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Research Tools

The Building Blocks, Biological Pathways and Networks program has transitioned from Common Fund support.  For more information, please visit https://commonfund.nih.gov/bbpn/index. Please note that since the Building Blocks, Biological Pathways and Networks program is no longer supported by the Common Fund, the program website is being maintained as an archive and will not be updated on a regular basis. 

 

 

 

 

DATASHEETS

Fluorogenic dye datasheets

  • Thiazole Orange with 2 unit PEG tail - TO1-2p
    view PDF
  • Malachite Green with 2 unit PEG tail - MG-2p-NH2 
    (membrane impermeant)  view PDF
  • Malachite Green with 11 unit PEG tail- MG-11p-NH2 
    (membrane impermeant) view PDF
  • modified Malachite Green with 11 unit PEG tail- MG-D-11p-NH2 
    (membrane impermeant) view PDF
  • Malachite Green Ester - MG-Ester 
    (membrane permeant) view PDF

 

COMPUTATIONAL & ANALYSIS

FoxS Fast SAXS profile computation with Debye formula
LigScore Pose & Rank - a web server for scoring protein-ligand complexes
ModEval Web server to model evaluation using TSVMod, DOPE and GA341
ModLoop Server for modeling of loops in protein structures
ModWeb Server for automated comparative protein structure modeling
PCSS Predicts peptide recognition specificity based on sequence and structure features
Flex-EM A method for fitting and refining a component structure within its map at intermediate resolution
IMP Integrative Modeling Platform
MODELLER Program for comparative protein structure modelling by satisfaction of spatial restraints
MDT MDT prepares a raw frequency table, given information from MODELLER alignments and/or PDB files

VECTOR AND SEQUENCE DATA

 
Primary scFv sequences

Vector map datasheets

  • General surface expression vector - pDisplayBlue view PDF
  • Surface expression HL1.1-TO1 (scFv1) - pDisplayB-scFv1  view PDF
  • General retroviral surface expression vector - pRetroDBlue  view PDF
  • Retroviral surface expression HL1.1-TO1 (scFv1) - pRetroDB-scFv1  view PDF
  • Random tagging retroviral vector - pStealthBlue view PDF
  • H6-PDGF fusion construct - pBabe H6-PDGFR TM-VACHT view PDF
  • General retroviral fusion protein expression vector - pBabeSacLac2 view PDF
Order Samples
 

The Clone Database (CD) currently includes approximately 3000 strains, many of which are tagged, and approximately 300 plasmids. Each strain is listed with details such as its descriptive and formal names, genotype, genetic background, and the location of frozen stock. The CD can be assessed via the NCDIR website here or directly here . If you have any problems accessing the website please contact Hua Jiang (hjiang01@mail.rockefeller.edu) Project Manger NCDIR.

The Standard Reference Materials (SRMs) serve a variety of clinical measurement needs. The frozen human sera and plasma materials can be used for helpful for metabolic profiling. NIST reference Standard for Serum and Plasma can be procured using the URL below.

SRM for Human Serum (frozen, liquid, and lyophilized forms)

 

 
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