Protein docking is used to check the structure, position and orientation of a protein when it interacts with small molecules like ligands. Protein receptor-ligand motifs fit together tightly, and are often referred to as a lock and key mechanism. There are both high specificity and induced fit within these interfaces with specificity increasing with rigidity. The foremost thing that we need to start with a docking search is the sequence of our protein of interest. (Halperin et al., 2002).
Protein-protein interactions occur between two proteins that are similar in size. The interface between the two molecules tends to be flatter and smoother than those in interfaces of these interactions do not have the ability to alter protein-ligand interactions. Protein-protein interactions are usually more rigid, the conformation in order to improve binding and ease movement. (Smith and Sternberg, 2002).
The process of drug development has revolved around a screening approach, as nobody knows which compound or approach could serve as a drug or therapy. Such almost blind screening approach is very time-consuming and laborious. The goal of structure-based drug design is to find chemical structures fitting in the binding pocket of the receptor. Based on the three-dimensional structure of the target protein, it can automatically build ligand molecules within the binding pocket and subsequently screen them (Weil et al., 2004).
A homology model of the housefly voltage-gated sodium channel was developed to predict the location of binding sites for the insecticides fenvalerate, a synthetic pyrethroid, and DDT, an early generation organochlorine. The model successfully addresses the state-dependent affinity of pyrethroid insecticides. (O’Reilly et al., 2006).
Interaction fingerprint: 1D representation of 3D protein-ligand complexesVladimir Chupakhin
Structural interaction fingerprint1 (IFP) was introduced in order to overcome the shortcomings of the existing scoring functions. IFP represent a binary string that encoding a presence or an absence of interactions of a ligand with amino acids of a protein binding site. It is a convenient way to compare and analyze binding poses of the ligands.
Protein docking is used to check the structure, position and orientation of a protein when it interacts with small molecules like ligands. Protein receptor-ligand motifs fit together tightly, and are often referred to as a lock and key mechanism. There are both high specificity and induced fit within these interfaces with specificity increasing with rigidity. The foremost thing that we need to start with a docking search is the sequence of our protein of interest. (Halperin et al., 2002).
Protein-protein interactions occur between two proteins that are similar in size. The interface between the two molecules tends to be flatter and smoother than those in interfaces of these interactions do not have the ability to alter protein-ligand interactions. Protein-protein interactions are usually more rigid, the conformation in order to improve binding and ease movement. (Smith and Sternberg, 2002).
The process of drug development has revolved around a screening approach, as nobody knows which compound or approach could serve as a drug or therapy. Such almost blind screening approach is very time-consuming and laborious. The goal of structure-based drug design is to find chemical structures fitting in the binding pocket of the receptor. Based on the three-dimensional structure of the target protein, it can automatically build ligand molecules within the binding pocket and subsequently screen them (Weil et al., 2004).
A homology model of the housefly voltage-gated sodium channel was developed to predict the location of binding sites for the insecticides fenvalerate, a synthetic pyrethroid, and DDT, an early generation organochlorine. The model successfully addresses the state-dependent affinity of pyrethroid insecticides. (O’Reilly et al., 2006).
Interaction fingerprint: 1D representation of 3D protein-ligand complexesVladimir Chupakhin
Structural interaction fingerprint1 (IFP) was introduced in order to overcome the shortcomings of the existing scoring functions. IFP represent a binary string that encoding a presence or an absence of interactions of a ligand with amino acids of a protein binding site. It is a convenient way to compare and analyze binding poses of the ligands.
Drug discovery take years to decade for discovering a new drug and very costly
Effort to cut down the research timeline and cost by reducing wet-lab experiment use computer modeling
Others have done the work. Some have used the work. I have spoken only on behalf of their behalf.
A lecture on molecular docking that I give for master students at University Paris Diderot.
Warning: this presentation has numerous animations which are not included in the slideshare document.
https://florentbarbault.wordpress.com/
molecular docking its types and de novo drug design and application and softw...GAUTAM KHUNE
This ppt deals with all the aspects related to molecular docking ,its types(rigid ,flexible and manual) and screening based on it and also deals with de novo drug design , various softwares available for docking methodologies and applications for molecular docking in new drug design
A short and quick presentation on predicting ligand binding sites which include four methods for prediction binding sites.First go through the references and then quick look at this presentation really helpful to you. Enjoy
Drug discovery take years to decade for discovering a new drug and very costly
Effort to cut down the research timeline and cost by reducing wet-lab experiment use computer modeling
Others have done the work. Some have used the work. I have spoken only on behalf of their behalf.
A lecture on molecular docking that I give for master students at University Paris Diderot.
Warning: this presentation has numerous animations which are not included in the slideshare document.
https://florentbarbault.wordpress.com/
molecular docking its types and de novo drug design and application and softw...GAUTAM KHUNE
This ppt deals with all the aspects related to molecular docking ,its types(rigid ,flexible and manual) and screening based on it and also deals with de novo drug design , various softwares available for docking methodologies and applications for molecular docking in new drug design
A short and quick presentation on predicting ligand binding sites which include four methods for prediction binding sites.First go through the references and then quick look at this presentation really helpful to you. Enjoy
Accurate protein-protein docking with rapid calculationMasahito Ohue
In PRIB2012 Talk (http://prib2012.org)
<reference>
Masahito Ohue, Yuri Matsuzaki, Takashi Ishida, Yutaka Akiyama: "Improvement of the Protein-Protein Docking Prediction by Introducing a Simple Hydrophobic Interaction Model: an Application to Interaction Pathway Analysis", In Proceedings of The 7th IAPR International Conference on Pattern Recognition in Bioinformatics (PRIB2012), Lecture Note in Bioinformatics 7632, 178-187, Springer Heidelberg, 2012.
http://link.springer.com/chapter/10.1007%2F978-3-642-34123-6_16
The Indian Dental Academy is the Leader in continuing dental education , training dentists in all aspects of dentistry and offering a wide range of dental certified courses in different formats.
Insilico Analysis towards Infuenza Virus- A Homology modelling and molecular ...Subhasree Pal
An Insilico attempt was made to characterize a newly sequenced Interferon induced GTP-binding protein MX1protein (organism: Mus musculus (mouse)) of influenza- A virus (H1N1) to deduce its structural information and to identify the potential drug to inhibit the protein. But, due to unavailability of further sequences a ‘template’ 3LJB (Interferon induced GTP-binding protein MX1protein (organism: Homo sapiens) is selected. For that an effort was taken to deduce the 3-D structure of this template protein and to identify and bind the active site of Interferon induced GTP-binding protein MX1protein with docking technique.
1. Scoring functions are the mathematical functions used to approximately predict the binding affinity between two molecules after they have been docked.
The evaluation and ranking of predicted ligand conformations is a crucial aspect of structure-based virtual screening.
2. Scoring functions implemented in docking programs make simplifications in the evaluation of modeled complexes.
3. Affinity scoring functions are applied to the energetically best pose found for each molecule, and comparing the affinity scores for different molecules gives their relative rank-ordering.
A QSAR is a mathematical relationship between a biological activity of a molecular system and its geometric and chemical characteristics.
QSAR attempts to find consistent relationship between biological activity and molecular properties, so that these “rules” can be used to evaluate the activity of new compounds.
Tim Cheeseright, Cresset, 'Introducing Fragment Growing in FieldStere and oth...Cresset
The upcoming release of FieldStere will enable fragment growing, This presentation will introduce the current operation and results then focus on the new features that enable more complex bioisostere searching experiments.
IOSR Journal of Applied Chemistry (IOSR-JAC) is an open access international journal that provides rapid publication (within a month) of articles in all areas of applied chemistry and its applications. The journal welcomes publications of high quality papers on theoretical developments and practical applications in Chemical Science. Original research papers, state-of-the-art reviews, and high quality technical notes are invited for publications.
Embracing GenAI - A Strategic ImperativePeter Windle
Artificial Intelligence (AI) technologies such as Generative AI, Image Generators and Large Language Models have had a dramatic impact on teaching, learning and assessment over the past 18 months. The most immediate threat AI posed was to Academic Integrity with Higher Education Institutes (HEIs) focusing their efforts on combating the use of GenAI in assessment. Guidelines were developed for staff and students, policies put in place too. Innovative educators have forged paths in the use of Generative AI for teaching, learning and assessments leading to pockets of transformation springing up across HEIs, often with little or no top-down guidance, support or direction.
This Gasta posits a strategic approach to integrating AI into HEIs to prepare staff, students and the curriculum for an evolving world and workplace. We will highlight the advantages of working with these technologies beyond the realm of teaching, learning and assessment by considering prompt engineering skills, industry impact, curriculum changes, and the need for staff upskilling. In contrast, not engaging strategically with Generative AI poses risks, including falling behind peers, missed opportunities and failing to ensure our graduates remain employable. The rapid evolution of AI technologies necessitates a proactive and strategic approach if we are to remain relevant.
June 3, 2024 Anti-Semitism Letter Sent to MIT President Kornbluth and MIT Cor...Levi Shapiro
Letter from the Congress of the United States regarding Anti-Semitism sent June 3rd to MIT President Sally Kornbluth, MIT Corp Chair, Mark Gorenberg
Dear Dr. Kornbluth and Mr. Gorenberg,
The US House of Representatives is deeply concerned by ongoing and pervasive acts of antisemitic
harassment and intimidation at the Massachusetts Institute of Technology (MIT). Failing to act decisively to ensure a safe learning environment for all students would be a grave dereliction of your responsibilities as President of MIT and Chair of the MIT Corporation.
This Congress will not stand idly by and allow an environment hostile to Jewish students to persist. The House believes that your institution is in violation of Title VI of the Civil Rights Act, and the inability or
unwillingness to rectify this violation through action requires accountability.
Postsecondary education is a unique opportunity for students to learn and have their ideas and beliefs challenged. However, universities receiving hundreds of millions of federal funds annually have denied
students that opportunity and have been hijacked to become venues for the promotion of terrorism, antisemitic harassment and intimidation, unlawful encampments, and in some cases, assaults and riots.
The House of Representatives will not countenance the use of federal funds to indoctrinate students into hateful, antisemitic, anti-American supporters of terrorism. Investigations into campus antisemitism by the Committee on Education and the Workforce and the Committee on Ways and Means have been expanded into a Congress-wide probe across all relevant jurisdictions to address this national crisis. The undersigned Committees will conduct oversight into the use of federal funds at MIT and its learning environment under authorities granted to each Committee.
• The Committee on Education and the Workforce has been investigating your institution since December 7, 2023. The Committee has broad jurisdiction over postsecondary education, including its compliance with Title VI of the Civil Rights Act, campus safety concerns over disruptions to the learning environment, and the awarding of federal student aid under the Higher Education Act.
• The Committee on Oversight and Accountability is investigating the sources of funding and other support flowing to groups espousing pro-Hamas propaganda and engaged in antisemitic harassment and intimidation of students. The Committee on Oversight and Accountability is the principal oversight committee of the US House of Representatives and has broad authority to investigate “any matter” at “any time” under House Rule X.
• The Committee on Ways and Means has been investigating several universities since November 15, 2023, when the Committee held a hearing entitled From Ivory Towers to Dark Corners: Investigating the Nexus Between Antisemitism, Tax-Exempt Universities, and Terror Financing. The Committee followed the hearing with letters to those institutions on January 10, 202
Welcome to TechSoup New Member Orientation and Q&A (May 2024).pdfTechSoup
In this webinar you will learn how your organization can access TechSoup's wide variety of product discount and donation programs. From hardware to software, we'll give you a tour of the tools available to help your nonprofit with productivity, collaboration, financial management, donor tracking, security, and more.
Honest Reviews of Tim Han LMA Course Program.pptxtimhan337
Personal development courses are widely available today, with each one promising life-changing outcomes. Tim Han’s Life Mastery Achievers (LMA) Course has drawn a lot of interest. In addition to offering my frank assessment of Success Insider’s LMA Course, this piece examines the course’s effects via a variety of Tim Han LMA course reviews and Success Insider comments.
Instructions for Submissions thorugh G- Classroom.pptxJheel Barad
This presentation provides a briefing on how to upload submissions and documents in Google Classroom. It was prepared as part of an orientation for new Sainik School in-service teacher trainees. As a training officer, my goal is to ensure that you are comfortable and proficient with this essential tool for managing assignments and fostering student engagement.
Unit 8 - Information and Communication Technology (Paper I).pdfThiyagu K
This slides describes the basic concepts of ICT, basics of Email, Emerging Technology and Digital Initiatives in Education. This presentations aligns with the UGC Paper I syllabus.
Synthetic Fiber Construction in lab .pptxPavel ( NSTU)
Synthetic fiber production is a fascinating and complex field that blends chemistry, engineering, and environmental science. By understanding these aspects, students can gain a comprehensive view of synthetic fiber production, its impact on society and the environment, and the potential for future innovations. Synthetic fibers play a crucial role in modern society, impacting various aspects of daily life, industry, and the environment. ynthetic fibers are integral to modern life, offering a range of benefits from cost-effectiveness and versatility to innovative applications and performance characteristics. While they pose environmental challenges, ongoing research and development aim to create more sustainable and eco-friendly alternatives. Understanding the importance of synthetic fibers helps in appreciating their role in the economy, industry, and daily life, while also emphasizing the need for sustainable practices and innovation.
Biological screening of herbal drugs: Introduction and Need for
Phyto-Pharmacological Screening, New Strategies for evaluating
Natural Products, In vitro evaluation techniques for Antioxidants, Antimicrobial and Anticancer drugs. In vivo evaluation techniques
for Anti-inflammatory, Antiulcer, Anticancer, Wound healing, Antidiabetic, Hepatoprotective, Cardio protective, Diuretics and
Antifertility, Toxicity studies as per OECD guidelines
2024.06.01 Introducing a competency framework for languag learning materials ...Sandy Millin
http://sandymillin.wordpress.com/iateflwebinar2024
Published classroom materials form the basis of syllabuses, drive teacher professional development, and have a potentially huge influence on learners, teachers and education systems. All teachers also create their own materials, whether a few sentences on a blackboard, a highly-structured fully-realised online course, or anything in between. Despite this, the knowledge and skills needed to create effective language learning materials are rarely part of teacher training, and are mostly learnt by trial and error.
Knowledge and skills frameworks, generally called competency frameworks, for ELT teachers, trainers and managers have existed for a few years now. However, until I created one for my MA dissertation, there wasn’t one drawing together what we need to know and do to be able to effectively produce language learning materials.
This webinar will introduce you to my framework, highlighting the key competencies I identified from my research. It will also show how anybody involved in language teaching (any language, not just English!), teacher training, managing schools or developing language learning materials can benefit from using the framework.
8. Simulated Annealing Finding a global minimium by lowering the temperature during the Monte Carlo/MD simulation
9.
10.
11.
12.
13.
14.
15.
16.
17.
18.
19. Empirical scoring Loss of entropy during binding Hydrogen-bonding Ionic interactions Aromatic interactions Hydrophobic interactions rot rot N G G G 0 bonds H neutral hb R f G . , . , int ionic io R f G int arom arom R f G . , . . , cont lipo lipo R f G
20.
21.
22. Distribution of interatomic distances is converted into energy functions by inverting Boltzmann’s law. F P (N,O)
23. Potential of Mean Force (PMF) ij seg i corr Vol B ij r r f T k r F _ ln r ij seg Number density of atom pairs of type ij at atom pair distance r Number density of atom pairs of type ij in reference sphere with radius R ij bulk ij bulk
24.
25.
26. Concluding remarks Although the reliability of docking methods is not so high, they can provide new suggestions for protein-ligand interactions that otherwise may be overlooked Scoring functions are the Achilles’ heel of docking programs . False positives rates can be reduced using several scoring functions in a consensus-scoring strategy
27.
28.
29.
30.
Editor's Notes
Explain docking is fitting ligand into the receptor, steric and electrostatic match