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Links tagged with 'protein engineering'

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CUPSATTool Content

http://cupsat.uni-koeln.de/

Protein > 3-D Structure Prediction
Protein > Biochemical Features

Cologne University Protein Stability Analysis Tool (CUPSAT) is a tool to analyse and predict protein stability changes upon point mutations (single amino acid mutations) for known protein structures.

NAR Web Server Issue 2006
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tagsmolecular structure point mutation protein databases protein denaturation protein engineering protein folding proteins secondary protein structure solvents

HotSpot WizardTool Content

http://loschmidt.chemi.muni.cz/hotspotwizard/

Protein > Annotation and Function
Protein > Biochemical Features
Protein > Sequence Comparison
Protein > Sequence Features

HotSpot Wizard is a web server for automatic identification of hot spots for engineering enzymes with substrate specificity, activity or enantioselectivity and for annotation of protein structures. Hot spots for mutagenesis are selected based on the integration of structural, functional and evolutionary information from various databases and tools.

NAR Web Server Issue 2009
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tagsbeta-lactamases glycoside hydrolases hydrolases phosphoric triester hydrolases protein engineering reproducibility of results

I-Mutant2.0Tool Content

http://gpcr2.biocomp.unibo.it/cgi/predictors/I-Mutant2.0/I-Mutant2.0.cgi

Protein > 3-D Structure Prediction
Protein > Molecular Dynamics and Docking

I-Mutant2.0 is a tool that can predict the effect of a single point mutation on protein stability from protein sequences or protein structures.

NAR Web Server Issue 2005
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tagsartificial intelligence point mutation protein engineering protein sequence analysis proteins tertiary protein structure thermodynamics

RosettaDesignTool Content

http://rosettadesign.med.unc.edu

Protein > 3-D Structure Prediction
Protein > Biochemical Features

RosettaDesign identifies low energy sequences for specified protein three dimensional (3D) structures and can been used to predict stable side chain conformations.

NAR Web Server Issue 2006
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tagsalgorithms amino acid sequence amino acid sequence homology bacterial proteins biomolecular nuclear magnetic resonance circular dichroism computational biology computer simulation crystallization dimerization dna-binding proteins guanidine kinetics magnetic resonance spectroscopy molecular models molecular sequence data monte carlo method mutagenesis mutation protein conformation protein databases protein denaturation protein engineering protein folding protein sequence analysis proteins secondary protein structure sequence alignment solubility temperature tertiary protein structure thermodynamics x-ray crystallography

SwissDockTool Content

http://www.swissdock.ch

Other Molecules > Small Molecules
Protein > Molecular Dynamics and Docking

SwissDock is a web server dedicated to the docking of small molecules on target proteins. It is based on the EADock DSS engine.

NAR Web Server Issue 2011
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tagsdrug design ligands molecular models protein conformation protein engineering

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