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 Biomedical Calculators

Biochemistry/DNA


Title: Align Two Polypeptide Chains
Description: Align Two Polypeptide Chains by Combinatorial Extension of the Optimal Path.
Inputs: Specify two polypeptide chains and optionally the similarity level and use of sequence information.
Requires: Forms capable browser.
Ref. No: 117


Title: All-to-All Protein Structure Comparison
Description: All-to-All Protein Structure Comparison by Combinatorial Extension of the Optimal Path.
Inputs: Specify a polypeptide chain to use as a search against a database of representative structures and optionally specify other than the default selection criteria.
Requires: Forms capable browser.
Ref. No: 915


Title: Biopolymer Calculator
Description: Calculate the molecular weight, the extinction coefficient, the concentration, and the melting temperature of a single stranded nucleic acid.
Inputs: sequence, Absorbance at 260nm, Counter Ion for Molecular Weight, Na+ concentration for Melting Temperature, many others.
Requires: forms capable browser.
Ref. No: 473


Title: Oligo Calculator
Description: Calculates Tm based on 0.195M monovalent cation (salt) concentration equal to 1x SSC.
Inputs: Oligo Sequence, Length, Melting Temperature, %GC content, Molecular Weight, OD/NanoMolar ratio.
Requires: forms capable browser.
Ref. No: 351


Title: All-to-All Protein Structure Comparison
Description: Compare a polypeptide chain to all chains from the polypeptide database.
Inputs: Specify a polypeptide chain to use as a search against the whole database and optionally specify other than the default selection criteria.
Requires: Forms capable browser.
Ref. No: 137


Title: Electronic PCR
Description: Detect PCR-based sequence tagged sites (STSs) in DNA sequences, potentially allowing their map locations to be determined.
Inputs: DNA sequence and sequence database.
Requires: forms based browser
Ref. No: 709


Title: Review Protein Families
Description: Explore Alignments for specific protein families.
Inputs: Select Protein Kinases or Esterases, Lipases databases to view detailed pairwise alignments for that protein family.
Requires: Forms capable browser
Ref. No: 995


Title: Oligo Dilution calculator
Description: Takes an oligo stock solution of higher concentration and determines how much volume to dilute down to final (desired) lower concentration.
Inputs: volumes of the stock solution (Start Point) and the diluted solution (End Point)
Requires: forms capable browser
Ref. No: 966


Title: Sequence Pattern Search
Description: Search DNA sequence Databases for a Nucleotide or Peptide sequence or pattern.
Inputs: Nucleotide or Peptide sequence. Patterns can be simple sequence strings (e.g. "ACCTA") or UNIX-style regular expressions.
Requires: forms capable browser.
Ref. No: 999


Title: Submit a polypeptide chain
Description: Submit a Structure to Find Structure Neighbors Using Combinatorial Extension of the Optimal Path.
Inputs: Enter a filename of a PDB formatted file containing the polypeptide chain for which you are seeking neighbors. Optionally specify your email address for notification of results.
Requires: Forms capable browser.
Ref. No: 488

 
Title: The Dali server
Description: The Dali server is a network service for comparing protein structures in 3D.
Inputs: Submit the coordinates of a query protein structure. Dali compares them against those in the Protein Data Bank. A multiple alignment of structural neighbours is mailed back.
Requires: Forms capable browser
Ref. No: 193


Title: Vector Alignment Search Tool (VAST)
Description: VAST is a computer algorithm used to examine distant evolutionary relationships based on similarities in three-dimensional structure of proteins.
Inputs: Coordinates of query protein.
Requires: Forms capable browser.
Ref. No: 138