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Links tagged with 'theoretical models'

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Found 16 links

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AD-ENMTool Content

http://enm.lobos.nih.gov

Protein > Annotation and Function
Protein > Domains and Motifs
Protein > Molecular Dynamics and Docking

Analysis of Dynamics of Elastic Network Model (AD-ENM) predicts the conformational changes a given protein structure can undergo.

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tagsactins adenosine triphosphate animals binding sites biophysical phenomena biophysics dictyostelium dna polymerase beta dna-directed rna polymerases elasticity humans kinesin ligands mice molecular conformation molecular models molecular motor proteins myosins nucleotides principal component analysis protein binding protein conformation proton-translocating atpases protozoan proteins secondary protein structure statistical models structure-activity relationship taq polymerase tertiary protein structure theoretical models thermodynamics viral proteins x-ray crystallography

BioNumbersDatabase Content

http://www.bionumbers.hms.harvard.edu

Literature > Databases

BioNumbers (http://www.bionumbers.hms.harvard.edu) is a database of key numbers in molecular and cell biology--the quantitative properties of biological systems of interest to computational, systems and molecular cell biologists. Contents of the database range from cell sizes to metabolite concentrations, from reaction rates to generation times, from genome sizes to the number of mitochondria in a cell. All numbers are taken directly from a literature source and that reference is provided with the number.

NAR Database Issue 2010
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tagsalgorithms animals biological models cell biology computational biology genetic databases humans molecular biology nucleic acid databases protein databases systems biology theoretical models

CAP3 Sequence Assembly ProgramTool Content

http://bioweb.pasteur.fr/seqanal/interfaces/cap3.html

DNA > Mapping and Assembly

Web-based contig assembly.

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tagsalgorithms bacterial chromosomes consensus sequence contig mapping dna sequence analysis factual databases genetic models reproducibility of results sequence alignment theoretical models

DINAMeltTool Content

http://mfold.rna.albany.edu/?q=DINAMelt

DNA > Tools For the Bench
RNA > Structure Prediction, Visualization, and Design

DINAMelt is a tool for predicting hybridization and folding (secondary structure) of DNA and RNA using equilibrium thermodynamic methods.

NAR Web Server Issue 2005
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tagsalgorithms animals bacterial rna base sequence calorimetry dna dna sequence analysis fungal rna genetic hybridization introns molecular sequence data nucleic acid conformation nucleic acid denaturation nucleic acid hybridization oligonucleotides oligoribonucleotides phylogeny rats rna rna sequence analysis single-stranded dna structure-activity relationship temperature theoretical models transition temperature

DisEMBLTool Content

http://dis.embl.de/

Protein > 2-D Structure Prediction
Protein > 3-D Structure Prediction

A computational tool for prediction of disordered/unstructured regions within a protein sequence.

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tagscircular dichroism humans ligands magnetic resonance spectroscopy neural networks (computer) protein conformation proteins proteome sensitivity and specificity src homology domains statistics as topic temperature theoretical models ultraviolet rays x-ray crystallography

ILMTool Content

http://cic.cs.wustl.edu/RNA/

RNA > Structure Prediction, Visualization, and Design

Server which provides iterated loop matching and maximum weighted matching algorithms for pseudoknot containing RNA secondary structure prediction. Algorithms can apply thermodynamic and comparative information, and thus can be used for either aligned or individual sequences.

NAR Web Server Issue 2004
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tagsalgorithms bacillus subtilis bacterial rna base composition base pairing base sequence escherichia coli feedback molecular models molecular sequence data nucleic acid conformation nucleic acid sequence homology phylogeny reproducibility of results rna rna sequence analysis sensitivity and specificity sequence alignment theoretical models thermodynamics transfer rna

M4TTool Content

http://manaslu.aecom.yu.edu/M4T/

Protein > 3-D Structure Prediction

M4T (Multiple Mapping Method with Multiple Templates) is a comparative protein structure modeling server that uses a combination of multiple templates and iterative optimization of alternative alignments.

NAR Web Server Issue 2007
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tagsalgorithms amino acid sequence biological models computational biology computer simulation molecular models molecular sequence data protein sequence analysis proteins secondary protein structure sequence alignment theoretical models

MEME SuiteTool Content

http://meme.nbcr.net/meme/intro.html

DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation
Protein > Domains and Motifs
Protein > Sequence Features
Sequence Comparison > Comparative Genomics

The MEME Suite web server is a unified portal for discovery and analysis of sequence motifs (e.g. DNA binding sites, protein interaction domains). Motifs with/without gaps may be discovered, searched for in DNA and protein databases, compared to other motifs and analyzed for putative function by association with gene ontology terms. MEME is a tool designed for discovering and searching for DNA motifs such as transcription factor binding sites (TFBS) or protein domains.

NAR Web Server Issue 2006NAR Web Server Issue 2009
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tagsalcohol dehydrogenase alcohol oxidoreductases algorithms amino acid motifs amino acid sequence amino acid sequence homology animals artificial intelligence automated pattern recognition automation bacterial proteins base sequence binding sites biopolymers chemical models consensus sequence dna dna sequence analysis entropy evaluation studies as topic factual databases ferredoxins genetic databases humans hydroxysteroid dehydrogenases mammals markov chains mathematical computing molecular models molecular sequence data nucleic acid repetitive sequences nucleic acid sequence homology oxidoreductases phylogeny protein sequence analysis proteins reproducibility of results secondary protein structure sequence alignment sequence analysis software design stochastic processes streptomyces tertiary protein structure theoretical models transcription factors transcriptional regulatory elements

MinActionPathTool Content

http://lorentz.immstr.pasteur.fr/joel/index.php

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

MinActionPath calculates the most-probable trajectory between two known structural states of a protein.

NAR Web Server Issue 2007
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tagsalgorithms amino acid sequence biological models chemical models computational biology computer simulation energy transfer molecular models molecular sequence data protein conformation proteins tertiary protein structure theoretical models thermodynamics

MobilomeFINDERTool Content

http://mml.sjtu.edu.cn/MobilomeFINDER/

Model Organisms > Microbes
Sequence Comparison > Comparative Genomics

MobilomeFINDER (Mobile Genome FINDER) is a tool for high-throughput genomic island discovery.

NAR Web Server Issue 2007
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tagsalgorithms bacterial genes bacterial genome bacterial rna computational biology enterobacteriaceae escherichia coli escherichia coli k12 fungal gene expression regulation genomic islands genomics oligonucleotide array sequence analysis polymerase chain reaction pseudomonas aeruginosa shigella shigella flexneri streptococcus suis theoretical models transfer rna

ModellerTool Content

http://salilab.org/modeller/

Protein > 3-D Structure Prediction

Homology or comparative modeling of 3D protein structures.

NAR Web Server Issue 2003
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tagsamino acid sequence amino acid sequence homology animals bacterial proteins biological models carrier proteins computer simulation enzymes factual databases genetic models genome genomics humans kallikreins l-lactate dehydrogenase mathematics molecular models molecular sequence data pancreatic elastase probability protein conformation protein databases protein folding protein structural homology proteins reproducibility of results sequence alignment sequence homology systems integration tertiary protein structure theoretical models thermodynamics tissue kallikreins trichomonas vaginalis trypsin

PhobiusTool Content

http://phobius.sbc.su.se/

Protein > 2-D Structure Prediction
Protein > Localization and Targeting

Phobius is a combined transmembrane topology and signal peptide predictor. The server also allows for constrained and homology-enriched predictions.

This content is being maintained by lukall.

NAR Web Server Issue 2007
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tagsalgorithms artificial intelligence computational biology computer simulation cytoplasm markov chains membrane proteins molecular models probability programming languages protein conformation protein databases protein sorting signals proteomics secondary protein structure statistical models theoretical models

QuadruplexTool Content

http://www.quadruplex.org

DNA > Structure and Sequence Feature Detection

A website to serve the quadruplex community. Contains conference information, forums, database and parsers.

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tagsanimals antineoplastic agents drug design g-quadruplexes gene expression regulation gene therapy genetic promoter regions guanine humans ligands molecular models molecular structure neoplasms neoplastic gene expression regulation nucleic acid conformation telomere theoretical models

Servers at University College LondonTool Content

http://bioinf.cs.ucl.ac.uk/web_servers/

Protein > 2-D Structure Prediction
Protein > 3-D Structural Features
Protein > 3-D Structure Prediction
Protein > Domains and Motifs
Protein > Localization and Targeting

A suite of tools that includes: PSIPRED, a protein structure prediction server; GenTHREADER, for genomic protein fold recognition; MEMSAT2, for transmembrane protein structure prediction; GTD, the genomic threading database; DISOPRED, a dynamic disorder prediction server; DomPred, a domain prediction server; and COPS, for the comparison of protein structure classifications. UCL web portal has been updated to include a fully automated 3-D modeling pipeline, BioSerf.

NAR Web Server Issue 2005NAR Web Server Issue 2010
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tagsalgorithms amino acid sequence amino acid sequence homology animals bacterial genome computational biology database management systems documentation factual databases false positive reactions fungal genome gene expression profiling genetic databases genome genomics humans london mathematics membrane proteins molecular evolution molecular models molecular sequence data neural networks (computer) open reading frames peptide fragments polypyrimidine tract-binding protein probability protein conformation protein databases protein folding protein sequence analysis proteins proteome proteomics reproducibility of results secondary protein structure sensitivity and specificity sequence alignment sequence analysis sequence homology structural models tertiary protein structure theoretical models

TreeDetTool Content

http://treedetv2.bioinfo.cnio.es/treedet/index.html

Protein > Annotation and Function
Protein > Domains and Motifs
Sequence Comparison > Analysis of Aligned Sequences

Tree Determinant (TreeDet) is a tool for predicting functional residues in protein sequence alignments.

NAR Web Server Issue 2006
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tagsalgorithms amino acid sequence conserved sequence cyclins gtp-binding proteins molecular models molecular sequence data multigene family phylogeny protein conformation protein databases protein sequence analysis proteins proto-oncogene proteins p21(ras) sequence alignment structure-activity relationship tertiary protein structure theoretical models