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Biophysics Core Handbook



ExPASy Molecular Biology Server

      The ExPASy (Expert Protein Analysis System) proteomics server of the Swiss Institute of Bioinformatics (SIB). This server is dedicated to the analysis of protein sequences and structures as well as 2-D PAGE.

      ProtParam tool

      A tool for computating various physical and chemical parameters for a given protein stored in SWISS-PROT or TrEMBL or for a user entered sequence. The computed parameters include the molecular weight, theoretical pI, amino acid composition, atomic composition, extinction coefficient, estimated half-life, instability index, aliphatic index and grand average of hydropathicity (GRAVY). (References).

CLAMP Software

      A software program designed to interpret complex interactions recorded on biosensors. It combines numerical integration and non linear global curve fitting routines.

Protein Interaction Facility

      David Myszka, Director. Some information about analytical ultracentrifugation, titration calorimetry and optical biosensors (Biacore).

Unit Conversions

      Temperature, length, energy, pressure, volume, density, specific volume, specific heat (entropy), enthalpy, thermal conductivity, viscosity, and coefficient of heat transfer conversions. Just enter a number and we will convert it for you!

Quadratic Formula Solver

      Enter your coefficients and receive the answers!

Constants

      Constant

      Value

      Unit

      Avogadro constant 6.022045 * 1023 mol-1
      Boltzmann constant 1.380662 * 10-23 J mol-1 K-1
        3.298 * 10-24 cal mol-1 K-1
      Electronic charge 1.602 * 10-19 C
      Faraday constant 96,485 C mol-1
      Molar gas constant 8.31441 J mol-1 K-1
        0.082057 * 10-3 m3 atm mol-1 K-1
        1.987 cal mol-1 K-1
      Plank's constant 6.626176 * 10-34 J s
      Velocity of light 2.998 * 108 m s-1
      Base of natural logarithms 2.7183  
      Pi 3.1416  

      More Information: E. R. Cohen & N. B. Taylor, J. Phys. Chem. Ref. Data, vol 2(4), 1973.

Circular Dichroism

      CD 222:208 ratio 1.10 => Coiled coil
      CD 222:208 ratio 0.90 => Helix

Molar Ellipticity Online Conversion

Thermo-dynamics of Protein Unfolding

      Protein

      pH

      Delta H° (kcal mol-1)

      Delta S° (kcal K-1 mol-1)

      Trypsin 2.0 67.6 213
      Soybean trypsin inhibitor 3.0 57.3 180
      Chymotrypsinogen 2.0 99.6 316
      Chymotrypsinogen 3.0 143 432

National Institute of Standards and Technology

      Elemental data index, physical constants, atomic spectroscopic data, molecular spectrscopic data, ionization data, x-ray and gamma-ray data, radiation dosimetry data, nuclear physics data, etc.

Reflexive Film