blog // protein

//

Books

2014

Notes for Systems Biology 25/Oct

Bioinformatics and Human Origins 8/Jun

Surface Area and Volume Tools for PDB files, written in easy to read Python 26/May

Structural alignment done right 22/May

2013

Installing TPP 4.6.2 on Mountain Lion Mac OSX 22/Apr

Vector Representation in Structural Biology 21/Jan

2011

★

A Fundamental Breakthrough in Protein Folding 27/Dec

★

Magic Numbers and unit conversions in Structural Biology 13/Dec

The infidelity of the theoretical protein backbone 15/Nov

The GPCR-G complex: the canonical structure of Cell Signaling (with interactive guide) 1/Aug

Purity in the atomic force-fields of molecular dynamics simulations 28/May

Multiple Widget Embedding for Jolecule 27/Apr

WebGL makes inroads into the browser for the foot soldiers of Biochemisty 6/Mar

Jolecule widgets for your embedding pleasure! 24/Feb

2010

Jolecule Example: RNase 23/Sep

Heating Water in Molecular Dynamics 11/Sep

HTML5 mojo: JOLECULE, a javascript protein viewer that runs on the web 10/Sep

Why bioinformatics !== compstructbio, or why Rosetta is not a glorified SVM 28/Jul

★

The 2 billion dollar protein sequencing error 11/Jul

The Theory of Single Domain Allostery 30/May

How the hell do I model this thing? 20/Mar

★

A Decade in Computational Structural Biology 4/Jan

2009

The bioinformatic-journal/software hydrid 25/Oct

Heat a residue in a protein, large loops pop out 12/Jul

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

★

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

Bioinformatics in the Near Concurrent Future 4/Mar

★

An Annotated History of Molecular Dynamics 25/Feb

How efficient is Molecular Dynamics? 9/Feb

2008

How the Serpin protein traps the digestive powers of the enzyme Serine Protease 13/Oct

How to Compute Chemistry, Conference Report 24/Sep

★

How to build a cathedral door out of 456 proteins 13/Mar

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

2007

★

Calculating the Solvent Accessible Surface-Area 19/Oct

★

Parsing PDB files: sometimes you really should reinvent the wheel 1/Oct

A Most Ugly Hack: translating from CHARMM to AMBER trajectories 12/Aug

Fetching PDB files remotely in pure Python code 10/Aug

Wet Holes in the Membrane 9/May

★

The Schrodinger Equation in Action 9/May

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

★

A Sign, a Flipped Structure, and a Scientific Flameout of Epic Proportions 21/Mar

★

Notes to a young computational biologist 13/Mar

Heating up a Protein, One residue at a time 11/Feb

2006

★

Come together, electrostatically, as one 31/Dec

Looking at the surface of a membrane 30/Dec

Structural features of the Beta-sheet 23/Sep

★

The Mysterious Regions of the Ramachandran Plot 7/Aug

2005

Of proteins, clusters and musical chairs 5/Oct

Transcription as Compilation 24/Sep

★

RMSD: Root Mean Square Deviation 1/Jul

2004

We can fold it for you wholesale 12/Jun

★

The Ten Commandments of Protein Folding 10/May