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Links tagged with 'mathematics'

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G2DTool Content

http://www.ogic.ca/projects/g2d_2/ [open in a new window]

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Human Genome > Health and Disease

G2D (Candidate Genes to Inherited Diseases) scans a human genomic region for genes related to an inherited disease. The G2D server also presents precomputed candidate genes for more than 600 genetically inherited diseases that have been mapped onto chromosomal regions without assignment of a particular gene.

links directory index: 486
TitlePublication YearGoogle Scholar Citation Count
Update of the G2D tool for prioritization of gene candidates to inherited diseases200737
Computational disease gene identification: a concert of methods prioritizes type 2 diabetes and obesity candidate genes200685
G2D: a tool for mining genes associated with disease2005112
Association of genes to genetically inherited diseases using data mining2002252
NAR Web Server Issue 2007
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tagsalgorithms alzheimer disease asthma chromosome mapping computational biology genes genetic databases genetic linkage genetic markers genetic predisposition to disease human genome humans inborn genetic diseases mathematics medline obesity phenotype type 2 diabetes mellitus

pKD ServerTool Content

http://enzyme.ucd.ie/cgi-bin/pKD/server_start.cgi [open in a new window]

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Protein > 3-D Structural Features
Protein > Biochemical Features

pKa Design (pKD) takes as input a protein structure and allows you to redesign the protein pKa value for that molecule. The server calculates a set of point mutations that will cause the desired pKa change.

links directory index: 178
TitlePublication YearGoogle Scholar Citation Count
pKD: re-designing protein pKa values200622
Optimizing the hydrogen-bond network in Poisson-Boltzmann equation-based pK(a) calculations2001156
NAR Web Server Issue 2006
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tagsamino acid sequence hydrogen bonding hydrogen-ion concentration mathematics molecular models point mutation protein conformation proteins static electricity x-ray crystallography

Protein Dipole ServerTool Content

http://bioportal.weizmann.ac.il/dipol/ [open in a new window]

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Protein > 3-D Structural Features
Protein > Biochemical Features

The Protein Dipole server calculates and displays the net charge, dipole moment and mean radius of any 3-dimensional protein structure.

This content is being maintained by Clifford Felder.

links directory index: 38
TitlePublication YearGoogle Scholar Citation Count
A server and database for dipole moments of proteins200738
NAR Web Server Issue 2007
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tagsbibliographic databases biophysics computational biology computer simulation enzymes fungal proteins mathematics molecular models protein conformation protein databases proteins secondary protein structure statistical models

PSATool Content

http://bmerc-www.bu.edu/psa/request.htm [open in a new window]

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Protein > 2-D Structure Prediction

Prediction of probable secondary structures and fold-class; good for visualizing amphipathic helices, where present.

links directory index: 324
TitlePublication YearGoogle Scholar Citation Count
Protein classification by stochastic modeling and optimal filtering of amino-acid sequences1994135
Structural analysis based on state-space modeling1993189
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tagsamino acid sequence chemical models flavodoxin markov chains mathematics molecular sequence data molecular structure probability proteins secondary protein structure structural models tertiary protein structure thioredoxins

Services from Zhou LaboratoryResource Content

http://cssb.biology.gatech.edu/skolnick/people/zhou.html [open in a new window]

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Protein > 2-D Structure Prediction
Protein > 3-D Structure Prediction
Protein > Localization and Targeting
Protein > Networks & Interactions, Pathways and Enzymes

Tools from the Zhou laboratory including predictors of transmembrane topology (THUMBUP, UMDHMM-TMHP, TUPS); prediction/analysis tools for tertiary structure (SPARKS2, SP3); and, prediction/analysis tools for interactions (DMONOMER, DLOOP, DMUTANT, DCOMPLEX, DDNA, TCD, DOGMA).

links directory index: 1058
TitlePublication YearGoogle Scholar Citation Count
Web-based toolkits for topology prediction of transmembrane helical proteins, fold recognition, structure and binding scoring, folding-kinetics analysis and comparative analysis of domain combinations200520
Fold recognition by combining sequence profiles derived from evolution and from depth-dependent structural alignment of fragments2005136
Accurate and efficient loop selections by the DFIRE-based all-atom statistical potential200473
Single-body residue-level knowledge-based energy score combined with sequence-profile and secondary structure information for fold recognition2004135
A physical reference state unifies the structure-derived potential of mean force for protein folding and binding200492
Predicting the topology of transmembrane helical proteins using mean burial propensity and a hidden-Markov-model-based method200360
Folding rate prediction using total contact distance2002139
Distance-scaled, finite ideal-gas reference state improves structure-derived potentials of mean force for structure selection and stability prediction2002403
NAR Web Server Issue 2005
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tagsalgorithms amino acid sequence amino acid sequence homology amino acids antigen-antibody complex binding sites biological evolution chemical models computational biology dimerization factual databases hydrogen bonding kinetics markov chains mathematics membrane proteins molecular evolution molecular structure peptide fragments peptide library plant proteins probability protein binding protein conformation protein databases protein folding protein sequence analysis proteins regression analysis reproducibility of results secondary protein structure sensitivity and specificity sequence alignment statistical models statistics as topic tertiary protein structure theoretical models thermodynamics time factors

WebScipio - eukaryotic gene identificationTool Content

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

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DNA > Gene Prediction
Expression > Splicing
RNA > General Resources
Sequence Comparison > Analysis of Aligned Sequences

Scipio is a tool to determine the precise exon-intron gene structure given a protein sequence and a genome. It identifies splice sites and is able to cope with sequencing errors and genes spanning several contigs. The output contains information about discrepancies that may result from sequencing errors. Scipio has also successfully been used to find homologous genes in related species. WebScipio, allows to search for mutually exclusive spliced exons and tandemly arrayed gene duplicates.

links directory index: 24
TitlePublication YearGoogle Scholar Citation Count
WebScipio: an online tool for the determination of gene structures using protein sequences20089
Scipio: using protein sequences to determine the precise exon/intron structures of genes and their orthologs in closely related species200815
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tagsacetylcholine action potentials algorithms alternative splicing amino acid sequence animals apomorphine atropine base sequence benserazide bromocriptine central nervous system dextroamphetamine diaphragm dna sequence analysis dopamine drosophila melanogaster drosophila proteins epinephrine exon-intron structure exons extrapyramidal tracts female gene duplicates gene prediction gene structure genetic databases genomics haloperidol human parainfluenza virus 3 humans hydroxylamines immunologic deficiency syndromes infant introns kinetics levodopa mathematics molecular sequence data motor activity muscle contraction muscle denervation mutually exclusive splicing nerve degeneration neurological models neuromuscular junction nucleic acid sequence homology oxidation-reduction paramyxoviridae infections physostigmine piribedil planarians protein sequence analysis proteins rats reading frames reserpine rna splice sites sequence alignment software species specificity superoxide dismutase superoxides synaptic transmission tandem gene duplication tetrodotoxin turbellaria user-computer interface viral pneumonia x chromosome

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