List of bioinformatic Tools related to Protein structure prediction and docking

 

Protein Structure Modeling

  1. Modellerhttp://caps.ncbs.res.in/iws/protmod.html

    https://modbase.compbio.ucsf.edu/modweb/

  2. Swiss-Modelhttp://swissmodel.expasy.org/
  3. I-Tasserhttp://zhanglab.ccmb.med.umich.edu/I-TASSER/

Protein Structure Validation

  1. The Structure Analysis and Verification Server

http://services.mbi.ucla.edu/SAVES/

Protein-Ligand docking

  1. Autodock
  2. SwissDockhttp://www.swissdock.ch/
  3. HADDOCKhttp://www.nmr.chem.uu.nl/haddock/
  4. Protein-Protein docking
  5. HADDOCKhttp://www.nmr.chem.uu.nl/haddock/
  6. Hexhttp://hex.loria.fr/hex.php

 

Retrieval of DNA and protein sequences

Biological databases: UniProt

UniProt is a comprehensive, high quality and freely accessible database of protein sequence and functional information. Databases: UniProtKB, UniRef, UniParc, UniMES ExPASy is a bioinformatics resource portal operated by the Swiss Institute of Bioinformatics (SIB). It is an extensive and integrative portal accessing many scientific resources, databases and software tools in life sciences. ExPASy (Expert Protein Analysis System) references the protein sequence knowledgebase UniProtKB.

PROCEDURE:

  1. Open the UniProt website
  2. Type the protein name in the text box titled enter keyword.
  3. On pressing search button the result page is displayed.
  4. Choose the first sequence by double clicking the accession number
  5. Retrieve sequence in both FASTA and GenBank format.
  6. Interpret the results.

Biological Databases: GenBank

To retrieve the DNA sequence of the uricase protein from GenBank database and to interpret the results.

DESCRIPTION:

The GenBank sequence database is an open access, annotated collection of all publicly available nucleotide sequences and their protein translations. The database is produced and maintained by the National Centre for Biotechnology Information (NCBI). NCBI is a part of National Institutes of Health (NIH). GenBank continues to grow at an exponential rate, doubling every 18 months.

PROCEDURE:

  1. Open the GenBank website.
  2. Type the protein name in the text box titled ‘enter keyword’.
  3. Select the appropriate database as gene/protein.
  4. On pressing search button the result page is displayed
  5. Choose the first sequence by double clicking the accession number
  6. Retrieve sequence in both FASTA and GenBank format.
  7. Interpret the results.

PubMed: articles

Omim: OMIM, Online Mendelian Inheritance in Man, a database of human genes and genetic disorders

ENTREZ: The Entrez Global Query Cross-Database Search System is a powerful federated search engine, or web portal that allows users to search many discrete health sciences databases at the National Center for Biotechnology Information (NCBI) website.

ENTREZ GENOME: The Entrez genome Query Cross-Database Search System is a powerful federated search engine, or web portal of genome that allows users to search many discrete health sciences databases with help of genome sequences.

GenBank: GenBank ® is the NIH genetic sequence database, an annotated collection of all publicly available DNA sequences

GENES & DISEASES: it is a query that make users search discrete health databases with are interlinked with gene sequences.
Pairwise comparison of sequences using BLAST
DESCRIPTION AND PRINCIPLE: The BLAST algorithm was developed as a new way to perform a sequence similarity search by an algorithm that is faster than FASTA while being as sensitive. A powerful computer system dedicated to running BLAST has been established at NCBI, National Library of Medicine. The BLAST algorithm increases the speed of sequence alignment by searching first for common words or k-tuples in the query sequence and each database sequence. Whereas FASTA searches for all possible words of the same length, BLAST confines the search to the words that are the most significant. For proteins, significance is determined by evaluating these word matches using log odds scores in the BLOSUM62 amino acid substitution matrix. For the BLAST algorithm, the word length is fixed at 3 (formerly 4) for proteins and 11 for nucleic acids (3 if the sequences are translated in all six reading frames). While BLAST is faster than Smith-Waterman, it cannot guarantee the optimal alignments of the query and database sequences as Smith-Waterman does.

Primer-BLAST : Provides primers specific to the PCR template sequence. Includes primer pair specificity checking against a selected database.
IgBLAST : Immunoglobulin BLAST (IgBLAST), a specialized variant of BLAST that is designed for the analysis of human or mouse immunoglobulin sequence data
Multiple Alignment Tool: is a general purpose multiple sequence alignment program for DNA
or proteins
SRA transcript and genomic libraries: Sequence Read Archive Nucleotide BLAST
RefSeqGene : Collection of curated gene-specific genomic sequences requested from, or with feedback, from Locus-Specific Databases (LSDB)

 

Secondary structure prediction of proteins

Primary Structure prediction:
1 Go to http://expasy.org/tools/ >Primary structure analysis> ProtParam, submit primary sequence
and compute physiochemical properties.
2 Go to http://expasy.org/tools/ >Primary structure analysis> Compute pI/WM, submit primary
sequence and compute molecular weight and isoelectric point.
3 Go to http://expasy.org/tools/ >Primary structure analysis> Radar, submit primary sequence and
compute repeated units.
4 Go to http://expasy.org/tools/ >Primary structure analysis> ProtScale, submit primary structure
and compute Hydrophobicity and other conformational parameters.
Secondary structure prediction:
1 Go to http://expasy.org/tools/ > Secondary structure prediction>GOR, submit primary sequence
and predict secondary structure.
2 Go to http://expasy.org/tools/ > Secondary structure prediction>CFSSP, submit primary sequence
and predict secondary structure.
3 Go to http://expasy.org/tools/ > Secondary structure prediction>HNN, submit primary sequence
and predict secondary structure.

4 Go to http://expasy.org/tools/ > Secondary structure prediction>Jpred, submit primary sequence
and predict secondary structure.
5 Go to http://expasy.org/tools/ > Secondary structure prediction>NetTurnP, submit primary
sequence and predict Beta-turn regions in protein sequences.
PROTEIN TERTIARY STRUCTURE:
PHYRE2 ­ Protein Homology/analogY Recognition Engine ­

Phyre2 uses the alignment of hidden Markov models via HHsearch to significantly improve accuracy of alignment and detection rate. It also incorporates a new ab initio folding simulation called Poing to model regions of your proteins with no detectable homology.
CPHModels (Center for Biological Sequence Analysis, Technical University of Denmark) ­ currently
consists of the following tools:

1)Sowhat: A neural network based method to predict contacts between C­alpha atoms from the amino acid sequence.

2)RedHom: A tool to find a subset with low sequence similarity in a database. Databases: Subsets of the Brookhaven Protein Data Bank (PDB) database with low sequence similarity produced using the RedHom tool.
SWISS­MODEL ­ (Glaxo­Wellcome Experimental Research, Switzerland) An automated comparative protein modelling server. Choose “First Approach mode”. N.B. results come by E­mail and require a viewer such as DeepView ­ Swiss­PdbViewer, Rasmol, Cn3D v3.0 or WebMol Java PDB Viewer to visualize.

I­TASSER ONLINE ­ 3D models are built based on multiple­threading alignments by LOMETS and iterative TASSER simulations; function inslights are then derived by matching the predicted models with protein function databases. I­TASSER was ranked as the No 1 server for protein structure prediction in recent CASP7 and CASP8 experiments.

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About YANAMALA VIJAY RAJ

Mtech in Clinical Eng Jointly offered by Indian institute of technology Madras& Christian medical college Vellore& Sree chitra tirunal institute for medical sciences and technology Trivandrum.
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