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Biological Function | Top

Searching Literature

  1. National Center for Biotechnology Information (NCBI)
  2. GO, Gene Ontology Database with medline links
  3. Eccles Library Catalog
  4. Marriott Librart Catalog
  5. Direct to Journal:   Science | Nature | Cell | Mol Cell | NSB | JBC | ACS-all (Biochem) | Acta Cryst D | JMB
  6. Local UofU Experts - Find A Researcher and SciVal Experts

Genome Resources | Top

  1. ATCC
  2. Open Reading Frame Consortium
  3. Addgene
  4. DF/HCC DNA resource Core
  5. TIGR The Institute of Genome Resources
  6. Yeast Genome
  7. Candida Genome
  8. Arabidopsis Genome
  9. Human Genome (NCBI)
  10. E.coli strain database (EGSC)
  11. Local hORF library at core facility

Genomic/Proteomic Large scale Studies | Top

  1. BioGRID (searchable linked databases of interactions and information)
  2. Jena Center for Bioinformatics Protein-Protein Interaction Website
  3. STRING - Search Tool for the Retrieval of Interacting Genes/Proteins
  4. Human Protein Reference database (similar, human only)
  5. Structural Genomic Portal (including Target Database at the rcsb)
  6. IntAct : EBI's interaction database from the literature.
  7. Omics Data Repositories
  8. Omics Integration Techniques
  9. References

Sequences/Alignments/Comparisons| Top

  1. National Center for Biotechnology Information
  2. pBLAST nBLAST PSI-BLAST or align 2 seqs
    BLAST specific genomes: Human, Mouse, Plants, Eukaryotic genomes, Structural Genomics Target DB
  3. MATTFash and SEEKQUENCHER multisequence structure-based alignments. (2014 best option) First use SEEKQUENCHER to pull sequences and structures from databanks - then it automatically sends to MATTFash for alignment.
  4. EMMBOSS a suite of bioinformatics tools.
  5. T-Coffee, T-Expresso: 3D versions combine structural and sequence alignments
  6. CLUSTALW2
  7. ESPript - color alignments with secondary structure (easy to advanced)
  8. Quick DNA->Protein translation
  9. SMART (Simple Modular Architecture Research Tool)
  10. HMMER (also installed locally) (A tutorial)
  11. Wise2 (Algorithums for DNA searching)

Domain Prediction | Top

  1. HHpred - homology detection and structure prediction
  2. Phyre2 - Protein Homology/analogY Recognition Engine V 2.0
  3. Expasy
  4. Sanger institute Software and Database resources
  5. Pfam home at WashU
  6. CDART(NCBI box domains with link to pfam domain number and alignments)
  7. CDD(Conserved Domain Database @ NCBI, standard output of blast with links to domains identified)
  8. DomPred Domain prediction.
  9. DomPro Domain Prediction
  10. DISPROT - CASP6 best disorder predictor
  11. DISOPRED - Disorder Prediction Server
  12. ANCHOR - A disorder and protein:protein interaction predictor
  13. DisMeta (A meta server for disorder prediction)
  14. PONDR - Predictor of Natural Disorder Regions
  15. SSEP - Protein Domain Prediction Server

Secondary Structure Prediction and Modeling | Top

  1. Protein Structure Initiative (PSI) Knowledge Database (model portal)
  2. Multiple Mapping Method with Multiple Templates (M4T) Server
  3. CaspR - Comparative Modeling for Molecular Replacement (CCMR)
  4. SAM Applications (Sequence Alignment and Modeling)
  5. Swiss-Model
  6. Ribosome A helix generator
  7. Robetta (Full chain predictions)
  8. PEPstr - peptide structure prediction (up to 75 residues)
  9. Helical Wheel mapping
  10. PSIPRED - simple predcition - output can be funneled into ESPript
  11. 3Djigsaw - like SwissModel
  12. PHOBIUS to predict transmembrane and signal peptide
  13. SSPRO - Secondary Structure Prediction Program
  14. PHYRE2 - A new Secondary Structure Modeling program (similar to SwissModel?)

Cloning and Expression | Top

  1. Serial Cloner (for Macs and PCs)

Vector Maps

  1. List of TOPO vectors at Invitrogen
  2. List of pET vectors at EMD (novagen).
  3. Invitrogen Gateway Vectors
  4. Novagen's pET vector manual (expression, toxcicity tips, etc)
  5. pET151-TOPO Cloning site map and full vector map
  6. DUET Vectors: pACYDuet-1, pCDFDuet-1, pCOLADuet-1, pRSFDuet-1, pETDuet-1
  7. pET Vectors: pET16b, pET26b-TEV, pET14b, pET9a, pET3a, pET19b, pET11a, pET21a, pET22, pET28, pET32, pET42, pET52 (Sundquist Lab)
  8. Modified pET Vectors: pET11a-His(7)-PP, pET16b-TEV
  9. pGEX Vectors: pGEXvectors, pGST-parallel, pGST-PP and pGST-TEV vectors from Steve (additional GST-PP and TEV vector sequences)
  10. Fusion vectors: AVI-tag, pTYB2 (intein)
  11. pLys Vectors: pLysE/ , pLysS
  12. Yeast Vectors: pYES2.0, pTF162, Stuff from Tim's lab about this series of vectors
  13. BaculoVirus Vectors: pAcGP67-A for expression with a signal sequence for secretion
  14. MPB Vectors: pMAL_c2X, Sequence, Picture
  15. Kathy's pKA8 Vectors (Mechler et al. (2000) A modular Set of Prokaryotic and Eukaryotic Expression Vectors Analytical Biochemistry 277, 109-120): pKA8 complete DNA sequence, pKA8 Cloning Map, Original Cloning Paper description
  16. IP6-activated fusion proteins: maps, paper, protocol, Vector sequence

Primer design | Top

  1. Primer X Online Quickchange Primer Design
  2. Oligo Calculator
  3. E.coli(K12) codon usage table | Human Code |
  4. Codon Usage Analyzer 2.0
  5. Graphical Codon Usage Analyzer
  6. JCat Codon Adaption tool (provide protein seq and get optimized codon for Ecoli)
  7. Primer Design tool - Argonne High Throughput
  8. Ecoli expression Rare/Bad Codon detector
  9. Excel file for Invitrogen oligo order
  10. CCD Crystallization Construct Design tool with bioinformatics analysis

Oligo Synthesis and Sequencing | Top

  1. Oligo Synthesis Core
  2. Sequencing - GNomEx

Protein Expression | Top

  1. Auto-Induction Method (ZY)- Studier paper.
  2. Autoinduction Miminal Media mix.
  3. SeMet labeling in mammalian cell culture Medline: 17001101

Protein Purification | Top

  1. Ammonium Sulfate Precipitation Calculator
  2. GE Healthcare Chromatography

Protein Analysis | Top

  1. Utah Mass Spectrometry Core | General MS submission form || General Core Facility Link
  2. UC Davis Mass Spec Services login is chris's email ask Heidi or Eric for password. (note email will go to Chris, so tell him what you are doing). Need a P.O. from Elisabeth added to the printed form mailed with submission.
  3. BioMolecular Interactions Core
  4. Expasy Proteomics Server, (ProtParam)
  5. Robetta Server (domain prediction)
  6. Refolded protein database

Protein Engineering | Top

  1. SER: Surface Entropy Reduction Prediction Server, reference
  2. Methylation of Lysine residues
  3. Disulfide-by-design

Crystallization | Top

Screens and Formulations

  1. Emeral Biosystems EZ Screen builder
  2. Bernard Rupp's Crystallization Predictor(based on pI)
  3. Crystallizability Predictor - XtalPred
  4. Hauptman and Woodward's High-Throughput Crystallization Lab.
  5. Hampton Research
  6. Jena Scientific Jena Hts I
  7. Qiagen: PACT screen
  8. Emerald Biosystems
  9. All Screens are available in this on-line database

Crystal Growth Videos | Top

  1. Lysozyme by Bernard Rupp

Phaseing | Top

  1. Heavy Atom Database - not as helpful as it sounds
  2. Anomalous Scattering (Eth an Meritts Anomalous Scatter Site w/ Periodic table and plotting)
  3. Another heavy atom database - based on peptide soaks with all heavy atoms and highlighted per pH.

Miscellaneous | Top

Structural Databases

  1. Protein Database (PDB)
  2. PDB Alert - keeps your sequence on file and alerts you if a homologous structure is deposited
  3. PDBeThe European PDB
  4. Cambridge Structural Database (CSD) - small molecule
  5. Database of Molecular Movements

Comparison Tools | Top

  1. Structural Comparisons
    • DaliLite - Structural Comparison Server
    • Theseus - Maximum Liklihood alignment (run locally) Manual
    • VAST - (NCBI) Vector Alignment of Search Tool - protein structural neighbors
    • MSDServer - Macromolecular Structure Database (Can provide %similarity cutoff to see entire structural family)
    • SSM - Secondary Structure Matching - multiple PDB comparison and sequence alignments.
    • STAMP - Structural Alignment of Multiple Proteins
    • MATRAS - MArkovian TRAnsition of Structure evolution - does multiple alignments
    • FATCAT - Flexible structure AlignmenT by Chaining Aligned fragment pairs allowing Twists - might be good conformational change?
    • POSA - Partial Order Structural Alignments
    • STRAP - Multiple Structural/Sequence Alignment
    • Indonesia - USF's biological sequence analysis (not installed) - multiple sequence alignments
    • MUSTANG - A MUtiple STructure AligNment alGorithm (installed - best for NMR files and close relatives) PDF
  2. SCOP - Structural Classification of Proteins
  3. PISA-Protein Interfaces, Surfaces and Assemblies (using PDB or new coordinates)
  4. ProtBud - PC program to evaluate multimer contacts and compare to related structures.
  5. ElNemo Elastic Network Model (conformational changes)
  6. EDS-Electron Density Server - Check other people's data
  7. PDBredo - a site where they re-refined everyone's structures
  8. PDBreport evaluations of PDB structures
  9. SiteEngine - wesite to define a active site and then search the PDB for similar sites.

High Throughput Tools and Ideas | Top

  1. Qfill2 - litte robot to put specificied amount of single liquid into each well.
  2. BGM technologies - microplate reader, optical density for bacterial growth, DNA detection, flurescence.
  3. Turner Biosystems - Picogreen dye and Modulus™ Fluorometer
  4. Northeast Structural Genomics Consortium
  5. Center for Eukaryotic Structural Genomics
  6. Joint Center for Structural Genomics

Crystallographic Software | Top

General

  1. SBGrid - documentation on supported software.
  2. CCP4 Program Documentation -
  3. CNS home page, CNS bulletin board
  4. PHENIX | Newsletter |Python-based Hierarchical Environment for INtegrated Xtallography, automated structure solutions
  5. Uppsala Software Factory (USF)
    • 6d_molman, 6d_mapman, voidoo, oops, and many more that I don't even know about
  6. CCMS - Computational Center for MacroMolecular Structure (SDSC)
  7. Helpful AWK primer
  8. Heidi s simple UNIX and vi primer

Data Collection and Indexing | Top

  1. Strategy don't forget to put "FORMAT RAXVERTICAL" in your com file
  2. HKLsuite hompage (manual)
  3. MOSFLM (starts with the command ipmosflm)
  4. D*TREK (not installed)
  5. XrayView - User friendly representations of the reciprocal lattice. cd to /home/local/LINUX/XrayView and run XRayView to access program and tutorials.
  6. Pointless - help on determing data and space group eveluation

Twinning | Top

  1. Twinning page at CCP4i
  2. Example of Bacteriorhodopsin twinning

Phasing (Heavy atom) | Top

  1. SOLVE - standard first choice.
  2. HKL2MAP - Shelx-based automatic phasing (to use source both xtalview and shelx)
  3. SnB Shake-n-Bake - atomic resolution - not installed
  4. SHARP- atomic resolution, see sysadmin for password
  5. ACORN(ccp4) - atomic resolution
  6. CRANK(ccp4)
  7. RANTAN(ccp4)
  8. SHELX
  9. AUTO-RICKSHAW - available only to EMBL beamline users

Phasing (molecular replacement) | Top

  1. PHASER (ccp4)
  2. MOLREP (ccp4)
  3. AMORE (ccp4)
  4. CNS
  5. EPMR (Cathy's tutorial covers using EMPR and CNS)
  6. BEAST (ccp4)
  7. GLRF - look for non-crystallographic symmetry
  8. CHAINSAW (CCP4) - mutate an starting model for Molecular replacement.
  9. NORMA - normal mode fitting of crystal structures into EM densities
  10. BALBES - Web-accesss full PDB supported molecular replacement.

Density Modification | Top

  1. RESOLVE
  2. PIRATE(ccp4)
  3. DMandDMMULTI(ccp4)
  4. SOLOMON(ccp4)
  5. Bias Removal Server - remove bias from a Molecular Replacement solution

Automated Structure Determination/ Building | Top

  1. CRANK (ccp4)
  2. Awp/Warp (ccp4)
  3. Buccaneer (ccp4) not yet installed 4-10-06
  4. RESOLVE (Solvent flattening and autobuild)
  5. RAPPER - ab initio conformational search algorithm for restraint-based protein modelling

Model Building | Top

  1. O | Molecular Model Building Software - might be better for new builds |
  2. COOT (ccp4) | Might be better for refinement/rebuilding/validation particularly at high resolution |
  3. XtalView (multi-task software, pattersons to refinement)
  4. Swiss-PDB Viewer (Frank has good experience with this)
  5. XPLEO - loop building program
  6. Ligand parameter files
  7. MFit
  8. Metal ions in crystal structures
  9. Nucleic Acid model building
  10. Pulchra- builds residues from CA tracce, let me know if you want it installed.

Refinement | Top

  1. REFMAC5 Found within CCP4. Here is a PDF of a lecture by Garib on new features. PDF
  2. CNS (1.1) (1.2), CNS bulletin board
  3. BUSTER-TNT (not installed)
  4. TLSMD (TLS Motion Determination) | Reference | Server to evaluate the anisotropic refinement PARVATI
  5. Xpleo (Help building loops)
  6. TNT (not installed)
  7. JLigand to produce a CIF file for coordinates
  8. PRODRG A server to generate CIF file for coordinates or smiles
  9. JLigand tutorial - showing how to make covalently attached modifications
  10. FiberDoc - Flexible yet rigid body refinement of modeled interactions (no X-ray data).

Structural Validation | Top

  1. COOT has lots of great validation.
  2. PROCHECK(installed locally)
  3. JCSG Quality Control
  4. PROSA - Protein Structure Analysis
  5. Biotech Validation Server
  6. JCSG web interface
  7. ADIT at the RCSB
  8. MOLPROBITY
  9. STAN - the STructure ANalysis server from the USF
  10. Verify3D Structure Evaluation Server
  11. ERRAT
  12. Ramachandran Server at Cambridge
  13. Asn/Gln Checker Server CAME
  14. Second Asn/Gln Server NQ flipper
  15. ValLigURL - ligand validator from Uppsala
  16. Zanuda - Structure validation of pseudo-translation structures to potentially correct space group.

Structural Evaluation | Top

  1. LIGPLOT - Interactions around a ligand of piece of structure
  2. DIMPLOT - Interactions between monomers of a dimer
  3. NACCESS - Surface area calculaitons, per residue, or atom
  4. Protein Interaction Server - to obtain surface calculations
  5. Monster - A tool for inferring non-covalant interactions in proteins
  6. VOIDOO - look for interior cavities, volumes of particular cavities (like active sites)
  7. SURFACE and AREAIMOL (ccp4) -surface programs
  8. GRASP - Runs on Sundance (unix) only
  9. Overview of Surface and Volume Programs
  10. CastP - Volume and surface calculation of pocket or cavity
  11. VADAR (Volume, Area, Dihedral Angle Reporter)
  12. 3Vweb GUI volume calculator
  13. NCONT - (ccp4) analyses contacts between subsets of atoms in a PDB file
  14. PARVATI anisotropic displacement parameters statistics
  15. FADE and PADRE - Shape and Complementarity Server
  16. STING Millenium - web-based suite of programs for visualizing molecular structure and comprehensive structure analysis:
  17. CASTp - webserver for identification and measurements of surface accessible pockets as well as interior inaccessible cavities

Final Graphics | Top

  1. Pymol - what a great program
  2. PDB2PQR - format conversion and adendum for electrostatic calculations with APBS.
  3. CCP4MG - molecular graphics from CCP4
  4. Molscript - molauto options and opengl available on some machines.
  5. Bobscript - currently not installed.
  6. TOPS - An Automated Topology Server, represented with triangles and circles
  7. ConSurf (Conservation automatically mapped to B-factor column, needs only PDB, does alignment for you)
  8. GRASP - Runs on Sundance (unix) only
  9. Chimera - /home/local/LINUX/chimera/bin
  10. Index of molecular visualization programs
  11. Movies - Hints about movie format conversion
  12. single AA and transmembrane bubble diagram TOPO2 Transmembrane Display, use with PHOBIUS to predict transmembrane and signal peptide

Modeling | Top

  1. Modeller - run "mod8v2" from the prompt
  2. WHATIF - molecular modeling and drug design
  3. DOT - A docking program for proteins of any size (sdsc)
  4. ClusPro - protein-protein docking
  5. Protein-Protein docking options
  6. HEX - David Richie's docking server, can also be downloaded

Other Crystallographic info | Top


Synchrotrons

  1. BioSync - Structural Biology Synchrotron Users Organization (statistics and information)
  2. Brookhaven National Labs (px)
  3. Mail-In Data Collection:
    Attn of (Annie or Howard)
    National Synchrotron Light Source
    Brookhaven National Laboratory
    75 Brookhaven Rd.
    Upton, NY 11973 USA
    Phone: (631) 344-7444
    Later call University Shipping office 1-6721 to get FedEx Tracking number, you'll need the internal reference number.
  4. APS - Chicago
  5. ALS - Berkely
  6. SSRL Homepage for users - Stanford: Our Proposal number as of 1/8/09 is 1C03, not sure if it's a zero or "O"
  7. Shipping form for SSRL dewars, Local Biochemistry FedEx Form to give to office
  8. Frank's remote user advice document
  9. remote users guide
  10. beamline guide
  11. beamline cell phones
  12. on-line DVD backup server
  13. On-line remote user tutorial
  14. Webice
  15. Cannister Template excel file
  16. Puck template Excel file
  17. SSRL page on how to handle and test a dewar
  18. RADDOSE - program to evaluate radiation decay (not installed)

Education | Top

  1. Bernard Rupp's Very educational Website and pictures to his new book
  2. Direct link to Ethan Merrit's Anamalous Scattering Website
  3. Kevin Cowtan's Website (cats and ducks)
  4. Salt Lake Valley Science Education Fair
  5. A graphic level discussion of various structures (DNA, hemaglobin, MHC, antibodies, lipids, flagella etc)
  6. Great set of movies detailing aspects of datacollection and refinement (James Holton)
  7. Commission on Crystallographic Teaching
  8. IUCr Teaching
  9. Articles

Structural Organizations | Top

  1. American Crystallographic Association
  2. International Union of Crystallography