I. Sillitoe

发表

Analysis and assessment of ab initio three‐dimensional prediction, secondary structure, and contacts prediction

C. Orengo, T. Hubbard, J. Bray, 1999, Proteins.

CATH: increased structural coverage of functional space

Radka Svobodová Vareková, Su Datt Lam, Jonathan G. Lees, 2020, Nucleic Acids Res..

Review: what can structural classifications reveal about protein evolution?

Frances M. G. Pearl, Gabrielle A. Reeves, C. Orengo, 2001, Journal of structural biology.

The CATH protein family database: A resource for structural and functional annotation of genomes

Frances M. G. Pearl, Daniel W. A. Buchan, David A. Lee, 2002, Proteomics.

Contrastive learning on protein embeddings enlightens midnight zone

B. Rost, C. Orengo, I. Sillitoe, 2021, bioRxiv.

The evolution of enzyme function in the isomerases

J. Thornton, I. Sillitoe, Nicholas Furnham, 2014, Current opinion in structural biology.

Sequence analysis MSAViewer : interactive JavaScript visualization of multiple sequence alignments

Ian Sillitoe, Suzanna E. Lewis, Burkhard Rost, 2016 .

Understanding enzyme function evolution from a computational perspective.

Jonathan D Tyzack, Janet M Thornton, Ian Sillitoe, 2017, Current opinion in structural biology.

Functional innovation from changes in protein domains and their combinations.

Ian Sillitoe, Natalie L Dawson, Jonathan G Lees, 2016, Current opinion in structural biology.

The history of the CATH structural classification of protein domains

Ian Sillitoe, Christine Orengo, Janet Thornton, 2015, Biochimie.

The CATH Hierarchy Revisited—Structural Divergence in Domain Superfamilies and the Continuity of Fold Space

Ian Sillitoe, Tony E. Lewis, Mark Dibley, 2009, Structure.

Functional classification of CATH superfamilies: a domain-based approach for protein function annotation

David A. Lee, Ian Sillitoe, Christine A. Orengo, 2015, Bioinform..

The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens

Jari Björne, Tapio Salakoski, Giorgio Valentini, 2019, Genome Biology.

Assessing strategies for improved superfamily recognition

Ian Sillitoe, Mark Dibley, Sarah Addou, 2005, Protein science : a publication of the Protein Society.

The Genome3D Consortium for Structural Annotations of Selected Model Organisms.

Daniel W. A. Buchan, David T. Jones, M. Sternberg, 2020, Methods in molecular biology.

Chapter 9 A Con fi gurable , Inexpensive , Portable , Multi-channel , Multi-frequency , Multi-chromatic RGB LED System for SSVEP Stimulation

R. Palaniappan, I. Sillitoe, Surej Mouli, 2015 .

Trees for Mapping the Local Environment in Mobile Robot Navigation

I. Sillitoe, 1994 .

SARS-CoV-2 spike protein predicted to form complexes with host receptor protein orthologues from a broad range of mammals

Su Datt Lam, Jonathan G. Lees, Harry M. Scholes, 2020, Scientific Reports.

Integrating Genome3D structural annotations and predicted secondary structures in InterPro 7

Robert D. Finn, Gustavo A. Salazar, Ian Sillitoe, 2019 .

AlphaFold2 reveals commonalities and novelties in protein structure space for 21 model organisms

Su Datt Lam, B. Rost, C. Orengo, 2022, bioRxiv.

Functional classification of CATH superfamilies: a domain-based approach for protein function annotation

David A. Lee, Jonathan G. Lees, C. Orengo, 2015, Bioinform..

The InterPro protein families and domains database: 20 years on

Silvio C. E. Tosatto, Cathy H. Wu, Gustavo A. Salazar, 2020, Nucleic Acids Res..

Genome3D: integrating a collaborative data pipeline to expand the depth and breadth of consensus protein structure annotation

Marcin J. Skwark, Gustavo A. Salazar, Daniel W. A. Buchan, 2019, Nucleic Acids Res..

Assigning protein function from domain-function associations using DomFun

C. Orengo, J. A. Ranea, I. Sillitoe, 2020, BMC Bioinform..

Dissecting peripheral protein-membrane interfaces

C. Orengo, N. Reuter, I. Sillitoe, 2022, bioRxiv.

Extensive prediction of globular domains in proteins.

David A. Lee, Tony E. Lewis, Su Datt Lam, 2017 .

3D-Beacons: decreasing the gap between protein sequences and structures through a federated network of protein structure data resources

Andrew M. Waterhouse, D. Hassabis, S. Salzberg, 2022, bioRxiv.

PDBe-KB: a community-driven resource for structural and functional annotations

Alfonso Valencia, Karel Berka, Jaroslav Koča, 2019, Nucleic Acids Res..

Comprehensive Collection and Prediction of ABC Transmembrane Protein Structures in the AI Era of Structural Biology

I. Sillitoe, H. Tordai, T. Hegedűs, 2022, bioRxiv.

VarSite: Disease variants and protein structure

Janet M Thornton, Ian Sillitoe, James D Stephenson, 2019, Protein science : a publication of the Protein Society.

InterPro in 2019: improving coverage, classification and access to protein sequence annotations

Silvio C. E. Tosatto, Neil D. Rawlings, Robert D. Finn, 2018, Nucleic Acids Res..

InterPro in 2017—beyond protein family and domain annotations

Silvio C. E. Tosatto, Neil D. Rawlings, Huaiyu Mi, 2016, Nucleic Acids Res..

CATH-Gene3D: Generation of the Resource and Its Use in Obtaining Structural and Functional Annotations for Protein Sequences.

Ian Sillitoe, Su Datt Lam, Natalie L Dawson, 2017, Methods in molecular biology.

The CATH Domain Structure Database and related resources Gene3D and DHS provide comprehensive domain family information for genome analysis

Frances M. G. Pearl, Andrew P. Harrison, David A. Lee, 2004, Nucleic Acids Res..

A structural perspective on genome evolution

David A. Lee, Ian Sillitoe, Christine A. Orengo, 2004, RECOMB.

Assigning genomic sequences to CATH

James E. Bray, Frances M. G. Pearl, Andrew P. Harrison, 2000, Nucleic Acids Res..

The InterPro protein families database: the classification resource after 15 years

Huaiyu Mi, Robert D. Finn, Matthew Fraser, 2014, Nucleic Acids Res..

Genome3D: a UK collaborative project to annotate genomic sequences with predicted 3D structures based on SCOP and CATH domains

Sameer Velankar, James Smith, Daniel W. A. Buchan, 2012, Nucleic Acids Res..

MSAViewer: interactive JavaScript visualization of multiple sequence alignments

Burkhard Rost, Ian Sillitoe, Suzanna Lewis, 2016, Bioinform..

Characterizing and explaining impact of disease-associated mutations in proteins without known structures or structural homologues

C. Orengo, S. Velankar, I. Sillitoe, 2021, bioRxiv.

CATHe: detection of remote homologues for CATH superfamilies using embeddings from protein language models

B. Rost, C. Orengo, I. Sillitoe, 2022, bioRxiv.

Characterizing disease-associated human proteins without available protein structures or homologues

C. Orengo, S. Velankar, I. Sillitoe, 2021 .

CATH: comprehensive structural and functional annotations for genome sequences

David A. Lee, Ian Sillitoe, Janet M. Thornton, 2014, Nucleic Acids Res..

Gene3D: Extensive prediction of globular domains in proteins

David A. Lee, Ian Sillitoe, Christine A. Orengo, 2017, Nucleic Acids Res..

CATH: an expanded resource to predict protein function through structure and sequence

David A. Lee, Ian Sillitoe, Christine A. Orengo, 2016, Nucleic Acids Res..

Exploring the Evolution of Novel Enzyme Functions within Structurally Defined Protein Superfamilies

Ian Sillitoe, Janet M. Thornton, Christine A. Orengo, 2012, PLoS Comput. Biol..

The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens

Tapio Salakoski, Feng Zhang, Paolo Fontana, 2019, Genome Biology.

An expanded evaluation of protein function prediction methods shows an improvement in accuracy

Tapio Salakoski, Paolo Fontana, Silvio C. E. Tosatto, 2016, Genome Biology.

The CATH classification revisited—architectures reviewed and new ways to characterize structural divergence in superfamilies

Ian Sillitoe, Janet M. Thornton, Christine A. Orengo, 2008, Nucleic Acids Res..

InterPro in 2022

Silvio C. E. Tosatto, Cathy H. Wu, Gustavo A. Salazar, 2022, Nucleic Acids Res..

ModelCIF: An extension of PDBx/mmCIF data representation for computed structure models

Ben M. Webb, C. Orengo, Augustin Zídek, 2022, bioRxiv.

CATH FunFHMMer web server: protein functional annotations using functional family assignments

David A. Lee, Ian Sillitoe, Christine A. Orengo, 2015, Nucleic Acids Res..

Using CATH‐Gene3D to Analyze the Sequence, Structure, and Function of Proteins

Tony E. Lewis, C. Orengo, I. Sillitoe, 2015, Current protocols in bioinformatics.

Gene3D: a domain-based resource for comparative genomics, functional annotation and protein network analysis

Ian Sillitoe, Christine A. Orengo, Jonathan G. Lees, 2011, Nucleic Acids Res..

The CATH domain structure database: new protocols and classification levels give a more comprehensive resource for exploring evolution

Frances M. G. Pearl, Ian Sillitoe, Janet M. Thornton, 2006, Nucleic Acids Res..

Recognizing the fold of a protein structure

Frances M. G. Pearl, Andrew P. Harrison, Ian Sillitoe, 2003, Bioinform..

Extending CATH: increasing coverage of the protein structure universe and linking structure with function

Ian Sillitoe, Janet M. Thornton, Christine A. Orengo, 2010, Nucleic Acids Res..

The CATH database: an extended protein family resource for structural and functional genomics

James E. Bray, Frances M. G. Pearl, Nigel J. Martin, 2003, Nucleic Acids Res..

KinFams: De-Novo Classification of Protein Kinases Using CATH Functional Units

C. Orengo, I. Sillitoe, N. Bordin, 2023, Biomolecules.

An overview of comparative modelling and resources dedicated to large-scale modelling of genome sequences

Ian Sillitoe, Su Datt Lam, Sayoni Das, 2017, Acta crystallographica. Section D, Structural biology.

Observing using sound and light – a short review of underwater acoustic and video-based methods

I. Sillitoe, Brian D. Dushaw, P. Jonsson, 2009 .

CATH: expanding the horizons of structure-based functional annotations for genome sequences

Ian Sillitoe, Janet M. Thornton, Christine A. Orengo, 2018, Nucleic Acids Res..

Gene3D: Extensive prediction of globular domains in proteins

David A. Lee, Ian Sillitoe, Christine A. Orengo, 2017, Nucleic Acids Res..

FLORA: A Novel Method to Predict Protein Function from Structure in Diverse Superfamilies

Ian Sillitoe, Christine A. Orengo, Benoit H. Dessailly, 2009, PLoS Comput. Biol..

Assessing strategies for improved superfamily recognition

Ian Sillitoe, Mark Dibley, James E. Bray, 2005, Protein Science.

Use of structure comparison methods for the refinement of protein structure predictions. I. Identifying the structural family of a protein from low‐resolution models

Ian Sillitoe, Christine Orengo, Xavier de la Cruz, 2002, Proteins.

Functional classification of CATH superfamilies: a domain-based approach for protein function annotation

David A. Lee, Ian Sillitoe, Christine A. Orengo, 2015, Bioinform..

Robot Navigation by Waypoints

Yang Wang, Ian P. W. Sillitoe, David J. Mulvaney, 2008, J. Intell. Robotic Syst..

Improving the Feature Stability and Classification Performance of Bimodal Brain and Heart Biometrics

Raveendran Paramesran, Ramaswamy Palaniappan, Andrews Samraj, 2015, SIRS.

New functional families (FunFams) in CATH to improve the mapping of conserved functional sites to 3D structures

David A. Lee, Ian Sillitoe, Janet M. Thornton, 2012, Nucleic Acids Res..

A rapid classification protocol for the CATH Domain Database to support structural genomics

James E. Bray, Frances M. G. Pearl, Nigel J. Martin, 2001, Nucleic Acids Res..

Tracing Evolution Through Protein Structures: Nature Captured in a Few Thousand Folds

Jonathan G. Lees, C. Orengo, J. Lees, 2021, Frontiers in Molecular Biosciences.

CATH: comprehensive structural and functional annotations for genome sequences

David A. Lee, Tony E. Lewis, Alison L. Cuff, 2014, Nucleic Acids Research.

Gene3D: expanding the utility of domain assignments

David A. Lee, Ian Sillitoe, Christine A. Orengo, 2015, Nucleic Acids Res..

BioJS: an open source standard for biological visualisation – its status in 2014

Aleksandra Pawlik, Leyla Jael García Castro, Henning Hermjakob, 2014, F1000Research.

Gene3D: Multi-domain annotations for protein sequence and comparative genome analysis

David A. Lee, Ian Sillitoe, Christine A. Orengo, 2013, Nucleic Acids Res..

Anatomy of BioJS, an open source community for the life sciences

Burkhard Rost, Devasena Inupakutika, Manuel Corpas, 2015, eLife.

Assigning protein function from domain-function associations using DomFun

C. Orengo, J. A. Ranea, I. Sillitoe, 2022, BMC Bioinformatics.

MSAViewer: interactive JavaScript visualization of multiple sequence alignments

B. Rost, S. Lewis, I. Sillitoe, 2016, Bioinform..

Associating Protein Domains with Biological Functions: A Tripartite Network Approach

Ian Sillitoe, Christine A. Orengo, Pedro Seoane, 2019, IWBBIO.

The Classification of Protein Domains.

Ian Sillitoe, Christine A Orengo, Russell L. Marsden, 2017, Methods in molecular biology.

Assessing strategies for improved superfamily recognition

C. Orengo, I. Sillitoe, Mark Dibley, 2005 .

cath-resolve-hits: a new tool that resolves domain matches suspiciously quickly

Ian Sillitoe, Tony E. Lewis, Jonathan G. Lees, 2018, Bioinform..

cath-resolve-hits: a new tool that resolves domain matches suspiciously quickly

Tony E. Lewis, J. Lees, I. Sillitoe, 2018, Bioinform..

Functional innovation from changes in protein domains and their combinations.

C. Orengo, J. Lees, I. Sillitoe, 2016, Current opinion in structural biology.

CATH: comprehensive structural and functional annotations for genome sequences

David A. Lee, Tony E. Lewis, Jonathan G. Lees, 2014, Nucleic Acids Res..

Predicting human and viral protein variants affecting COVID-19 susceptibility and repurposing therapeutics

Su Datt Lam, I. Sillitoe, N. Bordin, 2023, bioRxiv.

A granular approach to aggregation within sensor networks

I.P.W. Sillitoe, J. Bergstrom, I. Sillitoe, 2005, CIMSA. 2005 IEEE International Conference on Computational Intelligence for Measurement Systems and Applications, 2005..

The history of the CATH structural classification of protein domains

C. Orengo, J. Thornton, I. Sillitoe, 2015, Biochimie.

FunTree: a resource for exploring the functional evolution of structurally defined enzyme superfamilies

Ian Sillitoe, Janet M. Thornton, Christine A. Orengo, 2011, Nucleic Acids Res..

The Aquila Digital Community The Aquila Digital Community

Silvio C. E. Tosatto, Karin M. Verspoor, David A. Lee, 2022 .

Exploring Enzyme Evolution from Changes in Sequence, Structure, and Function.

Jonathan D Tyzack, Janet M Thornton, Ian Sillitoe, 2018, Methods in molecular biology.

LSHTM Research Online

J. Seeley, I. Sillitoe, D. Wight, 2020 .

A robust controller for wheel-slip attenuation

S. Szumko, I.P.W. Sillitoe, I. Sillitoe, 1991 .