A New Framework for Computational Protein Design through Cost Function Network Optimization
This page gives access to data, documentation and software to
reproduce the experiments presented in
our publication in Bioinformatics on a set of 35 Computational
Protein Design instances.
You can directly access from here:
- A QuickStart guide to help you
produce your own designs using OSPREY 2.0 and toulbar2 (and also
reproduce our results).
- The set of Open Source resources
(OSPREY 2.0, dependencies and toulbar2) needed to execute these
instructions on a Linux platform.
- The set of 35 energetic models, both in "OSPREY 2.0" and
"toulbar2 formats with corresponding results for GMEC
identification, enumeration of solutions and corresponding set
of sequences. Large files are compressed using the strong
compressor "xz" (readable using the 7-zip software).
List of instances (by PDB identifiers):
Design for 1BK2
Cpu-times in sec. (TO = Timeout/100h, MO = Memory out/128G)
| PDB Name | Conformation space | Osprey 2.0 | Cplex | Toulbar2 |
|---|
| 1BK2 | 1.18e+32 | 93.20 | 303.00 | 0.65 |
|---|
Energy matrices
GMEC
Solution enumeration
Design for 1BRS
Cpu-times in sec. (TO = Timeout/100h, MO = Memory out/128G)
| PDB Name | Conformation space | Osprey 2.0 | Cplex | Toulbar2 |
|---|
| 1BRS | 1.67e+64 | TO | 2.39e+05 | 426.0 |
|---|
Energy matrices
GMEC
Solution enumeration
Design for 1C9O
Cpu-times in sec. (TO = Timeout/100h, MO = Memory out/128G)
| PDB Name | Conformation space | Osprey 2.0 | Cplex | Toulbar2 |
|---|
| 1C9O | 3.77e+49 | 2.31e+03 | 1.40e+03 | 2.20 |
|---|
Energy matrices
GMEC
Solution enumeration
Design for 1CDL
Cpu-times in sec. (TO = Timeout/100h, MO = Memory out/128G)
| PDB Name | Conformation space | Osprey 2.0 | Cplex | Toulbar2 |
|---|
| 1CDL | 5.68e+65 | TO | TO | 191.1 |
|---|
Energy matrices
GMEC
Solution enumeration
Design for 1CM1
Cpu-times in sec. (TO = Timeout/100h, MO = Memory out/128G)
| PDB Name | Conformation space | Osprey 2.0 | Cplex | Toulbar2 |
|---|
| 1CM1 | 3.73e+63 | TO | 2.65e+04 | 19.2 |
|---|
Energy matrices
GMEC
Solution enumeration
Design for 1CSE
Cpu-times in sec. (TO = Timeout/100h, MO = Memory out/128G)
| PDB Name | Conformation space | Osprey 2.0 | Cplex | Toulbar2 |
|---|
| 1CSE | 8.35e+82 | 367.00 | 205.93 | 1.36 |
|---|
Energy matrices
GMEC
Solution enumeration
Design for 1CSK
Cpu-times in sec. (TO = Timeout/100h, MO = Memory out/128G)
| PDB Name | Conformation space | Osprey 2.0 | Cplex | Toulbar2 |
|---|
| 1CSK | 4.09e+32 | 41.70 | 24.90 | 0.15 |
|---|
Energy matrices
GMEC
Solution enumeration
Design for 1CSP
Cpu-times in sec. (TO = Timeout/100h, MO = Memory out/128G)
| PDB Name | Conformation space | Osprey 2.0 | Cplex | Toulbar2 |
|---|
| 1CSP | 5.02e+30 | 200.00 | 360.00 | 0.84 |
|---|
Energy matrices
GMEC
Solution enumeration
Design for 1CTF
Cpu-times in sec. (TO = Timeout/100h, MO = Memory out/128G)
| PDB Name | Conformation space | Osprey 2.0 | Cplex | Toulbar2 |
|---|
| 1CTF | 3.95e+51 | TO | 580.40 | 1.23 |
|---|
Energy matrices
GMEC
Solution enumeration
Design for 1DKT
Cpu-times in sec. (TO = Timeout/100h, MO = Memory out/128G)
| PDB Name | Conformation space | Osprey 2.0 | Cplex | Toulbar2 |
|---|
| 1DKT | 3.94e+58 | 5.42e+03 | 1.85e+03 | 3.95 |
|---|
Energy matrices
GMEC
Solution enumeration
Design for 1ENH
Cpu-times in sec. (TO = Timeout/100h, MO = Memory out/128G)
| PDB Name | Conformation space | Osprey 2.0 | Cplex | Toulbar2 |
|---|
| 1ENH | 6.65e+64 | TO | TO | TO |
|---|
Energy matrices
GMEC
Design for 1FNA
Cpu-times in sec. (TO = Timeout/100h, MO = Memory out/128G)
| PDB Name | Conformation space | Osprey 2.0 | Cplex | Toulbar2 |
|---|
| 1FNA | 3.02e+47 | 3.31e+03 | 419.00 | 0.73 |
|---|
Energy matrices
GMEC
Solution enumeration
Design for 1FYN
Cpu-times in sec. (TO = Timeout/100h, MO = Memory out/128G)
| PDB Name | Conformation space | Osprey 2.0 | Cplex | Toulbar2 |
|---|
| 1FYN | 5.04e+36 | 622.00 | 2.26e+03 | 3.79 |
|---|
Energy matrices
GMEC
Solution enumeration
Design for 1GVP
Cpu-times in sec. (TO = Timeout/100h, MO = Memory out/128G)
| PDB Name | Conformation space | Osprey 2.0 | Cplex | Toulbar2 |
|---|
| 1GVP | 1.51e+78 | TO | TO | 593.6 |
|---|
Energy matrices
GMEC
Solution enumeration
Design for 1HNG
Cpu-times in sec. (TO = Timeout/100h, MO = Memory out/128G)
| PDB Name | Conformation space | Osprey 2.0 | Cplex | Toulbar2 |
|---|
| 1HNG | 3.70e+88 | 5.59e+03 | 4.15e+03 | 6.97 |
|---|
Energy matrices
GMEC
Solution enumeration
Design for 1L63
Cpu-times in sec. (TO = Timeout/100h, MO = Memory out/128G)
| PDB Name | Conformation space | Osprey 2.0 | Cplex | Toulbar2 |
|---|
| 1L63 | 2.17e+94 | MO | 2.82e+03 | 6.41 |
|---|
Energy matrices
GMEC
Solution enumeration
Design for 1LZ1
Cpu-times in sec. (TO = Timeout/100h, MO = Memory out/128G)
| PDB Name | Conformation space | Osprey 2.0 | Cplex | Toulbar2 |
|---|
| 1LZ1 | 1.04e+72 | TO | 1.25e+03 | 2.11 |
|---|
Energy matrices
GMEC
Solution enumeration
Design for 1MJC
Cpu-times in sec. (TO = Timeout/100h, MO = Memory out/128G)
| PDB Name | Conformation space | Osprey 2.0 | Cplex | Toulbar2 |
|---|
| 1MJC | 4.36e+26 | 4.57 | 3.94 | 0.08 |
|---|
Energy matrices
GMEC
Solution enumeration
Design for 1NXB
Cpu-times in sec. (TO = Timeout/100h, MO = Memory out/128G)
| PDB Name | Conformation space | Osprey 2.0 | Cplex | Toulbar2 |
|---|
| 1NXB | 2.61e+41 | 11.10 | 21.20 | 0.24 |
|---|
Energy matrices
GMEC
Solution enumeration
Design for 1PGB
Cpu-times in sec. (TO = Timeout/100h, MO = Memory out/128G)
| PDB Name | Conformation space | Osprey 2.0 | Cplex | Toulbar2 |
|---|
| 1PGB | 5.10e+61 | TO | TO | TO |
|---|
Energy matrices
GMEC
Design for 1PIN
Cpu-times in sec. (TO = Timeout/100h, MO = Memory out/128G)
| PDB Name | Conformation space | Osprey 2.0 | Cplex | Toulbar2 |
|---|
| 1PIN | 5.32e+39 | 9.54e+03 | 3.00e+03 | 3.99 |
|---|
Energy matrices
GMEC
Solution enumeration
Design for 1POH
Cpu-times in sec. (TO = Timeout/100h, MO = Memory out/128G)
| PDB Name | Conformation space | Osprey 2.0 | Cplex | Toulbar2 |
|---|
| 1POH | 8.02e+43 | 77.90 | 31.80 | 0.45 |
|---|
Energy matrices
GMEC
Solution enumeration
Design for 1RIS
Cpu-times in sec. (TO = Timeout/100h, MO = Memory out/128G)
| PDB Name | Conformation space | Osprey 2.0 | Cplex | Toulbar2 |
|---|
| 1RIS | 1.23e+80 | TO | TO | 501.00 |
|---|
Energy matrices
GMEC
Solution enumeration
Design for 1SHF
Cpu-times in sec. (TO = Timeout/100h, MO = Memory out/128G)
| PDB Name | Conformation space | Osprey 2.0 | Cplex | Toulbar2 |
|---|
| 1SHF | 1.05e+34 | 44.30 | 11.10 | 0.17 |
|---|
Energy matrices
GMEC
Solution enumeration
Design for 1SHG
Cpu-times in sec. (TO = Timeout/100h, MO = Memory out/128G)
| PDB Name | Conformation space | Osprey 2.0 | Cplex | Toulbar2 |
|---|
| 1SHG | 2.13e+32 | 138.00 | 42.30 | 0.25 |
|---|
Energy matrices
GMEC
Solution enumeration
Design for 1STN
Cpu-times in sec. (TO = Timeout/100h, MO = Memory out/128G)
| PDB Name | Conformation space | Osprey 2.0 | Cplex | Toulbar2 |
|---|
| 1STN | 2.00e+249 | TO | MO | MO |
|---|
Energy matrices
GMEC
Design for 1TEN
Cpu-times in sec. (TO = Timeout/100h, MO = Memory out/128G)
| PDB Name | Conformation space | Osprey 2.0 | Cplex | Toulbar2 |
|---|
| 1TEN | 6.17e+43 | 113.00 | 81.70 | 0.33 |
|---|
Energy matrices
GMEC
Solution enumeration
Design for 1UBI
Cpu-times in sec. (TO = Timeout/100h, MO = Memory out/128G)
| PDB Name | Conformation space | Osprey 2.0 | Cplex | Toulbar2 |
|---|
| 1UBI | 2.43e+49 | TO | 704.00 | 2.14 |
|---|
Energy matrices
GMEC
Solution enumeration
Design for 2CI2
Cpu-times in sec. (TO = Timeout/100h, MO = Memory out/128G)
| PDB Name | Conformation space | Osprey 2.0 | Cplex | Toulbar2 |
|---|
| 2CI2 | 7.26e+75 | TO | TO | TO |
|---|
Energy matrices
GMEC
Design for 2DRI
Cpu-times in sec. (TO = Timeout/100h, MO = Memory out/128G)
| PDB Name | Conformation space | Osprey 2.0 | Cplex | Toulbar2 |
|---|
| 2DRI | 1.16e+47 | TO | | 2.92e+5 24.5 |
|---|
Energy matrices
GMEC
Solution enumeration
Design for 2PCY
Cpu-times in sec. (TO = Timeout/100h, MO = Memory out/128G)
| PDB Name | Conformation space | Osprey 2.0 | Cplex | Toulbar2 |
|---|
| 2PCY | 2.34e+52 | 2.08e+03 | 76.70 | 0.51 |
|---|
Energy matrices
GMEC
Solution enumeration
Design for 2RN2
Cpu-times in sec. (TO = Timeout/100h, MO = Memory out/128G)
| PDB Name | Conformation space | Osprey 2.0 | Cplex | Toulbar2 |
|---|
| 2RN2 | 3.68e+80 | MO | 1.14e+03 | 2.77 |
|---|
Energy matrices
GMEC
Solution enumeration
Design for 2TRX
Cpu-times in sec. (TO = Timeout/100h, MO = Memory out/128G)
| PDB Name | Conformation space | Osprey 2.0 | Cplex | Toulbar2 |
|---|
| 2TRX | 9.02e+59 | 487.00 | 1.34e+03 | 1.7 |
|---|
Energy matrices
GMEC
Solution enumeration
Design for 3CHY
Cpu-times in sec. (TO = Timeout/100h, MO = Memory out/128G)
| PDB Name | Conformation space | Osprey 2.0 | Cplex | Toulbar2 |
|---|
| 3CHY | 2.36e+92 | TO | 2.91e+04 | 171.00 |
|---|
Energy matrices
GMEC
Solution enumeration
Design for 3HHR
Cpu-times in sec. (TO = Timeout/100h, MO = Memory out/128G)
| PDB Name | Conformation space | Osprey 2.0 | Cplex | Toulbar2 |
|---|
| 3HHR | 2.98e+171 | TO | MO | TO |
|---|
Energy matrices
GMEC