Bavro, Vassiliy N; Pietras, Zbigniew; Furnham, Nicholas; Pérez-Cano, Laura; Fernández-Recio, Juan; Pei, Xue Yuan; Misra, Rajeev; Luisi, Ben; (2008) Assembly and channel opening in a bacterial drug efflux machine. Molecular cell, 30 (1). pp. 114-121. ISSN 1097-2765 DOI: https://doi.org/10.1016/j.molcel.2008.02.015

Benavente, Ernest D; Coll, Francesc; Furnham, Nick; McNerney, Ruth; Glynn, Judith R; Campino, Susana; Pain, Arnab; Mohareb, Fady R; Clark, Taane G; (2015) PhyTB: Phylogenetic tree visualisation and sample positioning for M. tuberculosis. BMC Bioinformatics, 16 (1). 155-. ISSN 1471-2105 DOI: https://doi.org/10.1186/s12859-015-0603-3

Borba, Joyce VB; Silva, Arthur C; Ramos, Pablo IP; Grazzia, Nathalia; Miguel, Danilo C; Muratov, Eugene N; Furnham, Nicholas; Andrade, Carolina H; (2019) Unveiling the Kinomes of Leishmania infantum and L. braziliensis Empowers the Discovery of New Kinase Targets and Antileishmanial Compounds. Computational and Structural Biotechnology Journal, 17. pp. 352-361. ISSN 2001-0370 DOI: https://doi.org/10.1016/j.csbj.2019.02.005

Coll, Francesc; Phelan, Jody; Hill-Cawthorne, Grant A; Nair, Mridul B; Mallard, Kim; Ali, Shahjahan; Abdallah, Abdallah M; Alghamdi, Saad; Alsomali, Mona; Ahmed, Abdallah O; +41 more... Portelli, Stephanie; Oppong, Yaa; Alves, Adriana; Bessa, Theolis Barbosa; Campino, Susana; Caws, Maxine; Chatterjee, Anirvan; Crampin, Amelia C; Dheda, Keertan; Furnham, Nicholas; Glynn, Judith R; Grandjean, Louis; Ha, Dang Minh; Hasan, Rumina; Hasan, Zahra; Hibberd, Martin L; Joloba, Moses; Jones-López, Edward C; Matsumoto, Tomoshige; Miranda, Anabela; Moore, David J; Mocillo, Nora; Panaiotov, Stefan; Parkhill, Julian; Penha, Carlos; Perdigão, João; Portugal, Isabel; Rchiad, Zineb; Robledo, Jaime; Sheen, Patricia; Shesha, Nashwa Talaat; Sirgel, Frik A; Sola, Christophe; Sousa, Erivelton Oliveira; Streicher, Elizabeth M; Van Helden, Paul; Viveiros, Miguel; Warren, Robert M; McNerney, Ruth; Pain, Arnab; Clark, Taane G; (2018) Author Correction: Genome-wide analysis of multi- and extensively drug-resistant Mycobacterium tuberculosis. Nature genetics, 50 (5). 764-. ISSN 1061-4036 DOI: https://doi.org/10.1038/s41588-018-0074-3 Full text not available from this repository.

Coll, Francesc; Phelan, Jody; Hill-Cawthorne, Grant A; Nair, Mridul B; Mallard, Kim; Ali, Shahjahan; Abdallah, Abdallah M; Alghamdi, Saad; Alsomali, Mona; Ahmed, Abdallah O; +41 more... Portelli, Stephanie; Oppong, Yaa; Alves, Adriana; Bessa, Theolis Barbosa; Campino, Susana; Caws, Maxine; Chatterjee, Anirvan; Crampin, Amelia C; Dheda, Keertan; Furnham, Nicholas; Glynn, Judith R; Grandjean, Louis; Minh Ha, Dang; Hasan, Rumina; Hasan, Zahra; Hibberd, Martin L; Joloba, Moses; Jones-López, Edward C; Matsumoto, Tomoshige; Miranda, Anabela; Moore, David J; Mocillo, Nora; Panaiotov, Stefan; Parkhill, Julian; Penha, Carlos; Perdigão, João; Portugal, Isabel; Rchiad, Zineb; Robledo, Jaime; Sheen, Patricia; Shesha, Nashwa Talaat; Sirgel, Frik A; Sola, Christophe; Oliveira Sousa, Erivelton; Streicher, Elizabeth M; Helden, Paul Van; Viveiros, Miguel; Warren, Robert M; McNerney, Ruth; Pain, Arnab; Clark, Taane G; (2018) Genome-wide analysis of multi- and extensively drug-resistant Mycobacterium tuberculosis. Nature genetics, 50 (2). pp. 307-316. ISSN 1061-4036 DOI: https://doi.org/10.1038/s41588-017-0029-0

Cuff, Alison L; Sillitoe, Ian; Lewis, Tony; Clegg, Andrew B; Rentzsch, Robert; Furnham, Nicholas; Pellegrini-Calace, Marialuisa; Jones, David; Thornton, Janet; Orengo, Christine A; (2010) Extending CATH: increasing coverage of the protein structure universe and linking structure with function. Nucleic acids research, 39 (Databa). D420-D426. ISSN 0305-1048 DOI: https://doi.org/10.1093/nar/gkq1001

Doré, Andrew S; Furnham, Nicholas; Davies, Owen R; Sibanda, Bancinyane L; Chirgadze, Dimitri Y; Jackson, Stephen P; Pellegrini, Luca; Blundell, Tom L; (2006) Structure of an Xrcc4-DNA ligase IV yeast ortholog complex reveals a novel BRCT interaction mode. DNA repair, 5 (3). pp. 362-368. ISSN 1568-7864 DOI: https://doi.org/10.1016/j.dnarep.2005.11.004 Full text not available from this repository.

Eccleston, Ruth Charlotte; Manko, Emilia; Campino, Susana; Clark, Taane G; Furnham, Nicholas; (2023) A computational method for predicting the most likely evolutionary trajectories in the stepwise accumulation of resistance mutations. eLife, 12. e84756-. ISSN 2050-084X DOI: https://doi.org/10.7554/eLife.84756

Farnell, Edward J; Tyagi, Nidhi; Ryan, Stephanie; Chalmers, Iain W; Pinot de Moira, Angela; Jones, Frances M; Wawrzyniak, Jakub; Fitzsimmons, Colin M; Tukahebwa, Edridah M; Furnham, Nicholas; +2 more... Maizels, Rick M; Dunne, David W; (2015) Known Allergen Structures Predict Schistosoma mansoni IgE-Binding Antigens in Human Infection. Frontiers in immunology, 6 (FEB). 26-. ISSN 1664-3224 DOI: https://doi.org/10.3389/fimmu.2015.00026

Furnham, Nicholas; Blundell, Tom L; DePristo, Mark A; Terwilliger, Thomas C; (2006) Is one solution good enough? Nature structural & molecular biology, 13 (3). pp. 184-185. ISSN 1545-9993 DOI: https://doi.org/10.1038/nsmb0306-184 Full text not available from this repository.

Furnham, Nicholas; Dawson, Natalie L; Rahman, Syed A; Thornton, Janet M; Orengo, Christine A; (2015) Large-Scale Analysis Exploring Evolution of Catalytic Machineries and Mechanisms in Enzyme Superfamilies. Journal of molecular biology, 428 (2 Pt A). pp. 253-267. ISSN 0022-2836 DOI: https://doi.org/10.1016/j.jmb.2015.11.010

Furnham, Nicholas; Doré, Andrew S; Chirgadze, Dimitri Y; de Bakker, Paul IW; Depristo, Mark A; Blundell, Tom L; (2006) Knowledge-based real-space explorations for low-resolution structure determination. Structure (London, England, 14 (8). pp. 1313-1320. ISSN 0969-2126 DOI: https://doi.org/10.1016/j.str.2006.06.014 Full text not available from this repository.

Furnham, Nicholas; Garavelli, John S; Apweiler, Rolf; Thornton, Janet M; (2009) Missing in action: enzyme functional annotations in biological databases. Nature chemical biology, 5 (8). pp. 521-525. ISSN 1552-4450 DOI: https://doi.org/10.1038/nchembio0809-521 Full text not available from this repository.

Furnham, Nicholas; Holliday, Gemma L; de Beer, Tjaart AP; Jacobsen, Julius OB; Pearson, William R; Thornton, Janet M; (2013) The Catalytic Site Atlas 2.0: cataloging catalytic sites and residues identified in enzymes. Nucleic acids research, 42 (Databa). D485-D489. ISSN 0305-1048 DOI: https://doi.org/10.1093/nar/gkt1243

Furnham, Nicholas; Laskowski, Roman A; Thornton, Janet M; (2013) Abstracting knowledge from the Protein Data Bank. Biopolymers, 99 (3). pp. 183-188. ISSN 0006-3525 DOI: https://doi.org/10.1002/bip.22107 Full text not available from this repository.

Furnham, Nicholas; Ruffle, Stuart; Southan, Christopher; (2004) Splice variants: a homology modeling approach. Proteins, 54 (3). pp. 596-608. ISSN 0887-3585 DOI: https://doi.org/10.1002/prot.10568 Full text not available from this repository.

Furnham, Nicholas; Sillitoe, Ian; Holliday, Gemma L; Cuff, Alison L; Laskowski, Roman A; Orengo, Christine A; Thornton, Janet M; (2012) Exploring the evolution of novel enzyme functions within structurally defined protein superfamilies. PLoS computational biology, 8 (3). e1002403-. ISSN 1553-734X DOI: https://doi.org/10.1371/journal.pcbi.1002403

Furnham, Nicholas; Sillitoe, Ian; Holliday, Gemma L; Cuff, Alison L; Rahman, Syed A; Laskowski, Roman A; Orengo, Christine A; Thornton, Janet M; (2011) FunTree: a resource for exploring the functional evolution of structurally defined enzyme superfamilies. Nucleic acids research, 40 (Databa). D776-D782. ISSN 0305-1048 DOI: https://doi.org/10.1093/nar/gkr852

Furnham, Nicholas; de Bakker, Paul Iw; Gore, Swanand; Burke, David F; Blundell, Tom L; (2008) Comparative modelling by restraint-based conformational sampling. BMC structural biology, 8 (1). 7-. ISSN 1472-6807 DOI: https://doi.org/10.1186/1472-6807-8-7

Furnham, Nicholas; de Beer, Tjaart AP; Thornton, Janet M; (2012) Current challenges in genome annotation through structural biology and bioinformatics. Current opinion in structural biology, 22 (5). pp. 594-601. ISSN 0959-440X DOI: https://doi.org/10.1016/j.sbi.2012.07.005 Full text not available from this repository.

Giuliani, Sandra; Silva, Arthur C; Borba, Joyce VVB; Ramos, Pablo IP; Paveley, Ross A; Muratov, Eugene N; Andrade, Carolina Horta; Furnham, Nicholas; (2018) Computationally-guided drug repurposing enables the discovery of kinase targets and inhibitors as new schistosomicidal agents. PLoS computational biology, 14 (10). e1006515-. ISSN 1553-734X DOI: https://doi.org/10.1371/journal.pcbi.1006515

Holliday, Gemma L; Rahman, Syed Asad; Furnham, Nicholas; Thornton, Janet M; (2014) Exploring the biological and chemical complexity of the ligases. Journal of molecular biology, 426 (10). pp. 2098-2111. ISSN 0022-2836 DOI: https://doi.org/10.1016/j.jmb.2014.03.008

Karmali, Anjum M; Blundell, Tom L; Furnham, Nicholas; (2009) Model-building strategies for low-resolution X-ray crystallographic data. Acta crystallographica Section D, Biological crystallography, 65 (Pt 2). pp. 121-127. ISSN 0907-4449 DOI: https://doi.org/10.1107/S0907444908040006

Li, Yutong; Cardoso-Silva, Jonathan; Kelly, John M; Delves, Michael J; Furnham, Nicholas; Papageorgiou, Lazaros G; Tsoka, Sophia; (2024) Optimisation-based modelling for explainable lead discovery in malaria. Artificial intelligence in medicine, 147. 102700-. ISSN 0933-3657 DOI: https://doi.org/10.1016/j.artmed.2023.102700

Martinez Cuesta, Sergio; Furnham, Nicholas; Rahman, Syed Asad; Sillitoe, Ian; Thornton, Janet M; (2014) The evolution of enzyme function in the isomerases. Current opinion in structural biology, 26 (1). pp. 121-130. ISSN 0959-440X DOI: https://doi.org/10.1016/j.sbi.2014.06.002

Martínez Cuesta, Sergio; Rahman, Syed Asad; Furnham, Nicholas; Thornton, Janet M; (2015) The Classification and Evolution of Enzyme Function. Biophysical journal, 109 (6). pp. 1082-1086. ISSN 0006-3495 DOI: https://doi.org/10.1016/j.bpj.2015.04.020

Mascotti, Maria Laura; Juri Ayub, Maximiliano; Furnham, Nicholas; Thornton, Janet M; Laskowski, Roman A; (2016) Chopping and Changing: the Evolution of the Flavin-dependent Monooxygenases. Journal of molecular biology, 428 (15). pp. 3131-3146. ISSN 0022-2836 DOI: https://doi.org/10.1016/j.jmb.2016.07.003

Melo-Filho, CC; Dantas, RF; Braga, RC; Neves, BJ; Senger, MR; Valente, WC; Rezende-Neto, JM; Chaves, WT; Muratov, EN; Paveley, RA; +5 more... Furnham, N; Kamentsky, L; Carpenter, AE; Silva-Junior, FP; Andrade, CH; (2016) QSAR-Driven Discovery of Novel Chemical Scaffolds Active against Schistosoma mansoni. Journal of chemical information and modeling, 56 (7). pp. 1357-72. ISSN 1549-9596 DOI: https://doi.org/10.1021/acs.jcim.6b00055

Moreira-Filho, José T; Silva, Arthur C; Dantas, Rafael F; Gomes, Barbara F; Souza Neto, Lauro R; Brandao-Neto, Jose; Owens, Raymond J; Furnham, Nicholas; Neves, Bruno J; Silva-Junior, Floriano P; +1 more... Andrade, Carolina H; (2021) Schistosomiasis Drug Discovery in the Era of Automation and Artificial Intelligence. Frontiers in immunology, 12. 642383-. ISSN 1664-3224 DOI: https://doi.org/10.3389/fimmu.2021.642383

Neves, BJ; Dantas, RF; Senger, MR; Melo-Filho, CC; Valente, WC; de Almeida, AC; Rezende-Neto, JM; Lima, EF; Paveley, R; Furnham, N; +6 more... Muratov, E; Kamentsky, L; Carpenter, AE; Braga, RC; Silva-Junior, FP; Andrade, CH; (2016) Discovery of New Anti-Schistosomal Hits by Integration of QSAR-Based Virtual Screening and High Content Screening. Journal of medicinal chemistry, 59 (15). pp. 7075-88. ISSN 0022-2623 DOI: https://doi.org/10.1021/acs.jmedchem.5b02038

Phelan, Jody; Coll, Francesc; McNerney, Ruth; Ascher, David B; Pires, Douglas EV; Furnham, Nick; Coeck, Nele; Hill-Cawthorne, Grant A; Nair, Mridul B; Mallard, Kim; +6 more... Ramsay, Andrew; Campino, Susana; Hibberd, Martin L; Pain, Arnab; Rigouts, Leen; Clark, Taane G; (2016) Mycobacterium tuberculosis whole genome sequencing and protein structure modelling provides insights into anti-tuberculosis drug resistance. BMC medicine, 14 (1). 31-. ISSN 1741-7015 DOI: https://doi.org/10.1186/s12916-016-0575-9

Pietras, Zbigniew; Bavro, Vassiliy N; Furnham, Nicholas; Pellegrini-Calace, Marialuisa; Milner-White, E James; Luisi, Ben F; (2008) Structure and mechanism of drug efflux machinery in Gram negative bacteria. Current drug targets, 9 (9). pp. 719-728. ISSN 1389-4501 DOI: https://doi.org/10.2174/138945008785747743 Full text not available from this repository.

Portelli, Stephanie; Myung, Yoochan; Furnham, Nicholas; Vedithi, Sundeep Chaitanya; Pires, Douglas EV; Ascher, David B; (2020) Prediction of rifampicin resistance beyond the RRDR using structure-based machine learning approaches. Scientific reports, 10 (1). 18120-. ISSN 2045-2322 DOI: https://doi.org/10.1038/s41598-020-74648-y

Portelli, Stephanie; Phelan, Jody E; Ascher, David B; Clark, Taane G; Furnham, Nicholas; (2018) Understanding molecular consequences of putative drug resistant mutations in Mycobacterium tuberculosis. Scientific reports, 8 (1). 15356-. ISSN 2045-2322 DOI: https://doi.org/10.1038/s41598-018-33370-6

Ragone, Stefania; Maman, Joseph D; Furnham, Nicholas; Pellegrini, Luca; (2008) Structural basis for inhibition of homologous recombination by the RecX protein. The EMBO journal, 27 (16). pp. 2259-2269. ISSN 0261-4189 DOI: https://doi.org/10.1038/emboj.2008.145

Rahman, Syed Asad; Cuesta, Sergio Martinez; Furnham, Nicholas; Holliday, Gemma L; Thornton, Janet M; (2014) EC-BLAST: a tool to automatically search and compare enzyme reactions. Nature methods, 11 (2). pp. 171-174. ISSN 1548-7091 DOI: https://doi.org/10.1038/nmeth.2803

Ribeiro, António JM; Holliday, Gemma L; Furnham, Nicholas; Tyzack, Jonathan D; Ferris, Katherine; Thornton, Janet M; (2017) Mechanism and Catalytic Site Atlas (M-CSA): a database of enzyme reaction mechanisms and active sites. Nucleic acids research, 46 (D1). D618-D623. ISSN 0305-1048 DOI: https://doi.org/10.1093/nar/gkx1012

Sillitoe, Ian; Cuff, Alison L; Dessailly, Benoit H; Dawson, Natalie L; Furnham, Nicholas; Lee, David; Lees, Jonathan G; Lewis, Tony E; Studer, Romain A; Rentzsch, Robert; +3 more... Yeats, Corin; Thornton, Janet M; Orengo, Christine A; (2012) New functional families (FunFams) in CATH to improve the mapping of conserved functional sites to 3D structures. Nucleic acids research, 41 (Databa). D490-D498. ISSN 0305-1048 DOI: https://doi.org/10.1093/nar/gks1211

Sillitoe, Ian; Furnham, Nicholas; (2015) FunTree: advances in a resource for exploring and contextualising protein function evolution. Nucleic acids research, 44 (D1). D317-D323. ISSN 0305-1048 DOI: https://doi.org/10.1093/nar/gkv1274

Sillitoe, Ian; Lewis, Tony E; Cuff, Alison; Das, Sayoni; Ashford, Paul; Dawson, Natalie L; Furnham, Nicholas; Laskowski, Roman A; Lee, David; Lees, Jonathan G; +4 more... Lehtinen, Sonja; Studer, Romain A; Thornton, Janet; Orengo, Christine A; (2014) CATH: comprehensive structural and functional annotations for genome sequences. Nucleic acids research, 43 (Databa). D376-D381. ISSN 0305-1048 DOI: https://doi.org/10.1093/nar/gku947

Silva, Arthur C; Borba, Joyce VVB; Alves, Vinicius M; Hall, Steven US; Furnham, Nicholas; Kleinstreuer, Nicole; Muratov, Eugene; Tropsha, Alexander; Andrade, Carolina Horta; (2021) Novel computational models offer alternatives to animal testing for assessing eye irritation and corrosion potential of chemicals. Artificial Intelligence in the Life Sciences, 1. p. 100028. ISSN 2667-3185 DOI: https://doi.org/10.1016/j.ailsci.2021.100028

Tan, Min Jie Alvin; Gaunt, Michael W; Hibberd, Martin L; Furnham, Nicholas; (2017) The complex relationship between the emerging flaviviruses: dengue and Zika. Biochemist, 39 (3). pp. 18-21. ISSN 0954-982X DOI: https://doi.org/10.1042/bio03903018 Item availability may be restricted.

Tunstall, Tanushree; Phelan, Jody; Eccleston, Charlotte; Clark, Taane G; Furnham, Nicholas; (2021) Structural and Genomic Insights Into Pyrazinamide Resistance in Mycobacterium tuberculosis Underlie Differences Between Ancient and Modern Lineages. Frontiers in molecular biosciences, 8. 619403-. ISSN 2296-889X DOI: https://doi.org/10.3389/fmolb.2021.619403

Tunstall, Tanushree; Portelli, Stephanie; Phelan, Jody; Clark, Taane G; Ascher, David B; Furnham, Nicholas; (2020) Combining structure and genomics to understand antimicrobial resistance. COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL, 18. pp. 3377-3394. ISSN 2001-0370 DOI: https://doi.org/10.1016/j.csbj.2020.10.017

Tyagi, Nidhi; Farnell, Edward J; Fitzsimmons, Colin M; Ryan, Stephanie; Tukahebwa, Edridah; Maizels, Rick M; Dunne, David W; Thornton, Janet M; Furnham, Nicholas; (2015) Comparisons of Allergenic and Metazoan Parasite Proteins: Allergy the Price of Immunity. PLoS computational biology, 11 (10). e1004546-. ISSN 1553-734X DOI: https://doi.org/10.1371/journal.pcbi.1004546

Tyzack, JD; Furnham, N; Sillitoe, I; Orengo, CM; Thornton, JM; (2019) Exploring Enzyme Evolution from Changes in Sequence, Structure, and Function. Methods in molecular biology (Clifton, NJ), 1851. pp. 263-275. ISSN 1064-3745 DOI: https://doi.org/10.1007/978-1-4939-8736-8_14 Full text not available from this repository.

Tyzack, Jonathan D; Furnham, Nicholas; Sillitoe, Ian; Orengo, Christine M; Thornton, Janet M; (2017) Understanding enzyme function evolution from a computational perspective. Current opinion in structural biology, 47. pp. 131-139. ISSN 0959-440X DOI: https://doi.org/10.1016/j.sbi.2017.08.003

Valasatava, Yana; Rosato, Antonio; Furnham, Nicholas; Thornton, Janet M; Andreini, Claudia; (2017) To what extent do structural changes in catalytic metal sites affect enzyme function? Journal of inorganic biochemistry, 179. pp. 40-53. ISSN 0162-0134 DOI: https://doi.org/10.1016/j.jinorgbio.2017.11.002

de Bakker, Paul IW; Furnham, Nicholas; Blundell, Tom L; DePristo, Mark A; (2006) Conformer generation under restraints. Current opinion in structural biology, 16 (2). pp. 160-165. ISSN 0959-440X DOI: https://doi.org/10.1016/j.sbi.2006.02.001 Full text not available from this repository.

de Souza Neto, Lauro Ribeiro; Moreira-Filho, José Teófilo; Neves, Bruno Junior; Maidana, Rocío Lucía Beatriz Riveros; Guimarães, Ana Carolina Ramos; Furnham, Nicholas; Andrade, Carolina Horta; Silva, Floriano Paes; (2020) In silico Strategies to Support Fragment-to-Lead Optimization in Drug Discovery. Frontiers in chemistry, 8. 93-. ISSN 2296-2646 DOI: https://doi.org/10.3389/fchem.2020.00093

Furnham, N; (2017) Complementary Sources of Protein Functional Information: The Far Side of GO. In: UNSPECIFIED, (ed.) The Gene Ontology Handbook. Humana Press, pp. 263-274. ISBN 1940-6029 DOI: https://doi.org/10.1007/978-1-4939-3743-1_19

Tunstall, T; (2023) Using Machine Learning to Anticipate Antimicrobial Resistance in Mycobacterium Tuberculosis. PhD thesis, London School of Hygiene & Tropical Medicine. DOI: https://doi.org/10.17037/PUBS.04670981