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Links tagged with 'amino acid substitution'

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ConSeqTool Content

http://conseq.bioinfo.tau.ac.il/

Protein > 3-D Structural Features
Protein > Phylogeny Reconstruction
Protein > Sequence Features

ConSeq is a tool for predicting functionally and structurally important amino acid residues in protein sequences. The predictions are based on the assumptions that residues of functional importance are often conserved and solvent-accessible, and those of structural importance are often conserved and located in the protein core. A multiple sequence alignment is used to predict the relative solvent accessibility state and the evolutionary rate at each residue. ConSeq has been integrated into ConSurf (2010).

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tagsalgorithms amino acid sequence amino acid sequence homology amino acid substitution amino acids molecular sequence data protein sequence analysis proteins sequence alignment structure-activity relationship

ConSurfTool Content

http://consurf.tau.ac.il/

Protein > 3-D Structural Features
Sequence Comparison > Analysis of Aligned Sequences

The ConSurf server allows one to map levels of amino acid conservation to known protein structures in order to study areas of potential functional importance on the surface of the protein. A PDB file is required as input, and a multiple sequence alignment is optional. If an alignment is not provided, ConSurf will build one by performing a search for homologous sequences and then aligning them. ConSurf 2010 combines ConSurf and ConSeq for an easier, more intuitive interface.

NAR Web Server Issue 2005NAR Web Server Issue 2010
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tagsamino acid sequence amino acid sequence homology amino acid substitution amino acids bacterial proteins base sequence bayes theorem bcl-x protein conserved sequence molecular evolution molecular models nucleic acid conformation phylogeny potassium channels protein conformation protein databases protein sequence analysis proteins proto-oncogene proteins c-bcl-2 sequence alignment sequence analysis

CRASPTool Content

http://wwwmgs.bionet.nsc.ru/mgs/programs/crasp/

Sequence Comparison > Analysis of Aligned Sequences

Correlation analysis of the amino acid substitutions in protein sequences (CRASP) takes multiple alignments of amino acid sequences as input, and detects coordinated residue substitutions. These substitutions may suggest dependent evolution of functionally related pairs of amino acids.

NAR Web Server Issue 2004
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tagsamino acid substitution protein sequence analysis sequence alignment

HarmonyTool Content

http://caps.ncbs.res.in/harmony/

Protein > 3-D Structural Features
Protein > 3-D Structure Prediction
Sequence Comparison > Analysis of Aligned Sequences

Harmony is a server to assess the compatibility of an amino acid sequence with a proposed three-dimensional structure.

NAR Web Server Issue 2006
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tagsalgorithms amino acid substitution amino acids hydrogen bonding molecular models protein conformation protein sequence analysis proteins solvents

MuDDatabase Content

http://MuD.tau.ac.il

Protein > Annotation and Function

Mutation Detector (MuD) is a web server uses structural and sequence derived features to assess the impact of a given substitution on the protein function.

NAR Web Server Issue 2010
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tagsalgorithms amino acid sequence homology amino acid substitution artificial intelligence protein conformation reproducibility of results

MutDBDatabase Content

http://www.mutdb.org/

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.

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

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.

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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

PupaSuiteTool Content

http://pupasuite.bioinfo.cipf.es

DNA > Sequence Polymorphisms
Human Genome > Sequence Polymorphisms

PupaSuite is a SNP analysis tool that allows for the selection of relevant SNPs within a gene based on the characteristics of the SNP. PupaSuite also provides information about LD parameters (based on genotype data from HapMap) and identifies haplotype blocks and tag SNPs. PupaSuite was created to join PupaSNP & PupasView.

NAR Web Server Issue 2004NAR Web Server Issue 2006
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tagsalgorithms amino acid substitution binding sites genetic transcription genotype haplotypes humans linkage disequilibrium molecular evolution nucleic acid databases phenotype rna splicing single nucleotide polymorphism transcription factors

RevTransTool Content

http://www.cbs.dtu.dk/services/RevTrans/

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.

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

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.

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/

DNA > Phylogeny Reconstruction
Sequence Comparison > Analysis of Aligned Sequences

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

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

SIFTTool Content

http://blocks.fhcrc.org/sift/SIFT.html

DNA > Sequence Polymorphisms
Human Genome > Sequence Polymorphisms
Protein > Annotation and Function

Sorting Intolerant From Tolerant (SIFT) is a sequence homology-based tool that will predict whether an amino acid substitution will affect protein function.

NAR Web Server Issue 2003
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tagsamino acid motifs amino acid sequence amino acid substitution bacterial proteins bacteriophage t4 chromosome mapping computational biology conserved sequence dna sequence analysis escherichia coli proteins false positive reactions genes genetic polymorphism hiv protease hiv-1 humans inborn genetic diseases lac repressors lactose missense mutation molecular sequence data muramidase mutation phenotype probability protein databases protein sequence analysis proteins pseudogenes repressor proteins sequence alignment single nucleotide polymorphism

SWAKKTool Content

http://oxytricha.princeton.edu/SWAKK/

DNA > Phylogeny Reconstruction
Protein > 3-D Structural Features
Protein > Phylogeny Reconstruction
Sequence Comparison > Pairwise Sequence Alignments

Sliding Window Analysis of Ka and Ks (SWAKK) is tool for detecting positive selection in proteins using a sliding window substitution rate analysis. The program can display the results on a 3D protein structure.

NAR Web Server Issue 2006
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tagsamino acid substitution computational biology dna sequence analysis genetic selection protein conformation proteins sequence alignment

WurstTool Content

http://www.zbh.uni-hamburg.de/wurst/

Protein > 3-D Structure Prediction

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

NAR Web Server Issue 2004
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tagsamino acid substitution molecular models protein conformation protein sequence analysis