Protein Design and Protein Folding

Ever since 1999, this site is dedicated to bringing the latest news on protein folding/protein design research. Proteins are the machinery of life, and as the rules behind their folding & structures are unfolded (no pun intended), the mysteries of biology will be unraveled one after another. One day we will be able to harness the knowledge to design proteins to solve thousands of problems and cure any disease.

Google Runs a Scam?

Posted by: david on Thursday/July 07/2011 - 12:03 AM
Protein News 
Okay- so this is not about protein folding- more of a rant. I'm finding evidence that Google is giving its own domains preference in the search engines. I wrote an article called "How the Heart Works: A Basic Overview" which is blatantly copied by Google's site. When you search for "How the Heart Works: A Basic Overview by David Yee" in Google, you will see that some bogus spam site called is ranked higher than me. What a freaking joke. This is the last straw- I'm switching to Bing and I am encouraging others to do so as well. Ironic how Google's mantra is "Do no evil". If that is not hilarious I do not know what is.

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How the Heart Works: A Basic Overview by David Yee

Posted by: david on Wednesday/March 31/2010 - 11:10 PM
Protein News 
How the Heart Works: A Basic Overview by David Yee (Originally Written 10-5-1994)
I. Location
A. the heart is located in the chest; it lies left of the body's midline, above and in contact with the diaphragm
B. situated immediately behind the breastbone, or sternum, and between the lungs, with apex tiled to the body cavity's left side
II. Heart has two cavities, divided by the cardiac septum
A. Right cavity takes in oxygen poor blood from the body and pumps it to the lungs
1. has an atrium (collecting chamber) and a ventricle (pumping chamber); atrium is on top of ventricle
a. atrium draws blood from veins, and ventricle pushes blood into arteries
b. thin walls for atrium and thick walls (=3x walls for atrium) for ventricle
2. has tricuspid (an atrioventricular valve) and pulmonary (a semilunar valve) valves
B. Left cavity takes in oxygen rich blood from the lungs and pumps it to the body
1.Same as A1, except walls are 2x as thick
2. has mitral (an atrioventricular valve), 2 flaps, also called bicuspid valve and aortic (a semilunar valve) valves
III. Two stages in each heartbeat cycle: diastole and systole
A. Diastole
1. Heart muscle relaxes, blood is thus drawn into the two atria from veins.
a. oxygen-poor blood into the right atrium from major veins superior and inferior vena cava; each through a separate opening
b. oxygen-rich blood into the left atrium from four pulmonary veins (2 from each lung)
2. Rising pressure in each atrium opens the tricuspid and mitral valve and blood flows into the ventricles.
B. Systole
1. Sinoatrial (SA) node fires impulses, stimilating atria to contract.
2. All the blood are forced into the ventricles
3. Mitral and tricuspid valves close due to rising pressure in ventricles.
4. Ventricles fully contract.
5. Aotric and pulmonary valves are forced open.
6. Blood pushes out to the arteries (aorta and pulmonary arteries).
7. Heart relaxes, and the aortic and pulmonary valves close. Return to diastole.
V. Additional information
A. Amount of blood pumped
1. At rest, the heart pumps about 59 cc (2 oz) of blood per beat and 5 l (5 qt) per minute 2. During exercise, 120-220 cc (4-7.3 oz) per beat and 20-30 l (21-32 qt) per minute B. Size
1. The adult human heart is about the size of a fist and weighs about 250-350 gm (9 oz).
2. Thickness of heart muscles varies from 2 mm to 20 mm
C. Heart's wall has three layers
1. The outer layer of the heart is called the epicardium.
a. is in intimate contact with the pericardium (a serous membrane that is a closed sac covering the heart muscle's outside wall). Within the sac, a small amount of fluid reduces the friction between the two layers of tissue.
2. The middle layer is the myocardium (heart muscle)
3. The inner layer is the endocardium
a. consists of a thin layer of endothelial tissue overlying a thin layer of vascularized connective tissue

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free open-source software for automated protein design

Posted by: Anonymous on Thursday/May 03/2007 - 04:27 PM
Protein News 
EGAD is a free open-source program for protein design and mutant prediction. EGAD's main focus is performing protein design on fixed backbone scaffolds. It can also consider multiple structures simultaneously for designing specific binding proteins or locking proteins into specific conformational states. In addition to natural protein residues, EGAD can also consider free-moving ligands with or without rotatable bonds. It may even be possible to use EGAD for drug design. EGAD can be used with a single processor, but it can take advantage of the power of parallelization to perform certain jobs quickly.

Some of the tasks EGAD can perform are: prediction of mutation effects on protein stability and protein-complex formation to within ~1kcal/mol, automated scanning mutagenesis, including saturation mutagenesis, of proteins and protein complexes, total protein sequence design, design of ligand binding sites, optimization of sequences while considering multiple structures for the design of specific binding proteins and conformational switching, predicting the pK's of ionizable groups in proteins, and generating tables to display the distribution of energetic interactions in protein structures.

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New version of Protein Folding Database released

Posted by: david on Thursday/October 12/2006 - 02:32 AM
Protein News 
Ashley from Monash University in Australia would like to announce that the group she is working with have released a new version of the Protein Folding Database.

"The database aims to collect all folding data into one repository and, within the framework of the International Foldeomics Consortium, encourage sharing and data analysis. We are particularly interested in allowing the graphical analysis of raw-data on the site."

You can register to do advanced searches and to submit your own protein folding data.

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Request for contributors, help

Posted by: david on Wednesday/August 14/2002 - 10:33 PM
Hi- I'm looking for people who are interested in protein research who would like to contribute news, articles, opinions, etc. on a constant basis to the site. I simply don't have the time nor resources to update the site on a constant basis so any help would be great. Anyone who's interested please click on Contact Us on the main menu & drop me a note - thanks!

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Welcome to /!

Posted by: david on Saturday/May 19/2001 - 11:36 PM
Welcome to /! This site is dedicated to providing the latest news on the front of protein research. Whenever I find a relevent research paper I will also post a small excerpt here and link to it. The target audience of this site is anyone who is interested in protein science. I personally have a *fascination* with proteins and their amazing characteristics and capabilities. If you have any suggestions/comments, please feel free to let me know. And if you have any news you like to contribute, please send them over.

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Featured Protein Folding Essay
  • Introduction to Protein Folding - The Process and Factors Involved by David C. Yee
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