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Links tagged with 'nucleic acids'

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ClustalWTool Content

http://www.ebi.ac.uk/clustalw/

Sequence Comparison > Multiple Sequence Alignments

Standard multiple sequence alignment.

NAR Web Server Issue 2003
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tagsalgorithms amino acid sequence globins molecular sequence data nucleic acids phylogeny protein sequence analysis proteins secondary protein structure sensitivity and specificity sequence alignment sequence analysis

ClustalXTool Content

http://www.clustal.org/clustal2/

Sequence Comparison > Multiple Sequence Alignments

Clustal X is a version of the Clustal W multiple sequence alignment program with a graphical interface. The display colours allow conserved features to be highlighted for easy viewing in the alignment. It is available for several platforms, including Windows, Macintosh PowerMac, Linux and Solaris.

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tagsalgorithms amino acid sequence animals data display humans molecular sequence data nucleic acid sequence homology nucleic acids phylogeny protein sequence analysis sequence alignment sequence analysis transcription factor tfiib transcription factors

EBI ToolsTool Content

http://www.ebi.ac.uk/Tools/webservices/

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

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.

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

MASCOT (Matrix Science)Tool Content

http://www.matrixscience.com/

Protein > Biochemical Features
Protein > Proteomics

Protein identification by peptide mass; excellent documentation; incorporates code from MOWSE but allows more search methods on more sequence databases.

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tagsamino acid sequence amino acids factual databases mass spectrometry molecular sequence data molecular weight nucleic acids probability protein biosynthesis proteins

MolAxisTool Content

http://bioinfo3d.cs.tau.ac.il/MolAxis

Protein > 3-D Structural Features

The MolAxis web server allows users to identify transmembrane channels in proteins and channels in macromolecules that connect buried cavities to the external surface. Gating residues, channel lining residues and a 3D graphical representation of the channel surface are output.

NAR Web Server Issue 2008
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tagsalgorithms binding sites biological transport computational biology membrane proteins molecular models nucleic acids

MONSTERTool Content

http://monster.northwestern.edu/

Protein > 3-D Structure Retrieval/Viewing
Protein > Biochemical Features

MONSTER takes a PDB structure file as input, and predicts non-bonding interactions that have the potential to provide stability to the molecule. The output can be viewed or downloaded as XML or text, or can be viewed as a 3D structure or a 2D diagram. There is also a good tutorial available at the site.

This content is being maintained by samseaver.

NAR Web Server Issue 2004
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tagsmacromolecular substances molecular structure nucleic acids peptides proteins

MoViESTool Content

http://ang.cz3.nus.edu.sg/cgi-bin/prog/norm.pl

DNA > Structure and Sequence Feature Detection
Protein > Annotation and Function
Protein > Molecular Dynamics and Docking
RNA > Structure Prediction, Visualization, and Design

MoViES (Molecular Vibrations Evaluation Server) allows the computation of the vibrational and thermal fluctuations dynamics for the chemical bonds of biomolecules. The server takes as input a structure file in PDB format and returns results by email. Analysis of vibrational motions and thermal fluctuational dynamics can give insights into the functional properties of both proteins and nucleic acids.

NAR Web Server Issue 2004
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tagscomputational biology hydrogen bonding nucleic acids proteins thermodynamics vibration

PBILTool Content

http://pbil.univ-lyon1.fr/

Education > Directories and Portals

Pole Bio-Informatique Lyonnais (PBIL) provides access to sequence databanks (EMBL, GenBank, SWISS-PROT, PIR) and to many tools of nucleic acid and protein sequence analyses.

NAR Web Server Issue 2003
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tagsdna sequence analysis genetic databases molecular models nucleic acids protein conformation protein sequence analysis proteins rna sequence analysis secondary protein structure sequence alignment sequence homology systems integration

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

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

SEMTool Content

http://dicsoft2.physics.iisc.ernet.in/sem/

Protein > 3-D Structure Retrieval/Viewing
RNA > Structure Prediction, Visualization, and Design

Symmetry Equivalent Molecules (SEM) is a tool for generating symmetrically equivalent three-dimensional (3D) molecules. This web based tool incorporates the graphics package of RASMOL for visualization; some configuration necessary.

NAR Web Server Issue 2003
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tagsmolecular models nucleic acids proteins

SPACETool Content

http://ligin.weizmann.ac.il/space/

Protein > 3-D Structure Prediction

SPACE (Structure Prediction and Analysis based on Complementarity with Environment) is a suite of tools for predicting and analyzing structures of biomolecules and their complexes.

NAR Web Server Issue 2005
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tagsalgorithms amino acids automation bacterial proteins binding sites biotin computational biology factual databases formycins hydrogen bonding ligands molecular conformation molecular models molecular structure nucleic acids point mutation protein binding protein conformation protein databases proteins ribonucleotides ricin site-directed mutagenesis solvents streptavidin thermodynamics water x-ray crystallography

The European Bioinformatics Institute (EBI)Database Content

http://www.ebi.ac.uk

DNA > Databases
DNA > Sequence Retrieval and Submission
Education > Community
Education > Directories and Portals
Expression > Databases
Expression > Transcript Expression Analysis
Human Genome > Databases
Literature > Databases
Model Organisms > Databases
Other Molecules > Databases
Protein > 3-D Structure Retrieval/Viewing
Protein > Annotation and Function
Protein > Databases
Protein > Domains and Motifs
Protein > Sequence Retrieval
RNA > Databases
Sequence Comparison > Multiple Sequence Alignments
Sequence Comparison > Similarity Searching

The European Bioinformatics Institute (EMBL-EBI) provides access to a comprehensive, integrated set of biological data. Resources include information on genes, genomes, proteins, expression, literature, and molecular interactions as well as many other useful resources.

NAR Database Issue 2010NAR Web Server Issue 2004
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tagsalgorithms animals biology computational biology europe gene expression profiling genetic databases humans nucleic acid databases nucleic acids phylogeny protein databases proteins sequence analysis sequence homology
setsEuropean Bioinformatics Institute (EBI)

WebFEATURETool Content

http://feature.stanford.edu/webfeature/

Protein > 3-D Structural Features
Protein > Domains and Motifs
RNA > Motifs
RNA > Structure Prediction, Visualization, and Design

WebFEATURE is a structural analysis tool for identifying 3D physiochemical motifs in molecular structures.

NAR Web Server Issue 2003
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tagsalgorithms bayes theorem binding sites calcium calcium-binding proteins computational biology factual databases genomics likelihood functions macromolecular substances molecular models molecular structure nucleic acid conformation nucleic acids protein conformation proteins reproducibility of results sensitivity and specificity statistical models