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Links tagged with 'zinc fingers'

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enoLOGOSTool Content

http://biodev.hgen.pitt.edu/enologos/

Sequence Comparison > Alignment Editing and Visualization

enoLOGOS creates sequence logos based on a variety of input, including sequence alignments, probability and alignment matrices and energy measurements.

NAR Web Server Issue 2005
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tagsamino acids binding sites dna sequence analysis dna-binding proteins sequence alignment zinc fingers

JEvTraceTool Content

http://www.cmpharm.ucsf.edu/~marcinj/JEvTrace/

Protein > 3-D Structure Comparison
Protein > 3-D Structure Retrieval/Viewing
Protein > Annotation and Function
Protein > Phylogeny Reconstruction
Sequence Comparison > Analysis of Aligned Sequences

Jevtrace is a tool that combines multiple sequence alignments, phylogenetic, and structural data for identification of functional sites in proteins.

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tagsamino acid sequence amino acid sequence homology animals bacterial proteins binding sites carrier proteins conserved sequence dna-binding proteins factual databases genetic variation glucocorticoid receptors haemophilus influenzae humans molecular evolution molecular models molecular sequence data mutation phylogeny protein conformation proteins quaternary protein structure rats rna-binding proteins sequence alignment src homology domains streptococcus pneumoniae zinc fingers

ReadOutTool Content

http://gibk26.bio.kyutech.ac.jp/jouhou/readout/

DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation
Protein > 3-D Structural Features

Readout is a server for the calculation of direct and indirect readout energy Z-scores which estimate the degree of sequence specificity of the protein-DNA complex. Readout can be useful for checking the quality of protein-DNA interactions in three dimensional (3D) structures.

NAR Web Server Issue 2006
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tagsbacterial proteins base sequence binding sites biological models dimerization dna dna primers dna-binding proteins endonucleases gene expression regulation genetic promoter regions glucocorticoid receptors hydrogen bonding macromolecular substances metalloproteins molecular models nucleic acid conformation protein binding protein conformation protein kinases protein subunits proteins repressor proteins saccharomyces cerevisiae proteins tertiary protein structure thermodynamics type ii site-specific deoxyribonucleases viral proteins viral regulatory and accessory proteins water zinc fingers

ZiFiTTool Content

http://bindr.gdcb.iastate.edu/ZiFiT/

DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation

ZiFiT (Zinc Finger Targeter) assists in the design of zinc finger proteins that can bind to specific DNA sequences. ZiFiT has been updated to integrate additional tools and resources including scoring schemes for modular assembly, an interface with the Zinc Finger Database of engineered ZFPs, and direct query of NCBI BLAST servers for identification of potential off-target sites within a host genome.

NAR Web Server Issue 2007NAR Web Server Issue 2010
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tagsbinding sites computational biology deoxyribonucleases dna sequence analysis dna-binding proteins humans protein conformation protein engineering secondary protein structure tertiary protein structure transcription factors zinc fingers

Zinc Finger ToolsTool Content

http://www.scripps.edu/mb/barbas/zfdesign/zfdesignhome.php

DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation

Zinc Finger Tools provides several tools for selecting zinc finger protein target sites and for designing the proteins that will target them.

NAR Web Server Issue 2006
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tagsamino acid sequence animals base sequence binding sites biomolecular nuclear magnetic resonance cell line combinatorial chemistry techniques computer simulation deoxyribonuclease i deoxyribonucleases dna dna primers dna sequence analysis dna-binding proteins down-regulation drug design enzyme-linked immunosorbent assay epidermal growth factor receptor erbb genes erbb-1 genes erbb-2 genes erbb-2 receptor erbb-3 receptor flow cytometry gene expression profiling gene expression regulation gene library gene targeting genetic promoter regions genetic transcription green fluorescent proteins histidine human genome humans kidney luminescent proteins lysine mice molecular cloning molecular models molecular sequence data mutation nucleic acid conformation oligonucleotides peptide library pliability polymerase chain reaction protein conformation protein engineering proteomics recombinant proteins reporter genes retroviridae secondary protein structure sequence analysis site-directed mutagenesis substrate specificity tertiary protein structure transcription factors transfection up-regulation x-ray crystallography zinc fingers