Bioorganic Chemistry

Links

Chemistry

Organic chemistry portal
Chemie im Alltag
Named reactions at organic-chemistry.org
Named reactions at uconn.edu
Top Pharmaceuticals
Nomenclature at qmul.ac.uk
Nomenclature at acdlabs
Nomenclature at adichemistry.com
Chemistry Education Resource Guide
IBM RXN for Chemistry AI-driven retrosynthesis and reaction outcome prediction
RetroBioCat A collection of tools for automated biocatalytic cascade design
Protein Engineering Portal Tools for protein engineering
eQuilibrator Calculation of deltaG for single reactions and metabolic pathways

Online-Tools for biocatalysis including a tool to calculate Enantioselectivity and a tool to simulate kinetic and dynamic kinetic resolutions

The tool IsoPat2 is provided as download here.

Molecular Biology & Biochemistry

Enzyan AI-supported process optimization
Calculations for Molecular Biology
Protocols for Molecular Biology
BLASTp Basic Local Alignment Search Tool
Hhblits Homology Protein search
ExPASy (Expert Protein Analysis System)
Tools at New England Biolabs
NEB Builder Primer Design for Gibson or HiFi assembly
NEB Goldengate Primer Design for Golden Gate assembly
NEBasechanger Mutagenenesis primer design and PCR protocol
SnapGene Viewer Sequence view and editing (Free version)
RNAfold Analysis of Secondary structure of single strand DNA and RNA at desired temperature
Tm Calculator Tm and Ta Calculator for Phusion polymerase
Ligation Calculator Gibson Mix or any type of Ligation Calculator
Codon Harmonizer Online Tool for Codon-Harmonization
Conversion Weight-Mole Protein
Check for Signal Peptide
Properties of primers
Checking restriction sites at New England Biolabs
Checking restriction sites Non cutter und Unique cutters can be searched for
Inverting DNA sequences, complements (useful for reverse primers)
Align protein sequences SIM – Alignment Tool for protein sequences
Translate DNA
Translate AA to DNA, Reverse Translate a protein
Info about primer design
GeneFisher2 – Interactive PCR Primer Design
Checking for N-glycosylation sites
PubChem – Public database for the bioactivity of small molecules
chEMBLdb – Database for chemical properties and biologialy active drug-like molecules
DrugBank – Fact sheet on drugs (chemical, pharmacological, pharmaceutical)
STITCH – Protein-Chemical Interactions database
Database on expression response of cancer cells on bioactive drug-like molecules
AcTOR – Chemical toxicity resources database
Online resource on side effects of marketed pharmaceuticals
GEO – gene expression omnibus
Comprehensive list on approved and experimental drugs
CSR-SALAD Prediction of mutation sites for reversal of NAD/NADP specificity

Structural Biology

DALI Protein Structure Comparison Server
PROSS the Protein Repair One-Stop Shop (design of proteins for high bacterial expression and stability)
Loschmidt Labs collection of online tools for structural biology
Innophore Computational solutions for structurel biology
PDB Protein Data Bank
PDBe Protein Data Bank Europe
AlphaFold2 how to use AlphaFold2 in Colab
AlphaFold Protein Structure Database
PDBsum at-a-glance overview of PDB and AlphaFold structures
EC➝PDB overview of PDB and AlphaFold structures
Pisa server Tools for protein interfaces
PDBredo updated and optimised crystallographic structures
ESM Metagenomic Atlas predicted metagenomic protein structures
MPNN Online-Server predicted sequences based on protein structures (see paper)
neurosnap bioinformatic tools and services by NVIDIA

Chemical Suppliers (Online Catalogues)

Check availability of chemicals
Acros
Activate Scientific
Bartelt
Chempur
Frontier Scientific
Alfa Aesar
Merck Millipore
MP Biomedicals
Sigma-Aldrich
TCI
Wako
AMT Isotope
Cambridge Isotope
Eurisotop
Icon Isotopes
CDN Isotopes

Department Chemicals
(use for Eigentümer (owner) = OBC-Lager or OBC-Feinchemikalien)

Suppliers of Enzymes

Almac
Amano
American Biosystems
ASA Spezialenzyme
Biocat Collection
Biozym
Calzyme
ChiralVision
CLEA Technologies
Codexis
c-Lecta
Diversa Verenium
EnzBank
Enzymicals
evoxx
Innotech MSU
Iris
Johnson Matthey
Libragen
Maxygen
Novozymes
Prozomix
Roche Diagnostics
Sigma-Aldrich
Strem (Codexis enzymes)
SyncoZymes
Toyobo

Culture Collections

Agricultural Research Service Culture Collection (NRRL)
American Type Culture Collection (ATCC)
ATCC-LGC Partnership
Centraalbureau voor Schimmelcultures (CBS)
Culture Collection, University of Göteborg
European Collection of Cell Cultures
German Culture Collection (DSMZ)
Biological Resource Center, NITE (NBRC)
National Collection of Industrial, Food and Marine Bacteria (NCIMB)
National Collection of Yeast Cultures (NCYC)
World Data Centre for Microorganisms (WDCM)

Further Culture Collections

Electronic Journals/Searching literature

Elektronische Zeitschriftenbibliothek
Universitätsbibliothek Graz (uni≡kat)
Reaxys
ChemWeb
Web of Science
Scopus
Scifinder
Journal abbreviations

Patents

Austrian Patent Office
German Patent Office
European Patent Office and European Patents
US Patents
World Intellectual Property Office

Online Databases

Biocatalysis/Biodegradation Database
BioCatNet Databases (Univ. Stuttgart)
Brenda
chemie-datenbanken.de
Combined Chemical Dictionary
ExPASy Expert Protein Analysis System
Macherey-Nagel Database for HPLC, GC, TLC and SPE methods NCBI homepage
PathPred – Pathway Prediction server
PDB structures
UniProt Protein Sequences

Biological Activity Screening

Antwerp Drug Discovery Network (ADDN; antimicrobial activity)
PerkinElmer – in vitro screening services
Harvard Neurodiscovery Center (neurodegenerative diseases)
National Cancer Institute (NCI; anti-cancer activity)
QPS Austria various in-vitro and in-vivo screenings

Others

Enzyan AI-supported process optimization
Innophore Computational solutions for structurel biology
bisy Biology for synthesis
Biokatalyse 2021 (industrial white biotechnology)
Microanalysis Laboratory (University of Vienna)
Synthetic Biology
Enzymes converting carbohydrates