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Links tagged with 'dimerization'

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Found 6 links

Displaying 6 links

GRAMM-XTool Content

http://vakser.bioinformatics.ku.edu/resources/gramm/grammx

Protein > Molecular Dynamics and Docking

GRAMM-X is a protein docking server.

NAR Web Server Issue 2006
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tagsalgorithms antigen-antibody complex automation binding sites computational biology computer simulation dimerization evaluation studies as topic influenza virus hemagglutinin glycoproteins ligands macromolecular substances molecular conformation molecular models multiprotein complexes protein conformation protein databases protein folding protein interaction mapping protein structural homology proteomics reproducibility of results statistical models tertiary protein structure viral antibodies

PDATool Content

http://dbb.nhri.org.tw/primer/

DNA > Tools For the Bench

Primer Design Assistant (PDA) is a PCR primer design tool that will accept batch submissions of query sequences.

NAR Web Server Issue 2003
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tagsdimerization dna primers dna sequence analysis gc rich sequence nucleic acid conformation nucleic acid denaturation polymerase chain reaction thermodynamics

PDB_HydroTool Content

http://lorentz.immstr.pasteur.fr/solvate_mutate.php

Protein > 3-D Structural Features
Protein > Biochemical Features

PDB_Hydro provides tools for mutating and solvating structures of biological macromolecules like proteins or DNA. It identifies strongly and poorly solvated exposed surfaces of structures in an effort to help identify potential interaction zones.

NAR Web Server Issue 2006
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tagsbinding sites dimerization lipids mathematical computing membrane proteins nucleic acids protein conformation protein databases proteins solvents static electricity water

ProtCIDDatabase Content

http://dunbrack2.fccc.edu/protcid

Protein > Databases

The protein common interface database (ProtCID) is a database that contains clusters of similar homodimeric and heterodimeric interfaces observed in multiple crystal forms (CFs). In ProtCID, protein chains in the protein data bank (PDB) are grouped based on their PFAM domain architectures. For a single PFAM architecture, all the dimers present in each CF are constructed and compared with those in other CFs that contain the same domain architecture. Interfaces occurring in two or more CFs comprise an interface cluster in the database. The same process is used to compare heterodimers of chains with different domain architectures. Our data therefore provide an independent check on publicly available annotations of the structures of biological interactions for PDB entries. Coordinates for all interfaces in a cluster are downloadable for further analysis.

This content is being maintained by dunbrack.

NAR Database Issue 2011
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tagsamino acid sequence homology dimerization molecular models phylogeny protein databases protein interaction domains and motifs protein interaction mapping proteins x-ray crystallography

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

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