Links tagged with 'hydrophobic and hydrophilic interactions'

Institute of Enzymology Servers

http://www.enzim.hu/index.php?option=com_content&task=blogcategory&id=30&Itemid=... [open in a new window]

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A set of severs developed by the Institute of Enzymology that includes tools for transmembrane protein structure prediction and structural analyses.

links directory index: 2004

Title	Publication Year	Google Scholar Citation Count
TMDET: web server for detecting transmembrane regions of proteins by using their 3D coordinates	2005	46
IUPred: web server for the prediction of intrinsically unstructured regions of proteins based on estimated energy content	2005	392
The pairwise energy content estimated from amino acid composition discriminates between folded and intrinsically unstructured proteins	2005	235
BiSearch: primer-design and search tool for PCR on bisulfite-treated genomes	2005	52
PDB_TM: selection and membrane localization of transmembrane proteins in the protein data bank	2005	138
Transmembrane proteins in the Protein Data Bank: identification and classification	2004	138
Locating the stabilizing residues in (alpha/beta)8 barrel proteins based on hydrophobicity, long-range interactions, and sequence conservation	2004	43
SCide: identification of stabilization centers in proteins.	2003	0
Servers for sequence-structure relationship analysis and prediction	2003	5
On filtering false positive transmembrane protein predictions	2002	57
The HMMTOP transmembrane topology prediction server.	2001	0
Principles governing amino acid composition of integral membrane proteins: application to topology prediction	1998	795
Stabilization centers in proteins: identification, characterization and predictions	1997	103

NAR Web Server Issue 2003

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tagsalgorithms amino acid sequence amino acids binding sites capsid proteins cell line chemical models computational biology computer simulation conserved sequence cysteine database management systems dna methylation dna primers drug stability energy transfer genome genomics humans hydrophobic and hydrophilic interactions kringles lipid bilayers markov chains membrane proteins molecular models molecular sequence data neural networks (computer) oxidation-reduction pliability polymerase chain reaction protein binding protein conformation protein databases protein engineering protein folding protein sequence analysis proteins reproducibility of results secondary protein structure sequence alignment statistical models structure-activity relationship sulfites temperature tertiary protein structure thermodynamics tissue plasminogen activator

POPS

http://mathbio.nimr.mrc.ac.uk/wiki/POPS [open in a new window]

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

links directory index: 114

Title	Publication Year	Google Scholar Citation Count
POPS: A fast algorithm for solvent accessible surface areas at atomic and residue level	2003	49
Parameter optimized surfaces (POPS): analysis of key interactions and conformational changes in the ribosome	2002	65

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

Qgrid

http://www.netasa.org/qgrid/index.html [open in a new window]

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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.

links directory index: 5

Title	Publication Year	Google Scholar Citation Count
Qgrid: clustering tool for detecting charged and hydrophobic regions in proteins	2004	5

NAR Web Server Issue 2004

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tagshydrophobic and hydrophilic interactions ions proteins

TBBpred

http://www.imtech.res.in/raghava/tbbpred/ [open in a new window]

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Transmembrane Beta Barrel prediction server predicts the transmembrane Beta barrel regions in a given protein sequence. The server uses a forked strategy for predicting residues which are in transmembrane beta barrel regions. Prediction can be done based only on neural networks or based on statistical learning technique - SVM or combination of two methods.

This content is being maintained by raghavagps.

links directory index: 75

Title	Publication Year	Google Scholar Citation Count
Prediction of transmembrane regions of beta-barrel proteins using ANN- and SVM-based methods	2004	75

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tagsalgorithms ANN bacterial proteins beta-barrel cell membrane computational biology computer simulation hydrophobic and hydrophilic interactions machine learning techniques membrane proteins molecular evolution molecular models neural networks (computer) pliability secondary protein structure sensitivity and specificity sequence alignment solvents SVM thermodynamics transmembrane