- #Serial cloner build construct full#
- #Serial cloner build construct Pc#
- #Serial cloner build construct series#
The supernatant from the in vivo excision is stable for at least a year at 4☌ without loss of titer.įresh colonies are plated weekly for preparation of plasmid DNA templates for sequencing. An aliquot of the packaged pBlue script is mixed with host cells (generally XL1–Blue) and plated on LB plates supplemented with 50 µg ml −1 ampicillin. The host strain chosen depends in part on the plasmid preparation method used. XL1-Blue is far superior for Qiagen preps, for instance, than DH5 or JM109 strains. STING Millenium - web-based suite of programs for visualizing molecular structure and comprehensive structure analysis:ĬASTp - webserver for identification and measurements of surface accessible pockets as well as interior inaccessible cavitiesOvernight cultures (5 ml) are split into two 500 µl fractions for storage at −70☌ and a 4-ml aliquot for plasmid DNA purification. PARVATI anisotropic displacement parameters statisticsįADE and PADRE - Shape and Complementarity Server NCONT - (ccp4) analyses contacts between subsets of atoms in a PDB file VADAR (Volume, Area, Dihedral Angle Reporter) SURFACE and AREAIMOL (ccp4) -surface programsĬastP - Volume and surface calculation of pocket or cavity VOIDOO - look for interior cavities, volumes of particular cavities (like active sites) Monster - A tool for inferring non-covalant interactions in proteins Protein Interaction Server - to obtain surface calculations NACCESS - Surface area calculaitons, per residue, or atom
LIGPLOT/LigPlus/DIMPLOT - Interactions around a ligand or interface SiteEngine - wesite to define a active site and then search the PDB for similar sites. PDBredo - a site where they re-refined everyone's structures
#Serial cloner build construct Pc#
ProtBud - PC program to evaluate multimer contacts and compare to related structures. PISA-Protein Interfaces, Surfaces and Assemblies (using PDB or new coordinates)
SCOP - Structural Classification of Proteins MUSTANG - A MUtiple STructure AligNment alGorithm Indonesia - USF's biological sequence analysis (not installed) - multiple sequence alignments STRAP - Multiple Structural/Sequence Alignment POSA - Partial Order Structural Alignments MATRAS - MArkovian TRAnsition of Structure evolution - does multiple alignments STAMP - Structural Alignment of Multiple Proteins (several choices) SSM - Secondary Structure Matching - multiple PDB comparison and sequence alignments. MSDServer - Macromolecular Structure Database (Can provide %similarity cutoff to see entire structural family) VAST - (NCBI) Vector Alignment of Search Tool - protein structural neighbors IP6-activated fusion proteins: maps, paper, protocol, Vector sequence (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
#Serial cloner build construct series#
Yeast Vectors: pYES2.0, pTF162, Stuff from Tim's lab about this series of vectorsīaculoVirus Vectors: pAcGP67-A for expression with a signal sequence for secretion PGEX Vectors: pGEXvectors, pGST-parallel, pGST-PP and pGST-TEV vectors from Steve (additional GST-PP and TEV vector sequences) Modified pET Vectors: pET11a-His(7)-PP, pET16b-TEV
#Serial cloner build construct full#
PET151-TOPO Cloning site map and full vector mapĭUET Vectors: pACYDuet-1, pCDFDuet-1, pCOLADuet-1, pRSFDuet-1, pETDuet-1 Novagen's pET vector manual (expression, toxcicity tips, etc) SLIC cloning, pGST-PP-GFP and pHIS-SUMO-GFP
Ligation Independent Cloning (LIC) vectors from Mark Connelly: pMCSG10, pMCSG7, pMCSG17-20, pMCSG19, pMCSG21 Yeast 2-hybrid vectors (sundquist lab) pGADT7 and pGBKT7 PDEST14 pDEST15, pDEST17, pENTR/TEV/D-TOPO, MCS PENTRL1pLaclacZaL4, pENTRL1pLaclacZaR5, pENTR元pLactetL2, pENTRL5LacIL4, pENTRL5pLacSpecL2, pENTRR4pLacSpecR3
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