Postings under ( protein )

27 August 2010
Explicitly heating your protein

28 July 2010
Why bioinformatics !== compstructbio, or why Rosetta is not a glorified SVM

11 July 2010
The 2 billion dollar protein sequencing error

30 May 2010
The Theory of Single Domain Allostery

20 March 2010
How the hell do I model this thing?

4 January 2010
A Decade in Computational Structural Biology

25 October 2009
The bioinformatic-journal/software hydrid

19 October 2009
Local Perturbations in Explicit Solvent

16 October 2009
Molecular Dynamics and things like that

3 September 2009
Protein Society Symposium Report

12 July 2009
Heat a residue in a protein, large loops pop out

23 May 2009
Thousands of hours of Molecular Dynamics saves you minutes of a Monte Carlo calculation

12 May 2009
Bionostalgia: Notes to an Even Younger Computational Biologist

17 April 2009
Structural alignment done right

31 March 2009
Gallery of Membrane Protein Structures

4 March 2009
Bioinformatics in the Near Concurrent Future

25 February 2009
An Annotated History of Molecular Dynamics

9 February 2009
How efficient is Molecular Dynamics?

4 February 2009
Lazy, lazy crystallographers

13 October 2008
How the Serpin protein traps the digestive powers of the enzyme Serine Protease

7 October 2008
What is Computational Biology?

1 October 2008
Computational Chemistry Challenge: the Power Stroke of Myosin that powers Muscle Contraction

24 September 2008
How to Compute Chemistry, Conference Report

23 August 2008
A Bird's Eye-View of Bioinformatic Journals

22 July 2008
How History affects Pattern Matching inside the Genome

11 June 2008
Finding fellow bottom feeders

13 March 2008
How to build a cathedral door out of 456 proteins

19 February 2008
Wicked Approximations: proteins move like a network of springs

7 February 2008
How to avoid futility: a guide to parameterizing non-standard amino acids in AMBER

4 February 2008
Interview Me

8 December 2007
Coding randomness not so naïvely

3 December 2007
Poking my eyes out with Amber, again

23 November 2007
asa.py - accessible surface area

19 November 2007
match.py - calculating the RMSD of PDB structures

19 October 2007
Calculating the solvent Accessible Surface Area (ASA)

1 October 2007
Parsing PDB files: sometimes you really should reinvent the wheel

16 September 2007
Grilling Juicy Steaks: The Best Introduction to Salt Effects in Cell Biology I have Ever Read

12 August 2007
A Most Ugly Hack: translating from CHARMM to AMBER trajectories

10 August 2007
Fetching PDB files remotely in pure Python code

9 May 2007
The Schrodinger Equation in Action

9 May 2007
Wet Holes in the Membrane

8 May 2007
Dragging an ion through the nicotonic channel

8 May 2007
Seeing a carbon-monoxide molecule escaping from the clutches of the Myoglobin protein

7 May 2007
Beautiful movies of X-ray Crystallography Refinement

21 March 2007
A Sign, a Flipped Structure, and a Scientific Flameout of Epic Proportions

13 March 2007
Notes to a young computational biologist

11 February 2007
Heating up a Protein, One residue at a time

25 January 2007
Simulating a very small peptide: enkephalin

31 December 2006
Come together, electrostatically, as one

30 December 2006
Looking at the surface of a membrane

13 November 2006
What is a molecule?

23 September 2006
Structural features of the Beta-sheet

7 August 2006
The Mysterious Regions of the Ramachandran Plot

14 July 2006
Why AMBER sticks a finger in its users eyes.

5 October 2005
Of proteins, clusters and musical chairs

24 September 2005
Transcription as Compilation

12 June 2004
We can fold it for you wholesale

31 December 1969
RMSD: Root Mean Square Deviation

3 September 2010
The Ten Commandments of Protein Folding