The Protein Data Bank (PDB) is a single worldwide database that stores 3D structural data of proteins and nucleic acids. It is operated by Rutgers University, the San Diego Supercomputer Center, and the Research Collaboratory for Structural Bioinformatics. The PDB is freely accessible online and contains over 76,000 biomolecular structure entries as of 2011. It uses a common file format to represent structural data and is updated weekly as new entries are submitted by researchers.
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
An integrated publicly accessible bioinformatics resource to support genomic/proteomic research and scientific discovery.
Established in 1984, by the National Biomedical Research Foundation (NBRF) Georgetown University Medial Center, Washington D.C., USA.
It is the source of annotated protein databases and analysis tools for the researchers.
Serve as primary resource for the exploration of protein information.
Accessible by text search for entry and list retrieval, and also BLAST search and peptide match.
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
An integrated publicly accessible bioinformatics resource to support genomic/proteomic research and scientific discovery.
Established in 1984, by the National Biomedical Research Foundation (NBRF) Georgetown University Medial Center, Washington D.C., USA.
It is the source of annotated protein databases and analysis tools for the researchers.
Serve as primary resource for the exploration of protein information.
Accessible by text search for entry and list retrieval, and also BLAST search and peptide match.
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.
This presentation gives you a detailed information about the swiss prot database that comes under UniProtKB. It also covers TrEMBL: a computer annotated supplement to Swiss-Prot.
SWISS-PROT- Protein Database- The Universal Protein Resource Knowledgebase (UniProtKB) is the central hub for the collection of functional information on proteins.
The Protein Information Resource, is an integrated public bioinformatics resource to support genomic and proteomic research, and scientific studies & contains protein sequences databases
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
Cytoscape plugins - GeneMania and CentiScapeNixon Mendez
Cytoscape is an open source software platform. It provides features for data integration, analysis and visualization.
Additional features are available in the form of apps (plugins).
These apps can be used for network analyses, molecular scripting and connection with databases.These apps are available in Cytoscape App Store.
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.
This presentation gives you a detailed information about the swiss prot database that comes under UniProtKB. It also covers TrEMBL: a computer annotated supplement to Swiss-Prot.
SWISS-PROT- Protein Database- The Universal Protein Resource Knowledgebase (UniProtKB) is the central hub for the collection of functional information on proteins.
The Protein Information Resource, is an integrated public bioinformatics resource to support genomic and proteomic research, and scientific studies & contains protein sequences databases
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
Cytoscape plugins - GeneMania and CentiScapeNixon Mendez
Cytoscape is an open source software platform. It provides features for data integration, analysis and visualization.
Additional features are available in the form of apps (plugins).
These apps can be used for network analyses, molecular scripting and connection with databases.These apps are available in Cytoscape App Store.
Ab Initio Protein Structure Prediction is a method to determine the tertiary structure of protein in the absence of experimentally solved structure of a similar/homologous protein. This method builds protein structure guided by energy function.
I had prepared this presentation for an internal project during my masters degree course.
Protecting Traditional Knowledge In IndiaIntepat IP
Traditional knowledge is the knowledge system possessed by various communities across the globe. Such knowledge has been accumulated over the years and has been used and passed down through several generations. It is usually with respect to the natural surroundings of the community and includes agricultural knowledge such as manner of cultivation, environmental knowledge and knowledge of natural medicines.
Clustering and Visualisation using R programmingNixon Mendez
Clustering Analysis is a collection of patterns into clusters based on similarity.
Here we will discuss on the following :
Microarray Data of Yeast Cell Cycle
Clustering Analysis :-
Principal Component Analysis (PCA)
Multidimensional Scaling (MDS)
K-Means
Self-Organizing Maps (SOM)
Hierarchical Clustering
Structural Bioinformatics - Homology modeling & its ScopeNixon Mendez
Homology modeling also known as comparative modeling uses homologous sequences with known 3D structures for the modelling and prediction of the structure of a target sequence
Homology modeling is one of the most best performing prediction methods that gives “accurate” predicted models.
PowerMV is a software environment for statistical analysis, molecular viewing, descriptor generation, and similarity search.
In this presentation we will study about two modules nearest neighbor search an molecular descriptor generation.
Protein Data Bank is a really important topic to civer in Bioinformatics for students. This presentation will help students to understand the Protein Data Bank in a really easy language.
BITS: Overview of important biological databases beyond sequencesBITS
Module 4 Other relevant biological data sources beyond sequences
Part of training session "Basic Bioinformatics concepts, databases and tools" - http://www.bits.vib.be/training
Protein Structure Prediction Using Support Vector Machine ijsc
Support Vector Machine (SVM) is used for predict the protein structural. Bioinformatics method use to protein structure prediction mostly depends on the amino acid sequence. In this paper, work predicted of 1-D, 2-D, and 3-D protein structure prediction. Protein structure prediction is one of the most important problems in modern computation biology. Support Vector Machine haves shown strong generalization ability protein structure prediction. Binary classification techniques of Support Vector Machine are implemented and RBF kernel function is used in SVM. This Radial Basic Function (RBF) of SVM produces better accuracy in terms of classification and the learning results.
PROTEIN STRUCTURE PREDICTION USING SUPPORT VECTOR MACHINEijsc
Support Vector Machine (SVM) is used for predict the protein structural. Bioinformatics method use to protein structure prediction mostly depends on the amino acid sequence. In this paper, work predicted of 1-
D, 2-D, and 3-D protein structure prediction. Protein structure prediction is one of the most important problems in modern computation biology. Support Vector Machine haves shown strong generalization ability protein structure prediction. Binary classification techniques of Support Vector Machine are implemented and RBF kernel function is used in SVM. This Radial Basic Function (RBF) of SVM produces better accuracy in terms of classification and the learning results.
BIOLOGICAL DATABASES :
A biological database is a large, organized body of persistent data, usually associated with computerized software designed to update, query, and retrieve components of the data stored within the system.
The chief objective of the development of a database is to organize data in a set of structured records to enable easy retrieval of information.
Example. A few popular databases are GenBank from NCBI (National Center for Biotechnology Information), SwissProt from the Swiss Institute of Bioinformatics and PIR from the Protein Information Resource.
IMPORTANCE OF DATABASES :
1. Databases act as a store house of information.
2. Databases are used to store and organize data in such a way that information can be retrieved easily via a variety of search criteria.
3. It allows knowledge discovery, which refers to the identification of connections between pieces of information that were not known when the information was first entered. This facilitates the discovery of new biological insights from raw data.
4. Secondary databases have become the molecular biologist’s reference library over the past decade or so, providing a wealth of information on just about any gene or gene product that has been investigated by the research community.
5. It helps to solve cases where many users want to access the same entries of data.
6. Allows the indexing of data.
7. It helps to remove redundancy of data.
TYPES OF BIOLOGICAL DATABASES:
Biological databases are classified on
1. Based on content of biological data
2. Based on the nature of data.
1. BASED ON CONTENT OF BIOLOGICAL DATA :
Based on their contents, biological databases can be roughly divided into two categories:
1. Primary databases
2. Secondary databases
The Roman Empire A Historical Colossus.pdfkaushalkr1407
The Roman Empire, a vast and enduring power, stands as one of history's most remarkable civilizations, leaving an indelible imprint on the world. It emerged from the Roman Republic, transitioning into an imperial powerhouse under the leadership of Augustus Caesar in 27 BCE. This transformation marked the beginning of an era defined by unprecedented territorial expansion, architectural marvels, and profound cultural influence.
The empire's roots lie in the city of Rome, founded, according to legend, by Romulus in 753 BCE. Over centuries, Rome evolved from a small settlement to a formidable republic, characterized by a complex political system with elected officials and checks on power. However, internal strife, class conflicts, and military ambitions paved the way for the end of the Republic. Julius Caesar’s dictatorship and subsequent assassination in 44 BCE created a power vacuum, leading to a civil war. Octavian, later Augustus, emerged victorious, heralding the Roman Empire’s birth.
Under Augustus, the empire experienced the Pax Romana, a 200-year period of relative peace and stability. Augustus reformed the military, established efficient administrative systems, and initiated grand construction projects. The empire's borders expanded, encompassing territories from Britain to Egypt and from Spain to the Euphrates. Roman legions, renowned for their discipline and engineering prowess, secured and maintained these vast territories, building roads, fortifications, and cities that facilitated control and integration.
The Roman Empire’s society was hierarchical, with a rigid class system. At the top were the patricians, wealthy elites who held significant political power. Below them were the plebeians, free citizens with limited political influence, and the vast numbers of slaves who formed the backbone of the economy. The family unit was central, governed by the paterfamilias, the male head who held absolute authority.
Culturally, the Romans were eclectic, absorbing and adapting elements from the civilizations they encountered, particularly the Greeks. Roman art, literature, and philosophy reflected this synthesis, creating a rich cultural tapestry. Latin, the Roman language, became the lingua franca of the Western world, influencing numerous modern languages.
Roman architecture and engineering achievements were monumental. They perfected the arch, vault, and dome, constructing enduring structures like the Colosseum, Pantheon, and aqueducts. These engineering marvels not only showcased Roman ingenuity but also served practical purposes, from public entertainment to water supply.
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.
Read| The latest issue of The Challenger is here! We are thrilled to announce that our school paper has qualified for the NATIONAL SCHOOLS PRESS CONFERENCE (NSPC) 2024. Thank you for your unwavering support and trust. Dive into the stories that made us stand out!
2. CONTENTS
Introduction
Supported and funded by
History
PDB Holdings list
Member organizations
Task forces
PDB ID
PDB File format
Browse to WWW.RCSB.ORG/PDB/
3. PROTEIN DATA BANK
PDB
Single worldwide database and hundreds of secondary databases categorize
the data differently.
Key resource in the area of structural biology, stores 3D structural data of
large biological molecules such as Proteins and Nucleic acids.
Data is submitted by Biologists and Biochemists from all around the world
to be freely accessible on internet via its member organizations’ websites
and is updated weekly.
The mission is to maintain a single Protein Data Bank Archive of
Macromolecular Structural data.
4. SUPPORTED AND FUNDED
The Protein Data Bank (PDB) is operated by:
Rutgers, The State University of New Jersey.
The San Diego Supercomputer Center at the University of California, San
Diego.
The Center for Advanced Research in Biotechnology of the National
Institute of Standards and Technology -- the Research Collaboratory for
Structural Bioinformatics (RCSB)
The PDB is supported by funds from the National Science Foundation, the
Department of Energy, and the National Institutes of Health.
5. PDB HISTORY
Two forces to initiate PDB:
Growing collection of sets of protein structural data by X-Ray diffraction.
Brookhaven Raster Display (BRAD), a molecular graphics display to
visualize protein structures in 3D, emerged in 1968.
In 1969, Dr Edger Meyer began to write software to store atomic
coordinates files in a common format to make them available for geometric
and graphical evaluation (with sponsorship of Dr Walton Hamilton at
Bookhaven National Laboratory.
In 1971, one of Dr Meyer’s programs- SEARCH- enabled networking i.e
enabled the researchers to access information from database to study protein
structures offline.
6. In 1973, upon Hamilton’s death, Dr Tom Koetzle took over direction of PDB
for 20 years.
mmCIF project completed and Structural genomics began in 1970s.
In 1980s, IUCr guidelines established, number of structures deposited increases
and independent biological databases established – e.g., the NDB.
In Oct, 1998; PDB was transferred to Research Collaboratory for Structural
Bioinformatics (RCSB), complete transfer since 1999. Dr Helen M Berman of
Rutgers University was the new director.
In 2003, with the formation of wwPDB, the PDB became an international
organization having three member organizations.
!n 2006, the BMRB joined PDB.
7. PDB HOLDINGS LIST ( AS OF 25 OCT, 2011)
Experimental Protein/Nucleic Acid
Proteins Nucleic Acids Other Total
Method complexes
X-ray diffraction 62750 1323 3050 2 67125
NMR 7962 960 179 7 9108
Electron microscopy 262 22 96 0 380
Hybrid 41 3 1 1 46
Other 133 4 5 13 155
Total: 71148 2312 3331 23 76814
8. MEMBER ORGANIZATIONS
Act as Data deposition, Data processing and Distribution centers for PDB data.
Three are founding member organizations:
PDBe…Protein Data Bank in Europe.
PDBj…Protein Data Bank in Japan.
RCSB…Research Collaboratory for Structural Bioinformatics.
The Biological Magnetic Resonance Data Bank (BMRB) joined later in 2006.
Another organization Worldwide Protein Data Bank (wwPDB) oversees PDB.
wwPDB reviews and annotates each submitted entry and then it is automatically
checked for plausibility( the source code for validation software is available.
9.
10.
11.
12.
13.
14. TASK FORCES
X-Ray diffraction (most of the structures)…approximations of the
coordinates of atoms of proteins are obtained. E.g lyzozyme.
NMR (about 15% e.g, haemoglobin)…estimations of distances between
pairs of atoms of proteins. Final conformation is obtained after solving
distance geometry problem.
Cryo Electron Microscopy (very few protein e.g, crsysalin).
15.
16.
17.
18. PDB IDENTIFIER (PDB ID)
Each structure published in PDB receives a four character alphanumeric
identifier or accession number. Like, 1ANG or 4hhb.
However, this cant be used as an identifier for biomolecules. Because
several structures for the same molecule in different environments or
conformations-are contained in PDB with different PDB IDs.
19. PDB FILE FORMAT
Standard data representation…encoded in data dictionary. The metadata
model supporting this representation is used by all PDB data processing and
database software tools.
PDB file format was restricted to 80 characters per line initially.
In 1996, macromolecular Crystallographic Information File (mmCIF) format
started.
In 2005, XML version called as PDBML, was described.
The structure files can be downloaded in any of these three formats.
The files are easily downloaded into graphics packages as well, using web
services.
20. PDB 3D data file format
ASCII
column based: 80 columns per line
KEYWORD for record type at col.#1
Header records
Structure records
Atom records (containing coordinates)
ATOM, HETATM, ..., TER
21. PDB format
Coordinate Section
ATOM record Biopolymer residue atom
HETATM record nonBiopolymer atom
TER record chain terminator
123456789012345678901234567890123456789012345678901234567
89012345678901234567890
ATOM 1 N ALA 1 11.104 6.134 -6.504 1.00 0.00 N
ATOM 2 CA ALA 1 11.639 6.071 -5.147 1.00 0.00 C
...
ATOM 293 1HG GLU 18 -14.861 -4.847 0.361 1.00 0.00 H
ATOM 294 2HG GLU 18 -13.518 -3.769 0.084 1.00 0.00 H
TER 295 GLU 18
HETATM 5555 CA 0.000 0.000 0.000
22. mmCIF
mmCIF is the acronym for the macromolecular Crystallographic
Information File.
mmCIF is based on a subset of the syntax rules for the Self
Defining Text Archive (STAR) file.
A Dictionary Description Language (DDL) defines the structure of
mmCIF dictionaries. Dictionaries provide the metadata which define
the content of mmCIF data files.
mmCIF data files, dictionaries and DDLs are all expressed in a
common syntax.
23. POINT YOUR BROWSER TO:
WWW.RCSB.ORG/PDB/
put either a search term (for example, a protein name) or a
PDB number
36. PROTEIN ANNOTATION
If the contents of the PDB are thought of as primary
data, then there are hundreds of derived (i.e.,
secondary) databases that categorize the data
differently. For example,
both SCOPand CATH categorize structures
according to type of structure and assumed
evolutionary relations; GO categorize structures
based on genes.
37.
38. The Structural Classification
of Proteins (SCOP) database is
a largely manual classification of
protein structural domains based
on similarities of
their structures and amino
acid sequences
39. Class:the overall secondary-structure content of the domain
Architecture:high structural similarity but no evidence
of homology.
Topology:a large-scale grouping of topologies which share
particular structural features
Homologous superfamily:indicative of a demonstrable
evolutionary relationship.
40.
41. Pfam is a
database
of protein
families that
includes their
annotations
and multiple
sequence
alignment
generated
using hidden
Markov models
57. VIEWING THE DATA
56,523 structures In PDB have structure factor files.
6410 structures In PDB have NMR restraint files.
198 structures In PDB have chemical shifts files.
Text file can be viewed or modified in editor.
Structure files may be viewed using various free and commercial
visualizations programs and Web browsers plug-ins like
OPEN SOURCE PDB softweres
Jmol
Molekel
MeshLab(able to import PDB data set and buildup surfaces from them)
QuteMol
Avogadro
And others open but not free , like
PYMOL , RASMOL, VIST PROT 3DS & STAR BIOCHEM
58. HTTP://WWW.RCSB.ORG/PDB/STATIC.DO
?P=SOFTWARE/SOFTWARE_LINKS/MOL
ECULAR_GRAPHICS.HTML
The RCSB PDB website contains
an extensive list of both free and
commercial molecule visualization
programs and web browser plug-in.
59.
60.
61. LIMITATION
The Protein Data Bank (PDB) is the central archive of
experimentally solved biomolecular structures. However, the PDB
only allows data retrieval and does not provide functionality for
collaboration or user feedback.
In contrast, PDBWiki allows for sharing expert knowledge about
structures deposited in the PDB. It provides tools for discussing and
annotating proteins in a collaborative way. The goal is to create a
central and freely-accessible repository of user-contributed
information that will be useful for anyone working with PDB
structures. As such PDBWiki can be considered a part of a wider
effort in community-based biological databases curation.