Resources

Crystallization

Other Crystallographic Info

This list compiled by Heidi Schubert.

Biological Function

Genomic/Proteomic Large scale Studies

  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. References

Sequences/Alignments/Comparisons

  1. National Center for Biotechnology Information

  2. BLAST

  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. EBI pairwise alignments

Domain Prediction

  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

Secondary Structure Prediction and Modeling

  1. Protein Structure Initiative (PSI) Knowledge Database (model portal)

  2. Protein Structure Prediction Center (CASP)

  3. Swiss-Model

  4. PHYRE2 homology model server

  5. Zhang Lab I-Tasser homology model server (recommended 2018)

  6. Ribosome A helix generator

  7. Robetta (Full chain predictions)

  8. PEPstr - peptide structure prediction (up to 75 residues)

  9. PSIPRED - simple predcition - output can be funneled into ESPript (also disopred)

  10. 3Djigsaw - like SwissModel

  11. PHOBIUS to predict transmembrane and signal peptide

  12. SSPRO - Secondary Structure Prediction Program

  13. PHYRE2 - A new Secondary Structure Modeling program (similar to SwissModel?)

Cloning and Expression

  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

  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

  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. E.coli expression Rare/Bad Codon detector

  8. Excel file for Invitrogen oligo order

  9. CCD Crystallization Construct Design tool with bioinformatics analysis

Protein Expression

  1. Auto-Induction Method (ZY)- Studier paper.

  2. Autoinduction Miminal Media mix.

  3. SeMet labeling in mammalian cell culture Medline: 17001101

Protein Analysis

  1. General Core Facility Link for Mass Spec, CryoEM, sequencing etc.

  2. U of Arizona Mass Spec Services See Heidi for login info

  3. Expasy Proteomics Server, (ProtParam)

  4. Robetta Server (domain prediction)

  5. Refolded protein database

Crystal Growth Videos

  1. Lysozyme by Bernard Rupp

Phasing

  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

Training Videos

  1. Sterile technique: Preparing yourself and your workplace, dealing with flame, bottle and plate lids. (Addgene.)

  2. Sterile technique: Bunson burner use, loops, spreading, different kinds of bacterial culture transfer, liquid/liquid, plate/liquid, etc. BioRad and Addgene

  3. Creation of bacterial glycerol stocks. (Addgene) (note our lab would use liquid N2 instead of dry ice)

  4. AKTA: How to transfer a SEC column. Drop-to-drop. (Cytiva). Using the spring-loaded syringe. (Cytiva)

  5. How to calibrate the Denver Instruments pH meter (Abnova)

  6. How to design PCR primers (Addgene)

  7. How to calculate molarity (TheChemistrySolution)

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

  1. Structural Comparisons

    • Dali - Structural Comparison Server

    • Theseus - Maximum Liklihood alignment

    • 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 (several choices)

    • MATRAS - MArkovian TRAnsition of Structure evolution - does multiple alignments

    • 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

  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. PDBredo - a site where they re-refined everyone's structures

  6. PDBreport evaluations of PDB structures

  7. SiteEngine - wesite to define a active site and then search the PDB for similar sites.

High Throughput Tools and Ideas

  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

General

  1. SBGrid - documentation on supported software.

  2. CCP4 Program Documentation -

  3. PHENIX | Newsletter |Python-based Hierarchical Environment for INtegrated Xtallography, automated structure solutions

  4. Uppsala Software Factory (USF)

    • 6d_molman, 6d_mapman, voidoo, oops, and many more that I don't even know about

  5. CCMS - Computational Center for MacroMolecular Structure (SDSC)

  6. Helpful AWK primer

  7. Heidi s simple UNIX and vi primer

Indexing Raw Data

  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

  5. XrayView - User friendly representations of the reciprocal lattice. as part of SBGRid cd to /home/local/LINUX/XrayView and run XRayView to access program and tutorials.

  6. Pointless - help on determining data and space group evaluation

Phasing (Heavy atom)

  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)

  1. PHASER (ccp4)

  2. MOLREP (ccp4)

  3. AMORE (ccp4)

  4. BEAST (ccp4)

  5. GLRF - look for non-crystallographic symmetry

  6. CHAINSAW (CCP4) - mutate an starting model for Molecular replacement.

  7. NORMA - normal mode fitting of crystal structures into EM densities

Density Modification

  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

  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

  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. Ligand parameter files

  6. MFit

  7. Metal ions in crystal structures

  8. Nucleic Acid model building

  9. Pulchra- builds residues from CA tracce, let me know if you want it installed.

Refinement

  1. REFMAC5

  2. BUSTER-TNT (not installed)

  3. TLSMD (TLS Motion Determination)

  4. PARVATI

  5. JLigand to produce a CIF file for coordinates

  6. PRODRG A server to generate CIF file for coordinates or smiles

  7. FiberDoc - Flexible yet rigid body refinement of modeled interactions (no X-ray data).

Structural Validation

  1. 3dfsc server from Salk on 3D FSC calculations

  2. COOT has lots of great validation.

  3. PROCHECK

  4. JCSG Quality Control

  5. PROSA - Protein Structure Analysis

  6. Biotech Validation Server

  7. JCSG web interface

  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

  1. LIGPLOT/LigPlus/DIMPLOT - Interactions around a ligand or interface

  2. NACCESS - Surface area calculaitons, per residue, or atom

  3. Protein Interaction Server - to obtain surface calculations

  4. Monster - A tool for inferring non-covalant interactions in proteins

  5. VOIDOO - look for interior cavities, volumes of particular cavities (like active sites)

  6. SURFACE and AREAIMOL (ccp4) -surface programs

  7. GRASP - Runs on Sundance (unix) only

  8. Overview of Surface and Volume Programs

  9. CastP - Volume and surface calculation of pocket or cavity

  10. VADAR (Volume, Area, Dihedral Angle Reporter)

  11. 3Vweb GUI volume calculator

  12. NCONT - (ccp4) analyses contacts between subsets of atoms in a PDB file

  13. PARVATI anisotropic displacement parameters statistics

  14. FADE and PADRE - Shape and Complementarity Server

  15. STING Millenium - web-based suite of programs for visualizing molecular structure and comprehensive structure analysis:

  16. CASTp - webserver for identification and measurements of surface accessible pockets as well as interior inaccessible cavities

Final Graphics

  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. TOPS - An Automated Topology Server, represented with triangles and circles

  6. ConSurf (Conservation automatically mapped to B-factor column, needs only PDB, does alignment for you)

  7. GRASP - Runs on Sundance (unix) only

  8. Chimera Chimera

  9. Single AA and transmembrane bubble diagram TOPO2 Transmembrane Display, use with PHOBIUS to predict transmembrane and signal peptide

Modeling

  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

Other Crystallographic Info

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) 344-7444Later 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. On-line remote user tutorial

  11. Webice

  12. Cannister Template excel file

  13. SSRL page on how to handle and test a dewar

  14. RADDOSE - program to evaluate radiation decay

Comparison Tools

  1. Structural Comparisons

    • Dali - Structural Comparison Server

    • Theseus - Maximum Liklihood alignment

    • 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 (several choices)

    • MATRAS - MArkovian TRAnsition of Structure evolution - does multiple alignments

    • 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

  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. PDBredo - a site where they re-refined everyone's structures

  6. PDBreport evaluations of PDB structures

  7. SiteEngine - wesite to define a active site and then search the PDB for similar sites.

High Throughput Tools and Ideas

  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