> Tag > Links tagged with 'amino acid substitution'

Links tagged with 'amino acid substitution'

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MutDBDatabase Content

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

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DNA > Annotations
DNA > Sequence Polymorphisms

MutDB is a database that associates protein structural information with mutations and polymorphisms in gene sequences. The data is derived from dbSNP and Swiss-Prot, and can be browsed by gene name or searched by keyword or by various identifiers.

links directory index: 64
TitlePublication YearGoogle Scholar Citation Count
MutDB services: interactive structural analysis of mutation data200533
MutDB: annotating human variation with functionally relevant data200331
NAR Web Server Issue 2005
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tagsamino acid substitution database management systems documentation genetic databases genetic predisposition to disease genetic variation human genome humans molecular models mutation phenotype protein conformation protein databases protein sequence analysis proteins sequence alignment single nucleotide polymorphism structure-activity relationship

ProtTestTool Content

http://darwin.uvigo.es/software/prottest_server.html [open in a new window]

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Protein > Phylogeny Reconstruction

ProtTest is a program that determines the best-fit model of evolution, among a set of candidate models, for a given protein sequence alignment.

links directory index: 1077
TitlePublication YearGoogle Scholar Citation Count
ProtTest: selection of best-fit models of protein evolution20051077
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tagsalgorithms amino acid sequence amino acid substitution amino acids computer simulation dna mutational analysis genetic models humans molecular evolution molecular models molecular sequence data phylogeny protein sequence analysis proteins site-directed mutagenesis structure-activity relationship

RevTransTool Content

http://www.cbs.dtu.dk/services/RevTrans/ [open in a new window]

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Sequence Comparison > Multiple Sequence Alignments

RevTrans takes a set of DNA sequences, virtually translates them, aligns the peptide sequences, and uses this as a scaffold for constructing the corresponding DNA multiple alignment.

links directory index: 180
TitlePublication YearGoogle Scholar Citation Count
RevTrans: Multiple alignment of coding DNA from aligned amino acid sequences2003180
NAR Web Server Issue 2003
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tagsamino acid substitution base sequence codon dna sequence analysis mutation protein sequence analysis sequence alignment

SDM Tool Content

http://www-cryst.bioc.cam.ac.uk/~sdm/sdm.php [open in a new window]

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Protein > 3-D Structural Features

Site Directed Mutator (SDM) is a web server for predicting effects of mutations on protein stability and function. Users input a wild type structure and the position and amino acid type of the mutation. An environment specific amino acid substitution frequency for homologous protein families is used to calculate a stability score.

links directory index: 7
TitlePublication YearGoogle Scholar Citation Count
SDM--a server for predicting effects of mutations on protein stability and malfunction20117
NAR Web Server Issue 2011
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tagsamino acid substitution disease humans mutation protein conformation protein stability proteins thermodynamics

SelectonTool Content

http://selecton.tau.ac.il/ [open in a new window]

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DNA > Phylogeny Reconstruction
Sequence Comparison > Analysis of Aligned Sequences

Selecton is a server for the identification of site-specific positive selection and purifying selection.

links directory index: 129
TitlePublication YearGoogle Scholar Citation Count
Selecton 2007: advanced models for detecting positive and purifying selection using a Bayesian inference approach200775
Selecton: a server for detecting evolutionary forces at a single amino-acid site200554
NAR Web Server Issue 2007
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tagsalgorithms amino acid sequence amino acid substitution amino acids animals bayes theorem computational biology computer simulation dna mutational analysis genetic models hiv protease humans molecular evolution molecular models molecular sequence data phylogeny protein sequence analysis proteins site-directed mutagenesis structure-activity relationship

WurstTool Content

http://www.zbh.uni-hamburg.de/wurst/ [open in a new window]

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Protein > 3-D Structure Prediction

Wurst is a protein structure prediction tool that uses threading, aligning submitted sequences to thousands of PDB template structures.

links directory index: 42
TitlePublication YearGoogle Scholar Citation Count
Wurst: a protein threading server with a structural scoring function, sequence profiles and optimized substitution matrices200442
NAR Web Server Issue 2004
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tagsamino acid substitution molecular models protein conformation protein sequence analysis

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