Slides of Davide Bolchini's seminar at City University, London (UK), at Centre for HCI Design, on May 2 2008. Host: Prof. Neil Maiden.

1. Usability and Bioinformatics Experience and Challenges Davide Bolchini University College London, Dept. Computer Science University of Lugano, Faculty of Communication Sciences, TEC-Lab Joint work with Anthony Finkelstein (UCL), Vito Perrone (UCL), Paolo Paolini (POLIMI and USI), Luca Mainetti (UNILE) Seminar at City University, London, Centre for HCI Design – 2 May 2008

3. The context

5. Bioinformatics researchers Biomedical, industrial researchers use, feed design, use, feed […] designers, developers „ biologists“, „wet“ scientists

9. Research Goals

12. Ongoing work & results

14. Concept 4.0 – April 08 Protein Classification: Advanced Browsing

17. Current information architecture and navigation: CATH

21. Preliminary high-level concept

23. beta Navigating the Protein Classification Class Architecture Topology Homologous Superfamily + + + +

25. beta Navigating the Protein Classification Class Architecture Topology Homologous Superfamily - - - - Mainly Alpha Mainly Beta Mixed Alpha-Beta Few Secondary Structures Orthogonal Bundle Up-down Bundle Alpha Horseshoe Alpha solenoid Alpha/alpha barrel Ribbon Single Sheet Roll Beta Barrel Sandwich Distorted Sandwich Trefoil Orthogonal Prism ... (4) (40) (1084) (2091) Single alpha-helices Heat-Stable Enterotoxin B F1FO ATP Synthase Pheromone ER-1 Methane Monooxygenase Chorismate Mutase Domain Acyl-CoA Binding Protein Receptor-associated Protein ADP Ribosyl Cyclase Phospholipase A2 Chitosanase ... Protein binding High density lipoproteins Coiled-coil Complex (site-specific ... Blood coagulation Blood coagulation Integral membrane protein Virus coat protein Regulatory protein Oxidoreductase Transport protein Proteasome activator ...

26. 1. Visualizing the distribution between classification levels

29. 2. Navigating the full protein collection by any criterion

30. beta Filter classification by: Navigating the Protein Classification Protein Domains Architecture: Alpha Horseshoe (443 domains) 16 out of 443 domains Class (4) Topology (1084) Homologous Superfamily (2091) Ribbon Single Sheet Roll Beta Barrel Clam Sandwich Distorted Sandwich Trefoil Orthogonal Bundle Updown Bundle Alpha Horseshoe [ 443 domains ] Alpha solenoid [6 domains] Alpha/alpha barrel [… domains] Beta Barrel Clam Distorted Sandwich Orthogonal Bundle Alpha Horseshoe Alpha solenoid Alpha/alpha barrel + + + Sort by: name | domains | code 1mu5A02 1mu5A03 1mu5A05 4mu4A01 1mu5A02 1mu5A02 1mu5A02 1mu5A02 1mu5A02 1mu5A02 1mu5A02 1mu5A02 1mu5A02 1mu5A02 1mu5A02 1mu5A02 Architecture (40) _ 1mu5A02 1mu5A03 1mu5A05 4mu4A01 1mu5A02 1mu5A02 1mu5A02 1mu5A02 1mu5A02 1mu5A02 1mu5A02 1mu5A02 1mu5A02 1mu5A02 1mu5A02 1mu5A02

32. 3. Superimposing multiple classifications while browsing the protein collection

33. beta Filter classification by: Navigating the Protein Classification Protein Domains Architecture: Alpha Horseshoe (443 domains) 1mu5A02 1mu5A03 1mu5A05 4mu4A01 1mu5A02 1mu5A02 1mu5A02 1mu5A02 1mu5A02 1mu5A02 1mu5A02 1mu5A02 1mu5A02 1mu5A02 1mu5A02 1mu5A02 16 out of 443 domains Class (4) Topology (3) Ribbon Single Sheet Roll Beta Barrel Clam Sandwich Distorted Sandwich Trefoil Orthogonal Bundle Updown Bundle Alpha Horseshoe [ 443 domains ] Alpha solenoid [6 domains] Alpha/alpha barrel [… domains] Beta Barrel Clam Distorted Sandwich Orthogonal Bundle Alpha Horseshoe Alpha solenoid Alpha/alpha barrel + - Sort by: name | domains | code Architecture (40) _ Leucine-rich Repeat Variant [ 91 domains ] 70-kda Soluble Lytic Transglycosylase; domain 1 [ 3 domains ] Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat [ 349 domains ]

34. beta Filter classification by: Navigating the Protein Classification Protein Domains Architecture: Alpha Horseshoe (443 domains) 1mu5A02 1mu5A03 1mu5A05 4mu4A01 1mu5A02 1mu5A02 1mu5A02 1mu5A02 1mu5A02 1mu5A02 1mu5A02 1mu5A02 1mu5A02 1mu5A02 1mu5A02 1mu5A02 16 out of 443 domains Class (4) Topology (3) Alpha Horseshoe [ 443 domains ] Alpha solenoid [6 domains] + - Sort by: name | domains | code (13) T, H T T Architecture (40) _ Leucine-rich Repeat Variant [ 91 domains ] 70-kda Soluble Lytic Transglycosylase; domain 1 [ 3 domains ] Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat [ 349 domains ] Homologous Superfamily (2091) + Leucine-rich Repeat Variant [89 domains] Lipovitellin. Chain A, domain 2 [1 domain] IP3 receptor type 1 binding core, domain 2 [1 domain] 70-kda Soluble Lytic Transglycosylase, domain 1 [3 domains] Leucine-rich Repeat Variant [89 domains] Lipovitellin. Chain A, domain 2 [1 domain] IP3 receptor type 1 binding core, domain 2 [1 domain] 70-kda Soluble Lytic Transglycosylase, domain 1 [3 domains] Leucine-rich Repeat Variant [89 domains] Lipovitellin. Chain A, domain 2 [1 domain] IP3 receptor type 1 binding core, domain 2 [1 domain] 70-kda Soluble Lytic Transglycosylase, domain 1 [3 domains] Leucine-rich Repeat Variant [89 domains] Lipovitellin. Chain A, domain 2 [1 domain] IP3 receptor type 1 binding core, domain 2 [1 domain] 70-kda Soluble Lytic Transglycosylase, domain 1 [3 domains] Leucine-rich Repeat Variant [89 domains] Lipovitellin. Chain A, domain 2 [1 domain] IP3 receptor type 1 binding core, domain 2 [1 domain]

35. ...with progressive filtering

36. beta Filter classification by: Navigating the Protein Classification Protein Domains Architecture: Alpha Horseshoe (443 domains) 1mu5A05 4mu4A01 1mu5A02 3 out of 59 domains Class (4) Topology (3) Alpha Horseshoe [ 443 domains ] Alpha solenoid [6 domains] + - Sort by: name | domains | code (13) T, H T T Architecture (40) _ Leucine-rich Repeat Variant [ 91 domains ] 70-kda Soluble Lytic Transglycosylase; domain 1 [ 3 domains ] Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat [ 349 domains ] Homologous Superfamily (2091) + Leucine-rich Repeat Variant [89 domains] Lipovitellin. Chain A, domain 2 [1 domain] IP3 receptor type 1 binding core, domain 2 [1 domain] 70-kda Soluble Lytic Transglycosylase, domain 1 [3 domains] Leucine-rich Repeat Variant [89 domains] Lipovitellin. Chain A, domain 2 [1 domain] IP3 receptor type 1 binding core, domain 2 [1 domain] 70-kda Soluble Lytic Transglycosylase, domain 1 [3 domains] Leucine-rich Repeat Variant [89 domains] Lipovitellin. Chain A, domain 2 [1 domain] IP3 receptor type 1 binding core, domain 2 [1 domain] 70-kda Soluble Lytic Transglycosylase, domain 1 [3 domains] Leucine-rich Repeat Variant [89 domains] Lipovitellin. Chain A, domain 2 [1 domain] IP3 receptor type 1 binding core, domain 2 [1 domain] 70-kda Soluble Lytic Transglycosylase, domain 1 [3 domains] Leucine-rich Repeat Variant [89 domains] Lipovitellin. Chain A, domain 2 [1 domain] IP3 receptor type 1 binding core, domain 2 [1 domain]

37. 4. Associative navigation from the protein details

38. beta Filter classification by: Navigating the Protein Classification Class (4) Topology (3) Ribbon Single Sheet Roll Beta Barrel Clam Sandwich Distorted Sandwich Trefoil Orthogonal Bundle Updown Bundle Alpha Horseshoe [ 443 domains ] Alpha solenoid [6 domains] Alpha/alpha barrel [… domains] Beta Barrel Clam Distorted Sandwich Orthogonal Bundle Alpha Horseshoe Alpha solenoid Alpha/alpha barrel + - Sort by: name | domains | code Protein Domain: 1eyhA00 ATOM Sequence HNYSEAEIKVREATSNDPWGPSSSLMSEIADLTYNVVAFSEIMSMIWKRLNDHGKNWRHVYKAMTLMEYLIKTGSERVSQ QCKENMYAVQTLKDFQYVDRDGKDQGVNVREKAKQLVALLRDEDRLREERAHALKTKEKLAQTA COMBS Sequence HNYSEAEIKVREATSNDPWGPSSSLMSEIADLTYNVVAFSEIMSMIWKRLNDHGKNWRHVYKAMTLMEYLIKTGSERVSQ QCKENMYAVQTLKDFQYVDRDGKDQGVNVREKAKQLVALLRDEDRLREERAHALKTKEKLAQTA >> Chain: 1eyhA Summary Chain ID 1eyhA Insert Timestamp 05 Mar 2006 13:03 PDB code 1eyh Flow Stage Type Chopped Seq Length 144 Fraction of Non-Alpha Carbon Atoms 0.88 Chain History Chain chopped (05 Mar 2006: Auto) PDB chopped based on information from the domall file >> Pdb: 1eyh Status PDB code 1eyh Release Date 06 May 2000 Release Status PDB_RELEASE_STATUS_ACTIVE Superseded Architecture (40) _ Leucine-rich Repeat Variant [ 91 domains ] 70-kda Soluble Lytic Transglycosylase; domain 1 [ 3 domains ] Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat [ 349 domains ] See also domains of the same:  Class: alpha (19‘729 domains)  Architecture: alpha horseshoe (443 domains)  Topology: Serine… (349 domains)  Homologous Superfamily: cell cycle (46 domains) [by other levels]

39. beta Filter classification by: Navigating the Protein Classification Protein Domains Architecture: Alpha Horseshoe (443 domains) 1mu5A02 1mu5A03 1mu5A05 4mu4A01 1mu5A02 1mu5A02 1mu5A02 1mu5A02 1mu5A02 1mu5A02 1mu5A02 1mu5A02 1mu5A02 1mu5A02 1mu5A02 1mu5A02 16 out of 443 domains Class (4) Topology (1084) Homologous Superfamily (2091) Ribbon Single Sheet Roll Beta Barrel Clam Sandwich Distorted Sandwich Trefoil Orthogonal Bundle Updown Bundle Alpha Horseshoe [ 443 domains ] Alpha solenoid [6 domains] Alpha/alpha barrel [… domains] Beta Barrel Clam Distorted Sandwich Orthogonal Bundle Alpha Horseshoe Alpha solenoid Alpha/alpha barrel + + + Sort by: name | domains | code Architecture (40) _

41. Push communication (notifying local updates)

42. beta Filter classification by: Navigating the Protein Classification Class (4) Topology (3) Ribbon Single Sheet Roll Beta Barrel Clam Sandwich Distorted Sandwich Trefoil Orthogonal Bundle Updown Bundle Alpha Horseshoe [ 443 domains ] Alpha solenoid [6 domains] Alpha/alpha barrel [… domains] Beta Barrel Clam Distorted Sandwich Orthogonal Bundle Alpha Horseshoe Alpha solenoid Alpha/alpha barrel + - Sort by: name | domains | code Protein Domain: 1eyhA00 ATOM Sequence HNYSEAEIKVREATSNDPWGPSSSLMSEIADLTYNVVAFSEIMSMIWKRLNDHGKNWRHVYKAMTLMEYLIKTGSERVSQ QCKENMYAVQTLKDFQYVDRDGKDQGVNVREKAKQLVALLRDEDRLREERAHALKTKEKLAQTA COMBS Sequence HNYSEAEIKVREATSNDPWGPSSSLMSEIADLTYNVVAFSEIMSMIWKRLNDHGKNWRHVYKAMTLMEYLIKTGSERVSQ QCKENMYAVQTLKDFQYVDRDGKDQGVNVREKAKQLVALLRDEDRLREERAHALKTKEKLAQTA >> Chain: 1eyhA Summary Chain ID 1eyhA Insert Timestamp 05 Mar 2006 13:03 PDB code 1eyh Flow Stage Type Chopped Seq Length 144 Fraction of Non-Alpha Carbon Atoms 0.88 Chain History Chain chopped (05 Mar 2006: Auto) PDB chopped based on information from the domall file >> Pdb: 1eyh Status PDB code 1eyh Release Date 06 May 2000 Release Status PDB_RELEASE_STATUS_ACTIVE Superseded XML populated as updates occur RSS Architecture (40) _ Leucine-rich Repeat Variant [ 91 domains ] 70-kda Soluble Lytic Transglycosylase; domain 1 [ 3 domains ] Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat [ 349 domains ] See also domains of the same:  Class: alpha (19‘729 domains)  Architecture: alpha horseshoe (443 domains)  Topology: Serine… (349 domains)  Homologous Superfamily: cell cycle (46 domains) […]

43. beta Filter classification by: Navigating the Protein Classification Protein Domains Architecture: Alpha Horseshoe (443 domains) 1mu5A02 1mu5A03 1mu5A05 4mu4A01 1mu5A02 1mu5A02 1mu5A02 1mu5A02 1mu5A02 1mu5A02 1mu5A02 1mu5A02 1mu5A02 1mu5A02 1mu5A02 1mu5A02 16 out of 443 domains Class (4) Topology (1084) Homologous Superfamily (2091) Ribbon Single Sheet Roll Beta Barrel Clam Sandwich Distorted Sandwich Trefoil Orthogonal Bundle Updown Bundle Alpha Horseshoe [ 443 domains ] Alpha solenoid [6 domains] Alpha/alpha barrel [… domains] Beta Barrel Clam Distorted Sandwich Orthogonal Bundle Alpha Horseshoe Alpha solenoid Alpha/alpha barrel + + + Sort by: name | domains | code RSS XML populated as updates occur Architecture (40) _