How are close residues of protein structures distributed in primary sequence?

Native protein sequences are close to optimal for their structures.

How large is the volume of sequence space that is compatible with a given protein structure? Starting from random sequences, low free energy sequences were generated for 108 protein backbone structures by using a Monte Carlo optimization procedure and a free energy function based primarily on Lennard-Jones packing interactions and the Lazaridis-Karplus implicit solvation model. Remarkably, in t...

Biomarkers in psychiatry: how close are we?

Until recently, there has been an ongoing worldwide quest in search for disease-specific molecular biomarkers in medicine. These biological molecules can allow for: a reliable and accurate disease diagnosis and prognosis, better understanding of pathogenesis and pathophysiological mechanisms, and for predicting disease progression and monitoring therapy. Furthermore, biomarkers can provide majo...

Close sequence comparisons are sufficient to identify

Nanorobots for medicine: how close are we?

Since the pioneering vision of Feynman in his now famous lecture ‘There’s Plenty of Room at the Bottom’ first delivered at an American Physical Society meeting at Caltech in December 1959 [1], film and scientific exploration at the nanoscale have been lending each other imagery and targets to achieve. It took only 5 years from Feynman’s lecture for a fellow resident of Los Angeles, Harry Kleine...

Formal Software Verification: How Close Are We?

Spin and its immediate predecessors were originally designed for the verification of data communication protocols. It didn’t take long, though, for us to realize that a data communications protocol is just a special case of a general distributed process system, with asynchronously executing and interacting concurrent processes. This covers both multithreaded software systems with shared memory,...