Library: Biology & Biological Engineering (BBE): Biological Properties

Crystallography Tools

Crystallography LibGuide
Visit the Crystallography Guide for information on how to access the Cambridge Structural Database, as well as other biologically-related crystallography resources.

Properties of Biological Compounds

BioCyc This link opens in a new window
BioCyc is a collection of 14560 Pathway/Genome Databases (PGDBs), plus software tools for exploring them. Key aspects of BioCyc data include quality data curated from tens of thousands of publications, including curated databases for E. coli, B. subtilis, H. sapiens, and S. cerevisiae; computationally predicted metabolic pathways and operons; and data integrated from other databases including gene essentiality, regulatory networks, protein features, and GO annotations.
Please note that in order to use BioCyc beyond the limited free access amount, you must create an account on the BioCyc website and login to it while accessing BioCyc on the Caltech network. If you do not create an account and log in, you will be denied access after using up the free access amount.
Links: Introduction to BioCyc | Briefings in Bioinformatics article
Brenda: The Comprehensive Enzyme Information System
BRENDA is a freely available collection of enzyme functional data. Search with EC Number; Enzyme Name; Organism; Protein; Full Text. Advanced Search also offers: cofactors; metals/ions; organic..

ChEMBL
"ChEMBL is a database of bioactive drug-like small molecules ... 2-D structures, calculated properties (e.g. logP, Molecular Weight, Lipinski Parameters, etc.) and abstracted bioactivities (e.g. binding constants, pharmacology and ADMET data)."
Binding MOAD
A subset of the Protein Data Bank (PDB), containing well resolved protein crystal structures ... with ligands annotated with experimentally determined binding data.
DrugBank
The DrugBank database ... 6711 drug entries ... drug/chemical data and drug target/protein data.
PDBbind
Experimentally measured binding affinity data (Kd, Ki, and IC50) for the protein-ligand complexes available in the Protein Data Bank (PDB).
Therapeutic Targets Database
A database ... therapeutic protein and nucleic acid targets, the targeted disease, pathway information and the corresponding drugs directed at each of these targets.
Supertarget
Supertarget: an extensive web resource for analyzing 332828 drug-target interactions.
PDSP - NIMH Psychoactive Drug Screening Program
Screening of novel psychoactive compounds for pharmacological and functional activity at cloned human or rodent CNS receptors, channels, and transporters.
BindingDB
BindingDB is a public, web-accessible database of measured binding affinities, focusing chiefly on the interactions of protein considered to be drug-targets with small, drug-like molecules. BindingDB contains 1,419,347 binding data, for 7,000 protein targets and 635,301 small molecules. There are 2291 protein-ligand crystal structures with BindingDB affinity measurements for proteins with 100% sequence identity, and 5816 crystal structures allowing proteins to 85% sequence identity.
Guide to Pharmacology
Quantitative information on drug targets and the prescription medicines and experimental drugs that act on them. Searchable versions of the BPS Guide to Receptors and Channels (GRAC), and the IUPHAR database (IUPHAR-DB) ... properties of G protein-coupled receptors (GPCRs), ion channels and nuclear receptors and their ligands.
Nuclear Receptor Signaling Atlas (NURSA)
Funded/developed by: National Institute of Diabetes, Digestive and Kidney Diseases, Baylor College of Medicine (BCM), additional support from the National Institute of Child Health and Development. "The mission of NURSA is to accrue, develop, and communicate information that advances our understanding of the roles of nuclear receptors (NRs) and coregulators in human physiology and disease. The NURSA website has been developed over the past decade into a comprehensive source of information about NRs and their co-regulators, ligands, and downstream transcriptional targets."
DNA Data Bank of Japan
Part of the International Nucleotide Sequence Database Collaboration.
Division of AIDS Anti-HIV/OI/TB Therapeutics Database
EMDataBank - Unified Data Resource for 3-Dimensional Electron Microscopy
EMDataBank is a unified global portal for deposition and retrieval of 3DEM density maps, atomic models, and associated metadata, as well as a resource for news, events, software tools, data standards, validation methods for the 3DEM community.