1. Modelling Proteomes

2. Genetic code evolution
Biological Genetic Code T C A G
TTT Phe (F)
TCT Ser (S)
TAT Tyr (Y)
TGT Cys (C)
TTC Phe (F)
TCC Ser (S)
TAC Tyr (Y)
TGC Cys (C)
TTA Leu (L)
TCA Ser (S)
TAA Ter
TGA Ter
TTG Leu (L)
TCG Ser (S)
TAG Ter
TGG Trp (W)
CTT Leu (L)
CCT Pro (P)
CAT His (H)
CGT Arg (R)
CTC Leu (L)
CCC Pro (P)
CAC His (H)
CGC Arg (R)
CTA Leu (L)
CCA Pro (P)
CAA Gln (Q)
CGA Arg (R)
CTG Leu (L)
CCG Pro (P)
CAG Gln (Q)
CGG Arg (R)
ATT Ile (I)
ACT Thr (T)
AAT Asn (N)
AGT Ser (S)
ATC Ile (I)
ACC Thr (T)
AAC Asn (N)
AGC Ser (S)
ATA Ile (I)
ACA Thr (T)
AAA Lys (K)
AGA Arg (R)
ATG Met (M)
ACG Thr (T)
AAG "
AGG Arg (R)
GTT Val (V)
GCT Ala (A)
GAT Asp (D)
GGT Gly (G)
GTC Val (V)
GCC Ala (A)
GAC Asp (D)
GGC Gly (G)
GTA Val (V)
GCA Ala (A)
GAA Glu (E)
GGA Gly (G)
GTG Val (V)
GCG Ala (A)
GAG Glu (E)
GGG Gly (G) T C A G
TTT Lys (K)
TCT Ser (S)
TAT Met (M)
TGT Ala (A)
TTC Lys (K)
TCC Asp (D)
TAC Ile (I)
TGC Leu (L)
TTA Ile (I)
TCA Leu (L)
TAA Ter
TGA Ter
TTG Asp (D)
TCG Leu(L)
TAG Ter
TGG Ala (A)
CTT Ala (A)
CCT Val (V)
CAT Lys (K)
CGT Thr (T)
CTC Glu (E)
CCC His (H)
CAC Ile (I)
CGC Ser (S)
CTA Thr (T)
CCA Glu (E)
CAA Ser (S)
CGA Gly (G)
CTG Pro (P)
CCG Pro (P)
CAG Thr (T)
CGG Leu (L)
ATT Tyr (Y)
ACT Ser (S)
AAT Ala (A)
AGT Gly (G)
ATC Gly (G)
ACC Gly (G)
AAC Thr (T)
AGC Ile (I)
ATA Arg (R)
ACA Gln (Q)
AAA Leu (L)
AGA Glu (E)
ATG Ser (S)
ACG Phe (F)
AAG Val (V)
AGG Ala (A)
GTT Pro (P)
GCT Ala (A)
GAT Glu (E)
GGT Arg (R)
GTC Gln (N)
GCC Val (V)
GAC Ala (A)
GGC Phe (F)
GTA Lys (K)
GCA Gln (Q)
GAA Leu (L)
GGA Arg (R)
GTG Lys (K)
GCG Leu (L)
GAG Asp (D)
GGG Val (V)
Standard Genetic Code:
SWISSPROT
Correlations:
Genes:
Random:
Best Mutated Genetic Code:
SWISSPROT
Correlations:
Genes:
Random:
Mike Inouye

3. Decomposition of all-atom function using ICA
(blind separation of sources by maximising the statistical independence across various channels)
atom type 2
atom type 1
energy
distance (A)
Disulphide
bridges
atom type 1
atom type 2
distance (A)
energy
Main chain
hydrogen bonding
atom type 2
atom type 1
energy
distance (A)
Salt
bridges
atom type 2
atom type 1
energy
distance (A)
Side -> main chain
hydrogen bonding
Shing-Chung Ngan

4. Protein structure from combining theory and experiment
Ling-Hong Hung

5. Prediction for Invb using de novo fold recognition
Ram Samudrala

6. Prediction of HIV-1 protease-inhibitor binding energies with MD
1.0
0.5
with MD
without MD
Correlation coefficient ps
MD simulation time
Ekachai Jenwitheesuk

7. Bioverse – explore relationships among molecules and systems
Jason Mcdermott

8. Bioverse – explore relationships among molecules and systems
Jason Mcdermott

9. Bioverse – human protein-protein interaction network
Jason Mcdermott/Zach Frazier

10. Bioverse – salmonella protein-protein interaction network
Jason Mcdermott/Zach Frazier

11. Bioverse – human protein-protein similarity network
Jason Mcdermott/Zach Frazier