All 12 chromatic notes/pitches used for chords and tuplets; melody, bass, and bends in a fixed scale (default C major).

A  - A     - small hydrophobic
A# - P     - larger hydrophobic, ringed, least conformational freedom
B  - S,T   - small hydroxls
C  - C,M   - contains sulphur atom
C# - N,Q   - neutral versions of D and E
D  - D     - medium acidic negatively charged
D# - K,R   - basic positively charged
E  - E     - large acidic negatively charged
F  - F,W,Y - large ring hydrophobic
F# - I,L,V - medium branched hydrophobic
G  - G     - smallest, greatest conformational freedom
G# - H     - imidazole ring, can be positive and negative


melodies: main chain - notes in different scales from amino acid mappings by chemical logic below

drums: main chain - speed up in helices/slow down in sheets variants (sprinkling of drum/noise effects based based on tertiary structure)

bass: main chain - speed up in helices/show down in sheets

chords: notes current position note interacts with, played simultaneously with different instruments with distance dictacting octaves 

tuplets: similar to chords, except that component notes are played explicitly per measure

bends: log odds scores using the RAPDF scoring function are used to manipulate the pitchwheel (solos)

volumes: dictated by position in sequence

times: distances for different time lengths/signatures?

melodies/chords: based on atom types instead of main chain?


proteomusic web server (input patch changes and chords by a configuration file)
proteomusic project (60 minutes)

track ideas:

theme is an album around biological processes/functions: i.e.,
translation, design, transition, transcription, evolution, inhibition,

translation: prototype track from 1ctf 
design: new designer protein form top7 1qys-A
twisted helices: logo derived from 2lh4
transition: native->intermediate->transition states 
function: designer form to function from 2kdl-A and 2kdm-A?
discrimination: decoy track(s), finding the best model track
variation: different patches and scales of same structure track(s)
function:  mfs-based track?
protein protein interface track
protein dna interface track
proteome/interactome track
important/disease protein track(s)
song build up showcasing tracks track
evolution: multifunctional evolution from 1tim-A
evolutionary track(s)
 - evolutionary history of a protein 
 - mixing and match track?
 - alignment track
track buildup by complexity of protein (do both):
  - short helix+strand motif repeated (th repeated? no strands)
  - longer mixed protein slowly mixed up

for tracks involving multiple proteins, for example an evolutionary
track or an intermediate/translition state track, or even a decoy
track, perhaps single tracks from each of the proteins (for example, a
bassline from protein 1, a melody from protein 2, the drum tracks from
3) could all be merged. Alternately, each of the individual proteins
could all be mixed into two tracks and you could have a mash up of

Eqe could use the MFS scores to weight certain notes and beats more
too so it hightlights the functionally important regions. That's an
idea. But I feel the song is very complicated as it is.


Proteomusic || TWISTED HELICES || Ram Samudrala || ram@twisted-helices.com