Modelling Proteomes

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: .9949 Random: .7026 Best Mutated Genetic Code: SWISSPROT Correlations: Genes: .9683 Random: .9800 Mike Inouye

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

Protein structure from combining theory and experiment Ling-Hong Hung

Prediction for Invb using de novo fold recognition Ram Samudrala

Prediction of HIV-1 protease-inhibitor binding energies with MD 1.0 0.5 with MD without MD Correlation coefficient ps 0 0.2 0.4 0.6 0.8 1.0 MD simulation time Ekachai Jenwitheesuk

Bioverse – explore relationships among molecules and systems http://bioverse.compbio.washington.edu Jason Mcdermott

Bioverse – explore relationships among molecules and systems Jason Mcdermott

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

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

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