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Links tagged with 'hydrophobic and hydrophilic interactions'

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Found 11 links

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CAMPOTool Content

http://schubert.bio.uniroma1.it/CAMPO/index.html

Sequence Comparison > Analysis of Aligned Sequences

CAMPO is a tool to analyze conserved regions from a multiple sequence alignment

NAR Web Server Issue 2005
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tagscomputational biology hydrophobic and hydrophilic interactions molecular evolution molecular models potassium channels protein conformation proteins trypsin inhibitors

CHC_FINDTool Content

http://schubert.bio.uniroma1.it/CHC_FIND/index.html

Protein > 3-D Structural Features
Protein > 3-D Structure Comparison
Sequence Comparison > Analysis of Aligned Sequences

CHC_FIND is a tool to analyze conserved hydrophobic contacts (CHC) from multiple structural alignments. In addition to a multiple sequence alignment, a structural alignment which provides the superposition of structurally conserved regions (SCRs) (i.e., results from SCR_FIND) needs to be provided.

NAR Web Server Issue 2005
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tagscomputational biology hydrophobic and hydrophilic interactions molecular evolution molecular models potassium channels protein conformation proteins trypsin inhibitors

MolSurferTool Content

http://projects.villa-bosch.de/dbase/molsurfer/

Protein > 3-D Structural Features
Protein > Biochemical Features
Protein > Interactions, Pathways, Enzymes

Molsurfer is a graphical tool that links a 2D projection of a macromolecular interface to a 3D view of the macromolecular structures. It can be used to study protein-protein and protein-DNA/RNA interfaces.

NAR Web Server Issue 2003
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tagsamino acid sequence animals dna hydrophobic and hydrophilic interactions ligands macromolecular substances molecular models molecular sequence data protein conformation protein databases proteins rna static electricity

PI2PETool Content

http://pipe.scs.fsu.edu/

Protein > 3-D Structural Features
Protein > Biochemical Features
Protein > Interactions, Pathways, Enzymes

PI2PE (Protein Interface/Interior Prediction Engine) consists of three predictors (WESA, cons-PPISP, and DISPLAR) for predicting solvent accessibility and interface residues from the structure of a protein-binding or DNA-binding protein.

NAR Web Server Issue 2007
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tagsalgorithms amino acid sequence amino acid sequence homology amino acids animals artificial intelligence binding sites biomolecular nuclear magnetic resonance computational biology computer simulation dna dna-binding proteins factual databases genomic library hydrophobic and hydrophilic interactions membrane proteins molecular conformation molecular models molecular sequence data mutation mycoplasma neural networks (computer) open reading frames prions protein binding protein conformation protein sequence analysis proteins quaternary protein structure reproducibility of results rna-binding proteins saccharomyces cerevisiae secondary protein structure sequence alignment solvents

POPSTool Content

http://mathbio.nimr.mrc.ac.uk/wiki/POPS

Protein > 3-D Structural Features

Parameter OPtimised Surfaces (POPS) is an algorithm to calculate accessible surfaces areas at atomic and residue level.

NAR Web Server Issue 2003
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tagsalgorithms amino acids hydrophobic and hydrophilic interactions macromolecular substances molecular models molecular structure nucleic acid conformation nucleic acids protein binding protein conformation proteins ribosomal proteins ribosomal rna ribosomes solvents time factors transfer rna

PreBITool Content

http://pre-s.protein.osaka-u.ac.jp/prebi/

Protein > 3-D Structural Features

Prediction of Biological Interfaces (PreBI) is a server for predicting protein-protein interfaces in protein structures that maximizes both the degree of complementarity and the interface area.

NAR Web Server Issue 2006
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tagsdatabase management systems humans hydrophobic and hydrophilic interactions molecular models multiprotein complexes protein conformation protein databases proteins static electricity three-dimensional imaging x-ray crystallography

QgridTool Content

http://www.netasa.org/qgrid/index.html

Protein > Biochemical Features

Server which provides cluster tree diagrams of a protein based on the charged atoms or hydrophobicity of each of its residues. The diagram allows for visual inspection of the distribution of hydrophobic and charged regions in proteins.

NAR Web Server Issue 2004
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tagshydrophobic and hydrophilic interactions ions proteins

Scooby-domainTool Content

http://ibivu.cs.vu.nl/programs/scoobywww/

Protein > Domains and Motifs

Scooby-domain (sequence hydrophobicity predicts domains) is a method to identify globular domains in protein sequence, based on the observed lengths and hydrophobicities of domains from proteins with known tertiary structure.

NAR Web Server Issue 2005
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tagshydrophobic and hydrophilic interactions protein sequence analysis proteins tertiary protein structure

SCR_FINDTool Content

http://schubert.bio.uniroma1.it/SCR_FIND/

Protein > 3-D Structure Comparison
Sequence Comparison > Analysis of Aligned Sequences

SCR_FIND is a tool to analyze structurally conserved regions (SCRs) from superimposed structures and multiple sequence alignments.

NAR Web Server Issue 2005
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tagscomputational biology hydrophobic and hydrophilic interactions molecular evolution molecular models potassium channels protein conformation proteins trypsin inhibitors

SrideTool Content

http://sride.enzim.hu/

Protein > 3-D Structural Features

Sride is a tool for identificating stabilizing residues in protein structure.

NAR Web Server Issue 2005
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tagsamino acids conserved sequence hydrophobic and hydrophilic interactions molecular evolution molecular models pliability protein conformation protein folding proteins secondary protein structure temperature tertiary protein structure thermodynamics

TMH BenchmarkTool Content

http://cubic.bioc.columbia.edu/services/tmh_benchmark/

Protein > 2-D Structure Prediction
Protein > Localization and Targeting

The Transmembrane Helix (TMH) Benchmark server provides a standard benchmark evaluation for helical trans-membrane prediction methods.

NAR Web Server Issue 2003
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tagsalgorithms animals computational biology hydrophobic and hydrophilic interactions membrane proteins molecular models protein folding protein sequence analysis reproducibility of results secondary protein structure sensitivity and specificity