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Computer Assisted Drug Design
Exercises

Week-1 Exercise

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Lab 1: Introduction to Bioinformatics resources

Section - 1

Objective

The objective of this exercise is to learn the major bioinformatics resources. It will make students aware about the various available biological information and databases. Here we will learn to access NCBI for nucleic and protein sequences, EBI for gene and protein data and UniProt for proteins.

NCBI- National Center for Biotechnology Information

  1. Division of the National Library of Medicine (NLM) at the United States National Institutes of Health
  2. Established in November of 1988 at Bethesda, Maryland, USA.
  3. http://www.ncbi.nlm.nih.gov/

EMBL-EBI - European Molecular Biology Laboratory- European bioinformatics institute

  1. EMBL (European Molecular Biology Laboratory) is Europe's flagship laboratory for the life sciences
  2. Established in 1980 at the European Molecular Biology Laboratory in Heidelberg, Germany in September 1994
  3. EMBL-EBI was firmly established at Wellcome Trust Genome Campus in Hinxton in the UK.
  4. http://www.ebi.ac.uk/about

Uniprot

  1. The UniProt Knowledgebase (UniProtKB) is the central hub for the collection of functional information on proteins, with accurate, consistent and rich annotation.
  2. In addition to capturing the core data mandatory for each UniProtKB entry (mainly, the amino acid sequence, protein name or description, taxonomic data and citation information), as much annotation information as possible is added.
  3. https://www.uniprot.org/

Section - 2

Introduction to CADD resources

The objective of this exercise is to learn the major CADD resources.

Protein Data Bank

  1. The Protein Data Bank (PDB) was established as the 1st open access digital data resource in all of biology and medicine.
  2. It provides access to 3D structure data for large biological molecules.
  3. The Worldwide Protein Data Bank (wwPDB) was formed to maintain a single PDB archive of macromolecular structural data that is freely and publicly available to the global community.
  4. https://www.rcsb.org

Drugbank

  1. DrugBank started in 2006 in Dr. David Wishart’s lab at the University of Alberta.
  2. It is a comprehensive, free-to-access, online database containing information on drugs and drug targets.
  3. It acts as both a bioinformatics and a cheminformatics resource, combining detailed drug (i.e. chemical, pharmacological and pharmaceutical) data with comprehensive drug target (i.e. sequence, structure, and pathway) information.
  4. |(https://go.drugbank.com/)

Pubchem

  1. PubChem is an open chemistry database at the National Institutes of Health (NIH).
  2. PubChem mostly contains small molecules.
  3. It has information on chemical structures, identifiers, chemical and physical properties, biological activities, patents, health, safety, toxicity data, and many others.
  4. (https://pubchem.ncbi.nlm.nih.gov/)

KEGG DRUG Database

  1. KEGG DRUG database provide information associated with therapeutic targets, drug metabolism, and other molecular interaction network information.
  2. (https://www.genome.jp/kegg/drug/)

MalaCards

  1. MalaCards is a human disease database which includes 21837 disease entries.
  2. MalaCards provides data of pathogen, gene, pathways, drug and therapeutics etc.
  3. (https://www.malacards.org/)

SwissTargetPrediction

  1. SwissTargetPrediction is a freely available online tool.
  2. SwissTargetPrediction aims to predict the most probable protein targets of small molecules.
  3. The query molecule can be inputted either as SMILES in the left-hand dedicated text box or through the MarvinJS molecular editor on the right, which enables convenient drawing of chemical structures.

  4. (http://www.swisstargetprediction.ch)

SwissADME

  1. SwissADME is a freely available web tool.
  2. SwissADME can be used to evaluate pharmacokinetics, drug-likeness and medicinal chemistry friendliness of small molecules.

  3. (http://www.swissadme.ch/index.php)

ProTox-II

  1. ProTox-II can be used for prediction of various toxicity endpoints; such as acute toxicity, hepatotoxicity, cytotoxicity, carcinogenicity, mutagenicity, immunotoxicity and toxicity targets.

  2. (https://tox-new.charite.de/protox_II/index.php?site=compound_input)

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