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UCLA-DOE Institute for Genomics and Proteomics, in the
Molecular Biology Institute (Boyer Hall) at the
University of California, Los Angeles (UCLA)
- Quick Links to | PETC | Bowie (ProPort) | Lab Chemical Inventory | Crystal Screen Recipes | ChemFFX MSDS | EH&S Safety Training | HS Monthly Safety Training | Lab Book | Waste Tag |
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UCLA-DOE Biochemistry Instrumentation Facility & Biochemistry Shared Instrumentation Facility (Reservation)
EMBL (European Molecular Biology Laboratory) Home. Go to Computational for their web-based programs
Databases / Resources for Mol Bio Research
The Integrated Center for Structure and Function Innovation (ISFI) - a PSI 2 Specialized Technology Center
Mycobacterium tuberculosis Structure Genomics Consortium.
Genome & Proteome Database of Mycobacterium tuberculosis (old SGC page) for public information of the RV-genes, like DNA sequences & amino acid sequences, etc.
The Mycobacterium tuberculosis H37Rv Genome Sequence by the Sanger Institute. Here's their BLAST Search tool.
Mycobacterium abscessus strain ATCC 19977 genome sequence database
Proteome Database of the hyperthermophilic Pyrobaculum aerophilum
The Methanosarcina acetivorans (C2A) database with genome information, from the Broad Institute at Cambridge, MA.
PATRIC - bioinformatic website containing genomic and associated information
NCBI featured services | PubMed | Entrez | BLAST | OMIM | Taxonomy | Structure |
Libraries | UCLA Library | National Library of Medicine | NCBI PubMed |
Protein Data Bank (PDB) has a reservoir of 3D macromolecule structures solved by X-Ray, NMR, or Cryo-EM, provided by the Research Collaboratory for Structural Bioinformatics (RCSB).
- Here is the PDB structure Validation Server.
Search Engines for Structurally Similar Protein Homologs | SSM (former DALI) by EMBL-EBI | VAST (reference) by NCBI |
The Protein Quaternary Structure Query Form at EMBL-EBI provides structures found in PDB but only in their solution forms
Structural similarity search Aided by Ramachandran Sequential Transformation - | SARST (basic search) | CP-SARST (circular permutation) | DS-SARST (domain-swapping) | - developed by the Lyu P. C. laboratory at the National Tsing Hua University of Taiwan
Periodic Table of Elements from the Los Alamos National Laboratory.
International Tables for Crystallography (by the International Union of Crystallography) - "comprises articles and tables of data relevant to crystallographic research and to applications of crystallographic methods"
Links to more Crystallography Stuff
ChemFinder gives you structures & properties of chemicals
SWISS-PROT protein knowledgebase - protein database - type in the gene name of your protein of interest and find its info & publications, etc.
E. coli Codon-Amino Acid Abbreviation Table - quick reference of the 1-letter and 3-letter codes for codons and amino acids, and E. coli rare codons.
Codon Usage Database (Homo sapiens) by the Kazusa DNA Research Institute
Addgene - plasmid databast (its Vector DB Search)
Vector Data - sequences, MCS, & maps of our commonly used vectors, and links to their manufacturers.
Public Software for Mol Bio Research
Unit Conversion - converts units such as length, temperature, energy, and even curreny.
Oligo Calculator ( Alt Site 1 / Alt Site 2 ) that helps you to calculate the melting temperature of the primer that you're trying to design.
NEB Interactive Tools - including its Tm Calculator
Primer Prim'er - useful program for designing larger number of primers, but be sure to check them before ordering. Click HERE for the manual.
Stratagene Quikchange Primer Tm Calculator
Finnzymes Tm Calculator - for use with PhusionTM High-Fidelity DNA Polymerase (NEB)
ReadSeq - | Site 1 | Site 2 | Site 3 | - can rearrange your DNA or Amino Acid sequence into the format of your choice
Locate Restriction Sites of your DNA sequences with Webcutter 2.0
Convert your DNA sequence into Reverse and/or Complementary sequence
The EMBL Clustal Omega for comparing your query DNA sequence with the original ORF
Alternative: Multiple Alignments - Another tool for DNA sequence alignment
Translate DNA sequence into protein amino acid sequence using: | ExPASy Translate Tool | EMBOSS Transeq | Molecular Workshop DNS Translater |
The Rare Codon Caltor (by Edmund Ng) finds out rare E. coli RNA codons from a DNA sequence. It also shows cluster(s) of rare codons.
Alternative: Rare Codon Calculator RaCC (by Cameron Mura)
The ExPASy ProtParam Tool for amino acid sequence analysis - calculates MW, pI, extinction coefficient, etc.
Grid Screen Generator - generate grid screen with a click of the button
Bioinformatics / Prediction Software for Mol Bio Research
SERp (Surface Entropy Reduction prediction) server - "identification of mutations to enhance protein crystallization"
PSIPRED / DISOPRED 2 - protein secondary structure / disordered region prediction servers
DomPred - protein domain prediction server / ProDom - another protein domain prediction software
3D-Jury (from the BioInfobank Meta Server) - "a simple approach to improve protein structure predition"
The EMBL SMART (Simple Modular Architecture Research Tool), also for protein sequence analysis
STRING - prediction of protein-protein interactions, including direct (physical) and indirect (functional) associations
Pfam - "collection of multiple sequence alignments and hidden Markov models covering many common protein domains and families"
Pole Bioinformatique Lyonnais Lyon-Gerland (protein division) software for Consensus Secondary Structure Prediction
MSDmotif - for search / analysis of 3D structure motifs
SignalP and LipoP servers at for predicting signal peptides and lipoprotein signal peptides, respectively, and their cleavage sites
Public Services for Mol Bio Research
IDT (Integrated DNA Technologies) - Ordering Primers
ValueGene - Ordering Primers
Ambion - Primer Dilution Calculator
Genewiz (Login) - Sequencing Lab located in N.J. & S.D.
Eton Bioscience Inc - S.D.-based sequencing lab
Davis DNA Sequencing Laboratory - | Login Page | Short Form & Long Form | ($12 per reaction, as of 2007)
The UCLA Sequencing & Genotyping Core (Gonda Center Rm. 5309) provides DNA sequencing services. Their WebSeq service allows existing customers to view results online.
USC/Norris Comprehensive Cancer Center Microchemical Core Facility procides DNA & Amino Acid Sequencing Services
UC Davis Molecular Structure Facility provides services of Protein Sequencing, Amino Acid Analysis, & Mass Spectrometry, etc.
UC Riverside High Resolution Mass Spectrometry Facility specialized in mass spec of small molecules.
Hauptman-Woodward Medical Research Institute, Inc. - HT crystallization services
| GE Healthcare Life Sciences | Axygen | BioRad ( Criterion Std Chart / Mini-PROTEAN TGX ) | Fisher Scientific | Hampton Research ( Crystal Screens ) | Invitrogen | Jena Bioscience (nucleo-s/t-ides & analogs) | New Bruswick Scientific Co., Inc. | Millipore | New England Biolabs | Novagen | Phenix Research Products | Promega | Qiagen | Sigma-Aldrich | Stratagene | VWR |
Literature & Procedure Reference
UK HGMP Resource Centre Primer Prediction and Analysis
TEV protease purification, storage, & proteolysis, etc., from the School of Bioscience, Cardiff University, UK.
EMBL Discussions on | E. coli Expression | Increase Protein Expression | Improve Protein Solubility | Increase Protein Stability | Decrease Protein Toxicity |
Applied Molecular Genetics, a biochem course webpage from the University of Arizona. Little bit about the E. coli lac operon system, K-12 strain, drug resistance, & plasmid vector in light of applications in molecular biology research.
A website talking about Acids, bases and the Henderson-Hasselbalch Equation
Another website about the Henderson-Hasselbalch Equation
Crystallization Related | Microseeding techniques | X-tal protocols | Terese Bergfors | Stura Footprint |
Viewing Molecule on Browser | RasMol v2.6 manual | Select Commands in Chime and RasMol | XMol XYZ MultiFrame Animation |
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