Tags: proteins

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Description

Proteins are organic compounds made of amino acids arranged in a linear chain and folded into a globular form. The amino acids in a polymer are joined together by the peptide bonds between the carboxyl and amino groups of adjacent amino acid residues. The sequence of amino acids in a protein is defined by the sequence of a gene, which is encoded in the genetic code.

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Tools (1-6 of 6)

  1. Photosynthetic Protein Spectroscopy Lab

    Tools | 19 Oct 2020 | Contributor(s):: Safa Ahad, Chientzu Lin, Michael Earl Reppert

    This tool parses PDB structures of photosynthetic proteins to identify pigments, calculate inter-pigment interactions, and simulate optical spectra for the complex.

  2. Demo of Loading and Visualizing Proteins from the RCSB Protein Data Bank

    Tools | 14 Dec 2016 | Contributor(s):: Martin Hunt

    Demo of Loading and Visualizing Proteins from the RCSB Protein Data Bank

  3. cadnano to PDB File Converter

    Tools | 13 Nov 2013 | Contributor(s):: Jejoong Yoo, AbderRahman N Sobh, Chen-Yu Li, Aleksei Aksimentiev

    Accepts CadNano files in the form of *.json and outputs a file in *.pdb which can be read by programs such as VMD.

  4. Tensile Mechanics of alpha-Helical Polypeptides

    Tools | 30 Aug 2013 | Contributor(s):: Korosh Torabi, George C. Schatz

    This model is capable of making quantitatively accurate predictions of force-extension behavior of a given helix-forming polypeptide sequence including its dependence on pH, temperature and ionic strength.

  5. Stretching simulation of an alpha-helical protein domain

    Tools | 10 Jan 2011 | Contributor(s):: Markus Buehler, Justin Riley, Joo-Hyoung Lee, Jeffrey C Grossman

    Uses steered molecular dynamics (SMD) to apply a tensile load to the ends of a molecule (such as an alpha-helical protein domain)

  6. PNP Cyclic Peptide Ion Channel Model

    Tools | 04 Apr 2007 | Contributor(s):: Brian Radak, Hyonseok Hwang, George C. Schatz, Mark Ratner

    This tool simulates ion flow in a system modeled after cyclic peptide ion channels using Poisson-Nernst-Planck (PNP) theory.