folding.chemistry.msstate.edu folding.chemistry.msstate.edu

folding.chemistry.msstate.edu

Fitzkee Lab Web Archives

Fitzkee Lab Web Archives. Department of Chemistry,. This site contains resources on protein structure as well as analysis and simulation tools. To visit our main lab web page. Applications are now being accepted for the 30th Gibbs Symposium on Biothermodynamics. Lab Programs for Downloading. Monte Carlo Polypeptide Simulations. Generate a polypeptide chain. Calculate Conditional Hydrophobic Accessible Surface Area. Difference Distance Matrix Plot (DDMP). Generate a hydrophobicity profile.

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Fitzkee Lab Web Archives | folding.chemistry.msstate.edu Reviews
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Fitzkee Lab Web Archives. Department of Chemistry,. This site contains resources on protein structure as well as analysis and simulation tools. To visit our main lab web page. Applications are now being accepted for the 30th Gibbs Symposium on Biothermodynamics. Lab Programs for Downloading. Monte Carlo Polypeptide Simulations. Generate a polypeptide chain. Calculate Conditional Hydrophobic Accessible Surface Area. Difference Distance Matrix Plot (DDMP). Generate a hydrophobicity profile.
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1 protein folding
2 conformational entropy
3 hierarchy
4 hierarchic consensation
5 secondary structure
6 RNA
7 RNA folding
8 LINUS
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mississippi state university,lab members,nicholas fitzkee,becca hill,dinusha jinasena,randika perera,sri ramya tata,ailin wang,dinesh yadav,yue zhang,linus,ribosome,chasa,compare c alpha positions,lab web resources,an rna primer,pross,assign,tein,econdary
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Fitzkee Lab Web Archives | folding.chemistry.msstate.edu Reviews

https://folding.chemistry.msstate.edu

Fitzkee Lab Web Archives. Department of Chemistry,. This site contains resources on protein structure as well as analysis and simulation tools. To visit our main lab web page. Applications are now being accepted for the 30th Gibbs Symposium on Biothermodynamics. Lab Programs for Downloading. Monte Carlo Polypeptide Simulations. Generate a polypeptide chain. Calculate Conditional Hydrophobic Accessible Surface Area. Difference Distance Matrix Plot (DDMP). Generate a hydrophobicity profile.

INTERNAL PAGES

folding.chemistry.msstate.edu folding.chemistry.msstate.edu
1

LINUS Distribution

http://folding.chemistry.msstate.edu/dist/index.html

The LINUS distribution is a suite of programs for exploring conformational ensembles of peptides and proteins. The core of LINUS is a torsion angle Monte Carlo simulation application that allows a restrained Monte Carlo move set with a simple atomic interaction energy acceptance criterion. LINUS is written entirely in Python although some routines are also provided as C code. The C routines will be called if they are compiled but they are not necessary. LINUS was ported to Python with the goal of making ...

2

Estimate of Unfolded state Accessible Surface Area

http://folding.chemistry.msstate.edu/utils/unfolded.html

Estimate of Unfolded state Accessible Surface Area. This is a form that allows you to enter a sequence and compute an estimate of the accessible surface area of a protein in the unfolded state. Creamer, T.P., Srinivasan, R. and Rose, G.D. Modeling unfolded states of peptides and proteins. Biochemistry 34: 16245-16250, 1995. Sequence data ( amino acid one letter codes in UPPERCASE).

3

Java Animations

http://folding.chemistry.msstate.edu/~raj/javanim.html

The animations are available in two formats - GIF animations and Java animations. The gif animations load faster, while the quality of the java animations is better (read smoother). If you have a slow connection think hard before opting for the java animations. Choose a movie to view from the list:. Change in Heme upon ligand binding Java. Quaternary Structure change to T to R2 transformation of Hemoglobin Java. Illustration of hierarchy - Java.

4

Yue Zhang @ Fitzkee Lab – A PhD Candidate in Biophysics

http://folding.chemistry.msstate.edu/~yue

Lab Programs for Downloading. Monte Carlo Polypeptide Simulations. Generate a polypeptide chain. Calculate Conditional Hydrophobic Accessible Surface Area. Difference Distance Matrix Plot (DDMP). Generate a hydrophobicity profile. Unfolded State Accessible Surface Area. Adrian Parsegian's VDW Book. The Protein Coil Library. Calculate Conditional Hydrophobic Accessible Surface Area. Unfavorable conformations in polyalanine.

5

The Coil Library - Introduction

http://folding.chemistry.msstate.edu/coil

Search by PDB ID:. Welcome to the Protein Coil Library! This is the website for The Protein Coil Library, a library of protein structure fragments derived from the Protein Data Bank (PDB). The fragments in this library are those fragments in the PDB that cannot be classified as either alpha-helix or beta-strand. Three-dimensional structures as well as side-chain and backbone torsion angles are stored in the database. In addition to searching by PDB ID. It is possible to download a particular size class.

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Our group is affiliated with the Departments of Environmental Health. University of Cincinnati College of Medicine. As well as with the Division of Biomedical Informatics. Children's Hospital Research Foundation. See links below). Our research in the fields of bioinformatics. And the recognition of functional sites. In proteins, gene (genome) annotation. And the identification of predictive fingerprints. Var win = new Window(Application.getNewId(), {className: "spread", title: "Research Highlights", ...

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Fitzkee Lab Web Archives

Fitzkee Lab Web Archives. Department of Chemistry,. This site contains resources on protein structure as well as analysis and simulation tools. To visit our main lab web page. Applications are now being accepted for the 30th Gibbs Symposium on Biothermodynamics. Lab Programs for Downloading. Monte Carlo Polypeptide Simulations. Generate a polypeptide chain. Calculate Conditional Hydrophobic Accessible Surface Area. Difference Distance Matrix Plot (DDMP). Generate a hydrophobicity profile.

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