PyMol is a molecular graphics program that allows visualization and manipulation of protein structures. It takes protein data files in PDB format as input and outputs the 3D protein structure that can be visualized, animated, exported, and analyzed through various features and commands. PyMol is open-source, cross-platform software that is effective for protein structure analysis and commonly used in research.
The Protein Data Bank (PDB) is a database for the three-dimensional structural data of large biological molecules, such as proteins and nucleic acids. This presentation deals with what, why, how, where and who of PDB. In this presentation we have also included briefing about various file formats available in PDB with emphasis on PDB file format
INTRODUCTION.
NCBI.
EMBL.
DDBJ.
CONCLUSION.
REFERENSE.
The National Center for Biotechnology Information (NCBI) is part of the United States National Library of Medicine (NLM), a branch of the National Institutes of Health.
The NCBI is located in Bethesda, Maryland and was founded in 1988 through legislation sponsored by Senator Claude Pepper.
The NCBI houses a series of databases relevant to biotechnology and biomedicine. Major databases include GenBank for DNA sequences and PubMed, a bibliographic database for the biomedical literature.
All these databases are available online through the Entrez search engine.
The Protein Data Bank (PDB) is a database for the three-dimensional structural data of large biological molecules, such as proteins and nucleic acids. This presentation deals with what, why, how, where and who of PDB. In this presentation we have also included briefing about various file formats available in PDB with emphasis on PDB file format
INTRODUCTION.
NCBI.
EMBL.
DDBJ.
CONCLUSION.
REFERENSE.
The National Center for Biotechnology Information (NCBI) is part of the United States National Library of Medicine (NLM), a branch of the National Institutes of Health.
The NCBI is located in Bethesda, Maryland and was founded in 1988 through legislation sponsored by Senator Claude Pepper.
The NCBI houses a series of databases relevant to biotechnology and biomedicine. Major databases include GenBank for DNA sequences and PubMed, a bibliographic database for the biomedical literature.
All these databases are available online through the Entrez search engine.
Sequence alig Sequence Alignment Pairwise alignment:-naveed ul mushtaq
Sequence Alignment Pairwise alignment:- Global Alignment and Local AlignmentTwo types of alignment Progressive Programs for multiple sequence alignment BLOSUM Point accepted mutation (PAM)PAM VS BLOSUM
protein structure prediction methods. homology modelling, fold recognition, threading, ab initio methods. in short and easy form slides. after one time read you can easily understand methods for protein structure prediction.
In this presentation, I talk about the various tools for the submission of DNA or RNA sequences into various sequence databases. The sequence submission tools talked about in this presentation are BankIt, Sequin and Webin.
Secondary Structure Prediction of proteins Vijay Hemmadi
Secondary structure prediction has been around for almost a quarter of a century. The early methods suffered from a lack of data. Predictions were performed on single sequences rather than families of homologous sequences, and there were relatively few known 3D structures from which to derive parameters. Probably the most famous early methods are those of Chou & Fasman, Garnier, Osguthorbe & Robson (GOR) and Lim. Although the authors originally claimed quite high accuracies (70-80 %), under careful examination, the methods were shown to be only between 56 and 60% accurate (see Kabsch & Sander, 1984 given below). An early problem in secondary structure prediction had been the inclusion of structures used to derive parameters in the set of structures used to assess the accuracy of the method.
Some good references on the subject:
Sequence alig Sequence Alignment Pairwise alignment:-naveed ul mushtaq
Sequence Alignment Pairwise alignment:- Global Alignment and Local AlignmentTwo types of alignment Progressive Programs for multiple sequence alignment BLOSUM Point accepted mutation (PAM)PAM VS BLOSUM
protein structure prediction methods. homology modelling, fold recognition, threading, ab initio methods. in short and easy form slides. after one time read you can easily understand methods for protein structure prediction.
In this presentation, I talk about the various tools for the submission of DNA or RNA sequences into various sequence databases. The sequence submission tools talked about in this presentation are BankIt, Sequin and Webin.
Secondary Structure Prediction of proteins Vijay Hemmadi
Secondary structure prediction has been around for almost a quarter of a century. The early methods suffered from a lack of data. Predictions were performed on single sequences rather than families of homologous sequences, and there were relatively few known 3D structures from which to derive parameters. Probably the most famous early methods are those of Chou & Fasman, Garnier, Osguthorbe & Robson (GOR) and Lim. Although the authors originally claimed quite high accuracies (70-80 %), under careful examination, the methods were shown to be only between 56 and 60% accurate (see Kabsch & Sander, 1984 given below). An early problem in secondary structure prediction had been the inclusion of structures used to derive parameters in the set of structures used to assess the accuracy of the method.
Some good references on the subject:
The installation of IMPL is a straightforward procedure and requires the following prerequisites: two redistributable components from Microsoft and Intel , two open-source applications called Dia and Matplotlib (with NumPy) as well as two versions of the freely useable and distributable Python programming language where it is important to install each component in the order that they are found in this manual. Note that Dia, Matplotlib and Python are only required to create a model’s flowsheet graphically and to view a solution’s data in a Gantt chart with trend plots. If IMPL only is required then only Microsoft and Intel redistributable packages must be installed.
It is also possible to install the free Notepad++ to help configure IML files with syntax highlighting. In addition, the free Visual Studio 2010 C++ Express may also be installed to write C or C++ programs calling IPL similar to the IMPL console program as well as to increase the stack-size of Microsoft Excel to call IPL from VBA.
After the prerequisites have been installed, the installation of IMPL itself is simply a matter of extracting the files from the IMPL.zip file into directory such as C:\IMPL. To run IMPL from a DOS command window prompt or console, type inside the C:\IMPL directory the following:
impl –feed=IMLfile –filter=logistics|quality –fork=coinmp|glpk|lpsolve|ipopt|slpqpe_
where IMLfile is your *.iml filename without the IML extension and select either coinmp, glpk or lpsolve as the MILP solver with logistics and ipopt, slpqpe_coinmp, slpqpe_glpk or slpqpe_lpsolve with quality as the NLP solver.
Youtube video download using python project report.pdfKamal Acharya
In order to form a clear sketch of this project, here's a brief introduction of the features and scope of YouTube Video Downloader. This project consists of three modules which are inter-linked to each other. Each of the above modules has certain specific task to perform. Tkinter is the standard GUI library for Python. Python when combined with Tkinter provides a fast and easy way to create GUI applications. Tkinter provides a powerful object- oriented interface to the Tk GUI toolkit. Tkinter provides various controls, such as buttons, labels and text boxes used in a GUI application. These controls are commonly called widgets.Pytube library makes the video downloading very easy. Create the object of the YouTube module by passing the link as the parameter. Then, get the appropriate extension and resolution of the video. You can set the name of the file as your convenience, in another case original name will be kept. After that, download the file using the download function which has one parameter which is the location where to download the file. Python, this task is very easy. Few lines of code will download the video from YouTube for you.
For creating great software products it is key to have a good set of developing practices. In this talk I go over some of the most important patterns and strategies for developing products in Python.
The talk was given at Imperial College London in June 2018.
Image Detection and Count Using Open Computer Vision (Opencv)IJERA Editor
The purpose of this paper is to introduce and quickly make a reader to provide basics of OpenCV (Open Source Computer Vision) without having to go through the lengthy reference manuals and books. OpenCV is actually an open source library for image and video analysis, originally introduced more than decade ago by Intel. The latest major change took place in 2009 (OpenCV2) which includes main changes to the C++ interface. Nowadays the library has >2500 optimized algorithms. It is extensively used around the world, having >2.5M downloads and >40K people in the user group. Regardless of whether one is a novice C++ programmer or a professional software developer, unaware of OpenCV, the content should be interesting mainly for the researchers and graduate students in image processing and computer vision areas.
Matteo Valoriani, Antimo Musone - The Future of Factory - Codemotion Rome 2019Codemotion
In the last 3 years Mixed Reality devices and AI technology have opened the door to an infinite number of new disrupting opportunities, but it is not the only revolution underway. Thanks to the combination of new powerful cloud services, AI and local computation capabilities, we can evolve the traditional industrial applications to enter in Industry 4.0 In this session we will showcase and describe the implementation of an industrial application that uses an offline ONNX Model, trained online on cloud service but deployed locally on dedicated AI chip.
Model Attribute Check Company Auto PropertyCeline George
In Odoo, the multi-company feature allows you to manage multiple companies within a single Odoo database instance. Each company can have its own configurations while still sharing common resources such as products, customers, and suppliers.
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
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
How to Make a Field invisible in Odoo 17Celine George
It is possible to hide or invisible some fields in odoo. Commonly using “invisible” attribute in the field definition to invisible the fields. This slide will show how to make a field invisible in odoo 17.
The French Revolution, which began in 1789, was a period of radical social and political upheaval in France. It marked the decline of absolute monarchies, the rise of secular and democratic republics, and the eventual rise of Napoleon Bonaparte. This revolutionary period is crucial in understanding the transition from feudalism to modernity in Europe.
For more information, visit-www.vavaclasses.com
Palestine last event orientationfvgnh .pptxRaedMohamed3
An EFL lesson about the current events in Palestine. It is intended to be for intermediate students who wish to increase their listening skills through a short lesson in power point.
Acetabularia Information For Class 9 .docxvaibhavrinwa19
Acetabularia acetabulum is a single-celled green alga that in its vegetative state is morphologically differentiated into a basal rhizoid and an axially elongated stalk, which bears whorls of branching hairs. The single diploid nucleus resides in the rhizoid.
Introduction to AI for Nonprofits with Tapp NetworkTechSoup
Dive into the world of AI! Experts Jon Hill and Tareq Monaur will guide you through AI's role in enhancing nonprofit websites and basic marketing strategies, making it easy to understand and apply.
3. PyMOL is a molecular
graphics program built
upon Python that can be
freely downloaded and
installed on Windows or
Linux PCs as well as Apple
computers running MAC
OSX and other UNIX-based
systems.
Introduction
4. “PyMOL is a user-sponsored molecular
visualization system on an open-
source foundation, maintained and
distributed by Schrodinger.”
5. Objectives
Available on
It is cross-platform, can
be installed on
Windows, Linux, as
well as on Mac OS.
Research
Outcome
PyMol is the most cited and
commonly used protein
visualization & allows you to
make beneficial changes and
add new features in
PyMol.
Analyzes
PyMol is an effective
protein structure
visualization and
manipulation tool.
6. Input
The program
requires to upload
the file containing
the protein
structure in PDB
format.
The program
results in protein
3D structure
visualization and
manipulation.
Output
Input & Output
7. Animation
The animation of the
protein molecule to
make an animated
video
Exporting
Allow to export the
protein structure in
.png format.
Visualization
Program apply
different parameters
to visualize protein 3D
model
Scripting
Scripting can be done
within PyMol.
Figure
Provides different
features to generate a
publication quality
figure
Methodology
Manipulation
PyMol uses different
commands to
manipulate protein
structure.
8. PyMol is an efficient and
most cited, both command-
line and GUI based for an
effective protein structure
visualization and
manipulation tool.
Conclusion
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