( protein ) postings
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
4 July 2009
The Ten Commandments of Protein Folding

« | »