattie. Dovendo sequenziare solo circa 1/60 dell’intero genoma si ha la possibilità di avere una migliore accuratezza e di ridurre tempi e costi del sequenziamento. Per questo motivo il sequenziamento esomico è diventato uno dei metodi di diagnosi genetica più utilizzato dai medici (sopratutto nel caso in cui non ci siano ipotesi sui geni coinvolti nella malattia).
1) The document presents a method for spatial velocity analysis of near-surface seismic data using a global simultaneous multi-parameter optimization approach.
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3) The method is demonstrated on an example of ultra-shallow seismic data from a field survey, and velocity models derived from the analysis are used for stacking, tomography, and migration, improving the quality and interpretability of
Valentina Spanu: esempi di applicazioni di GIS Partecipativo; gestione delle riserve idriche, energia solare, ristrutturazione di un edificio scolastico in Marocco; riduzione del rischio di disastro naturale in Georgia.
Alfonso Damiano (Università di Cagliari) Tecnologie ICT per le reti intelligenti di energia - evoluzione dei sistemi di distribuzione elettrica, anche con riferimento alla situazione della Regione; smart grid, micro grid e virtual power plant; stato della ricerca nel settore; potenzialità offerte dall'integrazione tra sistema elettrico e sistema della mobilità; reti intelligenti in una visione di smart city.
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This document summarizes trends in mobile graphics presented by Marco Agus and Marcos Balsa at the Visual Computing conference at UniCa in June 2015. It discusses how mobile devices are using techniques like remote rendering, mixed mobile/remote rendering, image-based and model-based methods to render 3D graphics. It also explores hardware acceleration methods for mobile like parallel pipelines, real-time ray tracing, and multi-rate approaches to improve frame rates and rendering quality on mobile. The document focuses on visualization techniques for large meshes, complex lighting, and volume rendering on mobile devices.
This document provides an overview of mobile graphics and development. It discusses the evolution of mobile devices and graphics through movies and games. It outlines the increasing capabilities of mobile devices including processing power, memory, and connectivity. It covers operating systems, programming languages, CPU architectures including ARM and graphics processing unit architectures used in mobile devices. It provides details on graphics development for mobile systems.
This document summarizes a survey of compressed GPU-based direct volume rendering techniques. It begins with an introduction to volume visualization and direct volume rendering. It then discusses the challenges posed by increasingly large volumetric datasets. Various compact data representation models are covered, including pre-defined bases like wavelets and learned bases like dictionaries. Wavelets and dictionaries are explained in more detail. The survey aims to achieve high compression ratios while still enabling real-time reconstruction and rendering.
How information systems are built or acquired puts information, which is what they should be about, in a secondary place. Our language adapted accordingly, and we no longer talk about information systems but applications. Applications evolved in a way to break data into diverse fragments, tightly coupled with applications and expensive to integrate. The result is technical debt, which is re-paid by taking even bigger "loans", resulting in an ever-increasing technical debt. Software engineering and procurement practices work in sync with market forces to maintain this trend. This talk demonstrates how natural this situation is. The question is: can something be done to reverse the trend?
inQuba Webinar Mastering Customer Journey Management with Dr Graham HillLizaNolte
HERE IS YOUR WEBINAR CONTENT! 'Mastering Customer Journey Management with Dr. Graham Hill'. We hope you find the webinar recording both insightful and enjoyable.
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Key Takeaways:
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"$10 thousand per minute of downtime: architecture, queues, streaming and fin...Fwdays
Direct losses from downtime in 1 minute = $5-$10 thousand dollars. Reputation is priceless.
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We will focus special attention on the architectural patterns used in the design of the fintech system, microservices and event-driven architecture, which ensure scalability, fault tolerance, and consistency of the entire system.
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Northern Engraving | Nameplate Manufacturing Process - 2024Northern Engraving
Manufacturing custom quality metal nameplates and badges involves several standard operations. Processes include sheet prep, lithography, screening, coating, punch press and inspection. All decoration is completed in the flat sheet with adhesive and tooling operations following. The possibilities for creating unique durable nameplates are endless. How will you create your brand identity? We can help!
The Department of Veteran Affairs (VA) invited Taylor Paschal, Knowledge & Information Management Consultant at Enterprise Knowledge, to speak at a Knowledge Management Lunch and Learn hosted on June 12, 2024. All Office of Administration staff were invited to attend and received professional development credit for participating in the voluntary event.
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- Understand the value of KM and the benefits of engaging
- Define and reflect on your “what’s in it for me?”
- Share actionable ways you can participate in Knowledge - - Capture & Transfer
How to Interpret Trends in the Kalyan Rajdhani Mix Chart.pdfChart Kalyan
A Mix Chart displays historical data of numbers in a graphical or tabular form. The Kalyan Rajdhani Mix Chart specifically shows the results of a sequence of numbers over different periods.
5th LF Energy Power Grid Model Meet-up SlidesDanBrown980551
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Power Grid Model
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Power Grid Model is an open source project from Linux Foundation Energy and provides a calculation engine that is increasingly essential for DSOs. It offers a standards-based foundation enabling real-time power systems analysis, simulations of electrical power grids, and sophisticated what-if analysis. In addition, it enables in-depth studies and analysis of the electrical power grid’s behavior and performance. This comprehensive model incorporates essential factors such as power generation capacity, electrical losses, voltage levels, power flows, and system stability.
Power Grid Model is currently being applied in a wide variety of use cases, including grid planning, expansion, reliability, and congestion studies. It can also help in analyzing the impact of renewable energy integration, assessing the effects of disturbances or faults, and developing strategies for grid control and optimization.
What to expect
For the upcoming meetup we are organizing, we have an exciting lineup of activities planned:
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-An update on the latest advancements in Power Grid -Model technology during the first and second quarters of 2024.
-An interactive brainstorming session to discuss and propose new feature requests.
-An opportunity to connect with fellow Power Grid Model enthusiasts and users.
Must Know Postgres Extension for DBA and Developer during MigrationMydbops
Mydbops Opensource Database Meetup 16
Topic: Must-Know PostgreSQL Extensions for Developers and DBAs During Migration
Speaker: Deepak Mahto, Founder of DataCloudGaze Consulting
Date & Time: 8th June | 10 AM - 1 PM IST
Venue: Bangalore International Centre, Bangalore
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Your One-Stop Shop for Python Success: Top 10 US Python Development Providersakankshawande
Simplify your search for a reliable Python development partner! This list presents the top 10 trusted US providers offering comprehensive Python development services, ensuring your project's success from conception to completion.
The Microsoft 365 Migration Tutorial For Beginner.pptxoperationspcvita
This presentation will help you understand the power of Microsoft 365. However, we have mentioned every productivity app included in Office 365. Additionally, we have suggested the migration situation related to Office 365 and how we can help you.
You can also read: https://www.systoolsgroup.com/updates/office-365-tenant-to-tenant-migration-step-by-step-complete-guide/
zkStudyClub - LatticeFold: A Lattice-based Folding Scheme and its Application...Alex Pruden
Folding is a recent technique for building efficient recursive SNARKs. Several elegant folding protocols have been proposed, such as Nova, Supernova, Hypernova, Protostar, and others. However, all of them rely on an additively homomorphic commitment scheme based on discrete log, and are therefore not post-quantum secure. In this work we present LatticeFold, the first lattice-based folding protocol based on the Module SIS problem. This folding protocol naturally leads to an efficient recursive lattice-based SNARK and an efficient PCD scheme. LatticeFold supports folding low-degree relations, such as R1CS, as well as high-degree relations, such as CCS. The key challenge is to construct a secure folding protocol that works with the Ajtai commitment scheme. The difficulty, is ensuring that extracted witnesses are low norm through many rounds of folding. We present a novel technique using the sumcheck protocol to ensure that extracted witnesses are always low norm no matter how many rounds of folding are used. Our evaluation of the final proof system suggests that it is as performant as Hypernova, while providing post-quantum security.
Paper Link: https://eprint.iacr.org/2024/257
[OReilly Superstream] Occupy the Space: A grassroots guide to engineering (an...Jason Yip
The typical problem in product engineering is not bad strategy, so much as “no strategy”. This leads to confusion, lack of motivation, and incoherent action. The next time you look for a strategy and find an empty space, instead of waiting for it to be filled, I will show you how to fill it in yourself. If you’re wrong, it forces a correction. If you’re right, it helps create focus. I’ll share how I’ve approached this in the past, both what works and lessons for what didn’t work so well.
Discover top-tier mobile app development services, offering innovative solutions for iOS and Android. Enhance your business with custom, user-friendly mobile applications.
Northern Engraving | Modern Metal Trim, Nameplates and Appliance PanelsNorthern Engraving
What began over 115 years ago as a supplier of precision gauges to the automotive industry has evolved into being an industry leader in the manufacture of product branding, automotive cockpit trim and decorative appliance trim. Value-added services include in-house Design, Engineering, Program Management, Test Lab and Tool Shops.
What is an RPA CoE? Session 1 – CoE VisionDianaGray10
In the first session, we will review the organization's vision and how this has an impact on the COE Structure.
Topics covered:
• The role of a steering committee
• How do the organization’s priorities determine CoE Structure?
Speaker:
Chris Bolin, Senior Intelligent Automation Architect Anika Systems
2. Mi presento
Matteo Floris
Laurea in C.T.F., Univ di Padova
Master in Bioinformatica, Koeln Univ.
Dottorato in Biochimica, Univ. Roma “La Sapienza”
Chemoinformatica: sviluppo di metodi per ligand based
drug design
Bioinformatica presso il CRS4 per 6 anni (genomica
computazionale)
matteo.floris@gmail.com
5. Premessa
Drug design
Rational drug design o rational design
Ricerca di nuovi (potenziali!) farmaci sulla base della
conoscenza di un target biologico
6. Premessa
Drug design
Rational drug design o rational design
Ricerca di nuovi (potenziali!) farmaci sulla base della
conoscenza di un target biologico
Drug design spesso si serve di tecniche di modeling
computazionale (computer-aided drug design, CADD)
7. Premessa
Drug design
Rational drug design o rational design
Ricerca di nuovi (potenziali!) farmaci sulla base della
conoscenza di un target biologico
Drug design spesso si serve di tecniche di modeling
computazionale (computer-aided drug design, CADD)
Se la struttura tridimensionale del target molecolare è nota,
allora si parla di structure-based drug design.
9. Premessa
Ligand based CADD
Structure based CADD
Basato sulla conoscenza di altre
molecole che in grado di legarsi col
target biologico di interesse.
Queste altre molecole possono
essere utilizzate per costruire una
ipotesi farmacoforica che definisca
le caratteristiche minime richieste
per avere l'interazione.
In alternativa, le techiche
quantitative structure-activity
relationship (QSAR) permettono di
cercare una correlazione tra
proprietà chimico-fisiche della
molecola e l'attività biologica.
10. Premessa
Ligand based CADD
Structure based CADD
Basato sulla conoscenza di altre Si basa sulla conoscenza della
molecole che in grado di legarsi col struttura del target biologico di
target biologico di interesse.
interesse, ottenuta tramite tecniche
di x-ray crystallography o
Queste altre molecole possono spetroscopia NMR.
essere utilizzate per costruire una
ipotesi farmacoforica che definisca Qualora la struttura del target non
le caratteristiche minime richieste fosse a disposizione, si può ovviare
per avere l'interazione.
con la costruzione di modelli
tridimensionali per omologia.
In alternativa, le techiche
quantitative structure-activity Con l'ausilio di strumenti
relationship (QSAR) permettono di computazionali è possibile stimare
cercare una correlazione tra l'affinità e la selettività di uno o più
proprietà chimico-fisiche della composti per il target.
molecola e l'attività biologica.
11. A virtual space odyssey
One of the main goals in drug discovery is to identify and
develop new ligands with high binding affinity towards
a protein target. Today, there is increased reliance on
computer-based tools […]. These help select molecules
from the vast expanse of chemical space and aid
optimization of compounds of interest into drugs.
Cath O'Driscoll, Nature, 2004
14. L'universo chimico
Chemical space is the space spanned by all possible (i.e.
energetically stable) molecules and chemical compounds –
that is, all stoichiometric combinations of electrons and
atomic nuclei, in all possible topology isomers.
Chemical reactions allow us to move in chemical space.
15. L'universo chimico
Chemical space is the space spanned by all possible (i.e.
energetically stable) molecules and chemical compounds –
that is, all stoichiometric combinations of electrons and
atomic nuclei, in all possible topology isomers.
Chemical reactions allow us to move in chemical space.
The mapping between chemical space and molecular
properties is often not unique, meaning that there can be
multiple molecules which exhibit the same properties
16. L'universo chimico
CAS REGISTRY
is the most authoritative collection of disclosed chemical substance
information, containing more than 65 million organic and inorganic
substances and 63 million sequences
67,370,815
Commercially available chemicals in CAS
Pubchem
Pcsubstance contains about 85 million records.
Pccompound contains nearly 30 million unique structures.
PCBioAssay contains more than 585,000 BioAssays. Each BioAssay
contains a various number of data points.
17. L'universo chimico
GDB-13 enumerates small organic molecules up to 13
atoms of C, N, O, S and Cl following simple chemical
stability and synthetic feasibility rules.
With 977.468.314 structures, GDB-13 is the largest publicly
available small organic molecule database to date
19. L'universo chimico
150 possibili sostituenti
da mono a 14 sostituenti
10^29 derivati teorici
20. L'universo chimico
Navigating chemical space for biology and medicine
Christopher Lipinski
& Andrew Hopkins
Nature 432, 855–861 (16 December 2004) doi:10.1038/nature03193
Despite over a century of applying organic synthesis to the search for drugs, we are still far
from even a cursory examination of the vast number of possible small molecules that could
be created. Indeed, a thorough examination of all ‘chemical space’ is practically
impossible. Given this, what are the best strategies for identifying small molecules
that modulate biological targets?
21. L'universo chimico
Navigating chemical space for biology and medicine
Christopher Lipinski
& Andrew Hopkins
Nature 432, 855–861 (16 December 2004) doi:10.1038/nature03193
Despite over a century of applying organic synthesis to the search for drugs, we are still far
from even a cursory examination of the vast number of possible small molecules that could
be created. Indeed, a thorough examination of all ‘chemical space’ is practically
impossible. Given this, what are the best strategies for identifying small molecules
that modulate biological targets?
Il salvarsan (o arsfenamina o 606) è un
farmaco utilizzato nel trattamento della
sifilide e della tripanosomiasi africana. È
stato il primo agente chemioterapico
conosciuto.
24. Trust, but verify
Many scientists TRUST chemistry and biology databases that are so
often reused, reanalyzed and integrated with new cheminformatics or
bioinformatics tools.
The authors of such articles do not appear to analyze for problems
caused by poor DATA QUALITY or hypotheses that are incorrect due
to poor underlying data.
Antony Williams, ChemSpider
28. Rappresentare molecole
InChI
The IUPAC International Chemical Identifier (InChI) is a
non-proprietary identifier for chemical substances that can
be used in printed and electronic data sources thus
enabling easier linking of diverse data compilations
http://www.inchi-trust.org/
29. Rappresentare molecole
InChI is short for International Chemical Identifier.
InChIs are text strings comprising different layers and
sublayers of information separated by slashes (/).
Each InChI strings starts with the InChI version number
followed by the main layer. This main layer contains
sublayers for chemical formula, atom connections and
hydrogen atoms.
Depending on the structure of the molecule the main layer
may be followed by additional layers e. g. for charge,
stereochemical and/or isotop information.
InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H
32. Descrittori molecolari
"The molecular descriptor is the final result of a logic and mathematical
procedure which transforms chemical information encoded within a symbolic
representation of a molecule into a useful number or the result of some
standardized experiment.
The field of molecular descriptors is strongly interdisciplinary and involves a mass of
different theories. For the definition of molecular descriptors, a knowledge of
algebra, graph theory, information theory, computational chemistry, theories of
organic reactivity and physical chemistry is usually required, although at
different levels.
For the use of the molecular descriptors, a knowledge of statistics, chemometrics,
and the principles of the QSAR/QSPR approaches is necessary in addition to
the specific knowledge of the problem. Moreover, programming, sophisticated
software and hardware are often inseparable fellow-travelers of the researcher in
this field.
From the introduction to the "Handbook of Molecular Descriptors"
by Roberto Todeschini and Viviana Consonni, Wiley-VCH, 2000.
33. Descrittori molecolari
The main classes of theoretical molecular descriptors are:
• 0D-descriptors (i.e. constitutional descriptors, count descriptors),
• 1D-descriptors (i.e. list of structural fragments, fingerprints),
• 2D-descriptors (i.e. graph invariants),
• 3D-descriptors (such as, for example, 3D-MoRSE descriptors,
WHIM descriptors, GETAWAY descriptors, quantum-chemical
descriptors, size, steric, surface and volume descriptors),
• 4D-descriptors (such as those derived from GRID or CoMFA
methods, Volsurf).
34. QSAR
More than a century ago, Crum-Brown and Fraser
expressed the idea that the physiological action of a
substance in a certain biological system (A) was a
function (f) of its chemical constitution C:
A = f C
35. QSAR
More than a century ago, Crum-Brown and Fraser
expressed the idea that the physiological action of a
substance in a certain biological system (A) was a
function (f) of its chemical constitution C:
A = f C
To explain the complex relationships between molecules and
observed quantities, two main streams were developed, the first
related to the search for relationships between molecular
structures and physico-chemical properties (QSPR,
Quantitative Structure-Property Relationships) and the second
between molecular structures and biological activities (QSAR,
Quantitative Structure-Activity Relationships).
36. QSAR
There is a consensus among current predictive toxicologists that Corwin
Hansch is the founder of modern QSAR. In the classic article it was
illustrated that, in general, biological activity for a group of ‘congeneric’
chemicals can be described by a comprehensive model:
Log 1/C50 = a π + b ε + cS + d
in which C, the toxicant concentration at which an endpoint is manifested
(e.g. 50% mortality or effect), is related to a hydrophobicity term, p, an
electronic and a steric term, S, (typically Taft’s substituent constant,
ES).
44. Algoritmi: similarity search
Similarity measures, calculations that quantify the similarity
of two molecules, and screening, a way of rapidly
eliminating molecules as candidates in a substructure
search, are both processes that use fingerprints.
Fingerprints are a very abstract representation of certain
structural features of a molecule
45. Algoritmi: similarity search
Structural keys
• The presence/absence of each element, or if an element is common
(nitrogen, for example), several bits might represent "at least 1 N", "at
least 2 N", "at least 4 N", and so forth.
• Unusual or important electronic configurations, such as "sp3 carbon" or
"triple-bonded nitrogen."
• Rings and ring systems, such as cyclohexane, pyridine, or napthalene.
• Common functional groups, such as alcohols, amines, hydrocarbons, and
so forth.
• Functional groups of special importance in a particular database. For
example, a database of organo-metallic molecules might have bits
assigned for metal-containing functional groups; in a drug database one
might have bits for specific skeletal features such as steroids and
barbiturates.
46. Algoritmi: similarity search
For example, the molecule OC=CN would generate the
following patterns:
0-bond paths:
C
O
N
1-bond paths:
OC
C=C
CN
2-bond paths:
OC=C
C=CN
3-bond paths:
OC=CN
51. MMsINC 1.0
3.967.056 total compounds
3.297.001 parent compounds
449.482 ionic states
220.573 tautomers
283.464.647 conformers (about 30confs/mol);
ordered by empirical E-pot;
max 5 confs/mol (= about 4.6 conformers per compound)
Final number of conformers: 18.461.878 (for which we have ph4-FP and USR
descriptors)
Fanton et al, IEEE, 2008; Masciocchi et al, Nucleic acid research, 2009
52. MMsINC 2.0
92.355.744 compounds from 65 public data sources and commercial catalogs
71.206.303 after single-vendor-based cleaning
42.073.344 unique compounds after redundancy washing
40 M of alternative tautomers
5 M of ionic states
Expected number of conformers: about 220 M
Average intra-vendor redundancy: 14%
10 vendors with redundancy more than 40%!
4 vendors with redundancy = 0% (small sets, 100 - 2000 comp.)
54. L'impatto della tautomeria
250000
total pairs taut/neu
different pred
Different AD
diff pred & diff AD
200000
150000
100000
50000
0
Skin DevTox LC50DM LC50FM Carcinogenicity Mutagenicity BCF
59. Screening farmacoforico su larga scala
• 2 minutes for the screening of 1 ph4 model on the CRS4 cluster resources over 17
M of conformers (4 M of commercial compounds)
• Output: SDF with top commercial compounds with highest overlap with the original
pharmacophore hypothesis
• Possibility of multiple simultaneous screenings and parameter tuning in a
reasonable time lapse
60. La cassetta degli attrezzi del chemoinformatico
• Python, Java
• R, Weka
• Openbabel, CDK
• Marvin Beans
• un database personale
• il BlueObelisk
62. Ringraziamenti
• Alessandro Bulfone
• Prof Stefano Moro
• Silvana Urru, Andrea Cristiani, Ricardo Medda, Stefania Olla
• i colleghi di Outreach del CRS4
• i colleghi del CNR (IRGB-CNR, Prof F. Cucca)
• Marco Fanton, Mattia Sturlese, Fabian Cedrati, Davide Sabbadin
• tutti gli altri collaboratori: Alberto Manganaro, Emilio Benfenati, i
colleghi del gruppo ministeriale QSAR-Reach, i colleghi del
BlueObeslik, il gruppo TNBC
• la mia famiglia (Lolli, Ric, Vera, nonni assortiti, sorelle varie)
matteo.floris@gmail.com