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Links tagged with 'quaternary protein structure'

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Human Protein Reference DatabaseDatabase Content

http://www.hprd.org/ [open in a new window]

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Protein > Networks & Interactions, Pathways and Enzymes
Protein > Proteomics

The Human Protein Reference Database (HPRD) is a centralized resource for information about human proteins, their interactions with other human proteins, and protein-disease relationships. The information contained in HPRD is curated by experts, who manually extract it from published literature.

links directory index: 953
TitlePublication YearGoogle Scholar Citation Count
Human protein reference database as a discovery resource for proteomics2004264
Development of human protein reference database as an initial platform for approaching systems biology in humans2003689
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external linksLink on Wikipedia
tagsbrca1 protein computational biology controlled vocabulary disease genomics humans macromolecular substances medical genetics post-translational protein processing protein binding protein databases protein interaction mapping proteins proteome proteomics quaternary protein structure substrate specificity tertiary protein structure

JEvTraceTool Content

http://www.cmpharm.ucsf.edu/~marcinj/JEvTrace/ [open in a new window]

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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.

links directory index: 845
TitlePublication YearGoogle Scholar Citation Count
JEvTrace: refinement and variations of the evolutionary trace in JAVA200218
An evolutionary trace method defines binding surfaces common to protein families1996827
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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

PI2PETool Content

http://pipe.scs.fsu.edu/ [open in a new window]

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Protein > 3-D Structural Features
Protein > Biochemical Features
Protein > Networks & Interactions, Pathways and 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.

links directory index: 473
TitlePublication YearGoogle Scholar Citation Count
PI2PE: protein interface/interior prediction engine200718
DISPLAR: an accurate method for predicting DNA-binding sites on protein surfaces200751
Prediction of solvent accessibility and sites of deleterious mutations from protein sequence200549
Prediction of interface residues in protein-protein complexes by a consensus neural network method: test against NMR data2005111
Fold recognition and accurate query-template alignment by a combination of PSI-BLAST and threading200136
Prediction of protein interaction sites from sequence profile and residue neighbor list2001208
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

STING MilleniumTool Content

http://luna.bioc.columbia.edu/SMS/STINGm/ [open in a new window]

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Protein > 3-D Structural Features
Protein > 3-D Structure Comparison
Protein > Annotation and Function
Protein > Biochemical Features
Protein > Phylogeny Reconstruction
Protein > Sequence Comparison

STING is a suite of tools for the analysis of protein sequence, structure, stability and function - and the relationships between them.

links directory index: 168
TitlePublication YearGoogle Scholar Citation Count
The Diamond STING server200522
STING Report: convenient web-based application for graphic and tabular presentations of protein sequence, structure and function descriptors from the STING database200516
STING Contacts: a web-based application for identification and analysis of amino acid contacts within protein structure and across protein interfaces200415
Defining 3D residue environment in protein structures using SCORPION and FORMIGA20043
ConSSeq: a web-based application for analysis of amino acid conservation based on HSSP database and within context of structure200415
STING Millennium Suite: integrated software for extensive analyses of 3d structures of proteins and their complexes200422
JavaProtein Dossier: a novel web-based data visualization tool for comprehensive analysis of protein structure200422
STING Millennium: A web-based suite of programs for comprehensive and simultaneous analysis of protein structure and sequence200344
Analysis of structural and physico-chemical parameters involved in the specificity of binding between alpha-amylases and their inhibitors20009
NAR Web Server Issue 2003NAR Web Server Issue 2005
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tagsacid anhydride hydrolases algorithms alpha-amylases amino acid sequence amino acid sequence homology amino acids animals beetles binding sites chemical models chymotrypsin color computational biology computer simulation conserved sequence enzyme inhibitors fabaceae hiv integrase hydrogen bonding lectins medicinal plants molecular cloning molecular models molecular sequence data molecular structure online systems ovomucin plant lectins plant proteins proprotein convertases protein binding protein conformation protein databases protein interaction mapping protein sequence analysis protein structural homology proteins quaternary protein structure recombinant proteins sequence alignment structure-activity relationship systems integration x-ray crystallography

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