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Links tagged with 'proteins'

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Found 312 links

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DISULFINDTool Content

http://disulfind.dsi.unifi.it/ [open in a new window]

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Protein > Biochemical Features
Protein > Sequence Features

DISULFIND is a server for predicting the disulfide bonding state of cysteines and their disulfide connectivity given a protein sequence.

This content is being maintained by paolo.frasconi.

links directory index: 252
TitlePublication YearGoogle Scholar Citation Count
MetalDetector v2.0: predicting the geometry of metal binding sites from protein sequence20111
MetalDetector: a web server for predicting metal-binding sites and disulfide bridges in proteins from sequence200825
DISULFIND: a disulfide bonding state and cysteine connectivity prediction server200689
Disulfide connectivity prediction using recursive neural networks and evolutionary information2004137
NAR Web Server Issue 2006
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tagsalgorithms amino acid sequence artificial intelligence binding sites computational biology computer simulation cysteine disulfide bridges disulfides gene expression profiling histidine machine learning metalloproteins molecular evolution molecular sequence data neural networks (computer) protein binding protein databases protein sequence analysis proteins sequence alignment

DOMACTool Content

http://casp.rnet.missouri.edu/domac.html [open in a new window]

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Protein > 3-D Structure Comparison
Protein > 3-D Structure Prediction
Protein > Domains and Motifs
Sequence Comparison > Similarity Searching and Classification

DOMAC is an accurate, protein domain prediction server that integrates homology modeling, domain parsing, and ab initio methods together.

links directory index: 156
TitlePublication YearGoogle Scholar Citation Count
DOMAC: an accurate, hybrid protein domain prediction server200731
A machine learning information retrieval approach to protein fold recognition2006125
NAR Web Server Issue 2007
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tagsalgorithms amino acid sequence amino acid sequence homology animals artificial intelligence computational biology genetic databases humans molecular models molecular sequence data normal distribution protein databases protein folding protein sequence analysis proteins secondary protein structure sensitivity and specificity sequence alignment statistical models tertiary protein structure

DSSPcontTool Content

http://cubic.bioc.columbia.edu/services/DSSPcont/ [open in a new window]

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Protein > 2-D Structure Prediction

DSSPcont automates protein secondary structure prediction from PDB structures to reflect structural variations due to thermal fluctuations.

links directory index: 60
TitlePublication YearGoogle Scholar Citation Count
DSSPcont: Continuous secondary structure assignments for proteins200360
NAR Web Server Issue 2003
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tagsalgorithms amino acid sequence biomolecular nuclear magnetic resonance hydrogen bonding molecular models proteins secondary protein structure

EBI ToolsTool Content

http://www.ebi.ac.uk/Tools/webservices/ [open in a new window]

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Computer Related > Web Services
DNA > Sequence Retrieval and Submission
Education > Directories and Portals
Literature > Search Tools
Protein > 3-D Structure Comparison
Protein > Domains and Motifs
Protein > Sequence Retrieval
RNA > Sequence Retrieval
Sequence Comparison > Multiple Sequence Alignments
Sequence Comparison > Similarity Searching and Classification

EBI Tools is a project that aims to provide programmatic access to the various databases and retrieval and analysis services that the European Bioinformatics Institute (EBI) provides through Simple Object Access Protocol (SOAP) and other related web service technologies.

links directory index: 250
TitlePublication YearGoogle Scholar Citation Count
Web services at the European Bioinformatics Institute-2009200935
Web services at the European bioinformatics institute2007143
SOAP-based services provided by the European Bioinformatics Institute200554
Public web-based services from the European Bioinformatics Institute200418
NAR Web Server Issue 2005NAR Web Server Issue 2007NAR Web Server Issue 2009
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tagsbibliographic databases biotechnology computational biology europe genetic databases nucleic acids protein sequence analysis proteins sequence alignment sequence analysis sequence homology systems integration

eF-seekTool Content

http://ef-site.hgc.jp/eF-seek/index.jsp [open in a new window]

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Protein > 3-D Structural Features
Protein > 3-D Structure Comparison

eF-seek predicts protein functional sites by searching for similar electrostatic potential and molecular surface shapes against eF-site, a database of electrostatic surfaces for representative ligand binding sites.

This content is being maintained by Kenta Nakai.

links directory index: 409
TitlePublication YearGoogle Scholar Citation Count
eF-seek: prediction of the functional sites of proteins by searching for similar electrostatic potential and molecular surface shape200727
Identification of the ligand binding sites on the molecular surface of proteins200547
eF-site and PDBjViewer: database and viewer for protein functional sites200472
Identification of protein biochemical functions by similarity search using the molecular surface database eF-site2003118
Protein informatics towards function identification200352
Identification of protein functions from a molecular surface database, eF-site200293
NAR Web Server Issue 2007
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tagsalgorithms antibodies binding sites biological models computational biology computer simulation database management systems ligands molecular models protein conformation protein databases protein folding proteins proteomics s-adenosylhomocysteine static electricity structure-activity relationship three-dimensional imaging trypsin

ELMTool Content

http://elm.eu.org/ [open in a new window]

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Eukaryotic Linear Motif (ELM) resource is a tool for predicting eukaryotic protein functional sites that report domains, motifs, and sequence patterns based on the input sequence.

links directory index: 1035
TitlePublication YearGoogle Scholar Citation Count
ELM--the database of eukaryotic linear motifs201215
ELM: the status of the 2010 eukaryotic linear motif resource201090
ELM server: A new resource for investigating short functional sites in modular eukaryotic proteins2003465
ELM server: A new resource for investigating short functional sites in modular eukaryotic proteins2003465
NAR Database Issue 2010NAR Web Server Issue 2003
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external linksLink on Wikipedia
tagsamino acid motifs amino acid sequence amino acid sequence homology animals computational biology computer graphics disease eukaryota eukaryotic cells genetic databases humans information storage and retrieval internet molecular sequence data nucleic acid databases protein databases protein sequence analysis proteins software tertiary protein structure user-computer interface viral proteins

ELMTool Content

http://elm.eu.org/ [open in a new window]

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Eukaryotic Linear Motif (ELM) resource is a tool for predicting eukaryotic protein functional sites that report domains, motifs, and sequence patterns based on the input sequence.

links directory index: 1035
TitlePublication YearGoogle Scholar Citation Count
ELM--the database of eukaryotic linear motifs201215
ELM: the status of the 2010 eukaryotic linear motif resource201090
ELM server: A new resource for investigating short functional sites in modular eukaryotic proteins2003465
ELM server: A new resource for investigating short functional sites in modular eukaryotic proteins2003465
NAR Database Issue 2010NAR Web Server Issue 2003
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external linksLink on Wikipedia
tagsamino acid motifs amino acid sequence amino acid sequence homology animals computational biology computer graphics disease eukaryota eukaryotic cells genetic databases humans information storage and retrieval internet molecular sequence data nucleic acid databases protein databases protein sequence analysis proteins software tertiary protein structure user-computer interface viral proteins

ElNemoTool Content

http://igs-server.cnrs-mrs.fr/elnemo/start.html [open in a new window]

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Protein > 3-D Structure Retrieval/Viewing
Protein > Molecular Dynamics and Docking

ElNemo (The Elastic Network Model) is a tool for predicting the possible movements (ie. conformational changes and other structural changes) of macromolecules. This tool allows users to compute, visualize, and analyse low-frequency normal modes of a protein.

links directory index: 293
TitlePublication YearGoogle Scholar Citation Count
ElNemo: a normal mode web server for protein movement analysis and the generation of templates for molecular replacement2004293
NAR Web Server Issue 2004
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tagsmolecular models motion protein conformation proteins x-ray crystallography

EMAGEDatabase Content

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

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Expression > Databases
Model Organisms > Databases

EMAGE is a freely available online database of in situ gene expression patterns in the developing mouse embryo. Gene expression domains from raw images are extracted and integrated spatially into a set of standard 3D virtual mouse embryos at different stages of development, which allows data interrogation by spatial methods. An anatomy ontology is also used to describe sites of expression, which allows data to be queried using text-based methods. Data coverage has been increased by sourcing from a greater selection of journals.

links directory index: 30
TitlePublication YearGoogle Scholar Citation Count
The BioMart interface to the eMouseAtlas gene expression database EMAGE20112
EMAGE mouse embryo spatial gene expression database: 2010 update201028
NAR Database Issue 2010
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external linksLink on Wikipedia
tagsaccess to information animals automation computational biology database management systems developmental gene expression regulation embryonic development factual databases gene expression gene expression profiling genetic databases immunohistochemistry in situ hybridization information storage and retrieval internet mammalian embryo messenger rna mice molecular imaging nucleic acid databases programming languages proteins reporter genes software user-computer interface

EMDataBank.orgDatabase Content

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

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Other Molecules > Databases
Protein > Databases

EMDataBank.org is a resource for deposition and retrieval of cryoEM maps, models and associated metadata. The resource unifies public access to the two major archives containing EM-based structural data: EM Data Bank (EMDB) and Protein Data Bank (PDB), and facilitates use of EM structural data of macromolecules and macromolecular complexes.

links directory index: 15
TitlePublication YearGoogle Scholar Citation Count
EMDataBank.org: unified data resource for CryoEM201115
NAR Database Issue 2011
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tagscryoelectron microscopy factual databases macromolecular substances molecular models protein databases proteins

eShadowTool Content

http://eshadow.dcode.org/ [open in a new window]

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Sequence Comparison > Analysis of Aligned Sequences
Sequence Comparison > Multiple Sequence Alignments

A tool for phylogenetic shadowing of multiple sequences from closely related species. This analyses of multiple sequence alignments can be used to predict putative functional elements.

links directory index: 64
TitlePublication YearGoogle Scholar Citation Count
eShadow: a tool for comparing closely related sequences200464
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tagsanimals computational biology conserved sequence exons genetic databases humans intergenic dna papio peptides proteins software design tertiary protein structure

ESLpredTool Content

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

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Protein > Localization and Targeting

ESLpred is a tool for predicting subcellular localization of proteins using support vector machines. The predictions are based on dipeptide and amino acid composition, and physico-chemical properties.

This content is being maintained by raghavagps.

links directory index: 182
TitlePublication YearGoogle Scholar Citation Count
ESLpred: SVM-based method for subcellular localization of eukaryotic proteins using dipeptide composition and PSI-BLAST2004182
NAR Web Server Issue 2004
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tagsartificial intelligence dipeptides eukaryotic cells protein databases proteins reproducibility of results

EVATool Content

http://cubic.bioc.columbia.edu/eva/ [open in a new window]

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Computer Related > Math and Statistics
Protein > 2-D Structure Prediction
Protein > 3-D Structure Prediction

EValuation of Automatic protein structure prediction; provides a continuous, automated, statistical analysis of structure prediction servers.

links directory index: 448
TitlePublication YearGoogle Scholar Citation Count
EVA: Evaluation of protein structure prediction servers2003143
EVA: continuous automatic evaluation of protein structure prediction servers2001183
EVA: large-scale analysis of secondary structure prediction2001122
NAR Web Server Issue 2003
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external linksLink on Wikipedia
tagsautomation protein conformation protein databases protein folding protein sequence analysis protein structural homology proteins reproducibility of results secondary protein structure sequence alignment

ExPASy 2-D PAGE databases and servicesResource Content

http://us.expasy.org/ch2d/2d-index.html [open in a new window]

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Expression > Protein Expression
Protein > Protein Expression

References to known 2-D PAGE database servers, as well as to 2-D PAGE related servers and services.

links directory index: 122
TitlePublication YearGoogle Scholar Citation Count
Federated two-dimensional electrophoresis database: a simple means of publishing two-dimensional electrophoresis data1996122
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tagsautomatic data processing factual databases gel electrophoresis humans proteins publishing reproducibility of results

ExPASy Molecular Biology ServerResource Content

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

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Education > Directories and Portals
Protein > Do-it-all Tools for Protein

ExPASy is the bioinformatics resource portal for access to programs and databases for the analysis of proteomics, genomics, phylogeny, systems biology, population genetics, transcriptomics etc.

links directory index: 1342
TitlePublication YearGoogle Scholar Citation Count
ExPASy: The proteomics server for in-depth protein knowledge and analysis20031342
NAR Web Server Issue 2003NAR Web Server Issue 2012
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tagsenzymes gel electrophoresis internet molecular models protein conformation protein databases protein sequence analysis proteins proteomics software systems integration user-computer interface

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