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PETC Group Meeting

Presentation Main Page - Latest: < 2008 Spring > Quarter

Academic

The UCLA-DOE Institute for Genomics and Proteomics, which resides in the Molecular Biology Institute (Boyer Hall) at the University of California, Los Angeles (UCLA)

M230D - Structural Molecular Biology Laboratory at UCLA (Winter 2002)

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 Gemonics Consortium.

Proteome Database of Mycobacterium tuberculosis. You can go to the Quick Search (on upper right) 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.

Proteome Database of the hyperthermophilic Pyrobaculum aerophilum

Libraries | UCLA Library | National Library of Medicine | NCBI PubMed |

Protein Data Bank (PDB) has a reservoir of 3D macromolecule structures solved by X-ray or NMR, provided by the Research Collaboratory for Structural Bioinformatics (RCSB). Here is their 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"

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.

Codon-Amino Acid Abbreviation Table - quick reference of the 1-letter and 3-letter codes for codons and amino acids

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.

Primer Prim'er - "a PCR primer design tool that completely automates the primer design process". Click HERE for the manual.

Oligo Calculator that helps you to calculate the melting temperature of the primer that you're trying to design (Note: only input the part of the primer that will anneal to the template!)

Stratagene Quikchange Primer T_m Calculator

Finnzymes T_m Calculator - for use with Phusion^TM 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 a Reverse and/or Complementary sequence

The EMBL ClustalW for comparing your query DNA sequence with the original ORF

Multiple Alignments - Another tool for DNA sequence alignment

Transeq can translate your DNA sequence into the corresponding amino acid sequence.

DNA Translater - Another program that translates a DNA sequence into a amino acid sequence.

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.

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 - protein secondary structure prediction server

DISOPRED - protein disordered region prediction software (click HERE for the downloadable version)

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

Public Services for Mol Bio Research

Integrated DNA Technologies (IDT) - Ordering Primer

Ambion - Primer Dilution Calculator

Genewiz - Sequencing Lab located at N.J. & S.D. ($8 per reaction, as of 2007)

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

Biotech Companies

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.

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

Viewing Molecule on Browser | RasMol v2.6 manual | Select Commands in Chime and RasMol | XMol XYZ MultiFrame Animation |

News & Media

Newspapers - | UCLA Daily Bruin | CNN News ( Asia / Europe ) | L.A. Times ( Shopping Center ) |

Hong Kong TVB Video News | @ 8:00am | @ Noon | @ 6:30pm |

Hong Kong Online Radio Stations - | HKCR | Metro Radio (Finance) | RTHK (S2 Rev / News) |

Weather Forecast - | MAC MDR real-time | NOAA L.A. area | The Weather Channel ( MDR Boat Weather & L.A. Wave Map ) |

Other Miscellaneous Bookmarks You May Be Interested In

Arts - | UCLA Performing Arts | Los Angeles Philharmonic | the Getty Center & Villa |

Centers for Disease Control - learn about Anthrax & SARS, & of course Tuberculosis

Credit reports - get yours free annually at | Equifax | Exparian | TransUnion | and you may also want to check your FICO credit score.

Dining - | Japanese Restaurant Info.com | Japanese Restaurant Guides.com |

Yabu Japanese Restaurant - offers the best Japanese cuisine at a very reasonable price. Must Try!

E-cards - | Hallmark | Shockwave / Ynot (J) |

Family Watchdog - the national criem / sex offender registry

Ripoff Report - updates you on the latest consumer ripoff and other scams

Traffic report - SigAlert covering Los Angeles & Orange County

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