N. Borkakoti

发表

Analysis of catalytic residues in enzyme active sites.

Gail J. Bartlett, J. Thornton, C. T. Porter, 2002, Journal of molecular biology.

From structure to function: Approaches and limitations

Annabel E. Todd, C. Orengo, J. Thornton, 2000, Nature Structural Biology.

Catalysing new reactions during evolution: economy of residues and mechanism.

Gail J. Bartlett, J. Thornton, N. Borkakoti, 2003, Journal of molecular biology.

Identifying pseudoenzymes using functional annotation: pitfalls of common practice

Jonathan D. Tyzack, António J. M. Ribeiro, J. Thornton, 2020 .

Discovery of novel low molecular weight inhibitors of IMPDH via virtual needle screening.

Neera Borkakoti, Stephen D Pickett, N. Borkakoti, 2003, Bioorganic & medicinal chemistry letters.

Structural studies of matrix metalloproteinases

N. Borkakoti, 2000, Journal of Molecular Medicine.

A global analysis of function and conservation of catalytic residues in enzymes

Neera Borkakoti, Janet M. Thornton, Gemma L. Holliday, 2019, The Journal of Biological Chemistry.

Inhibition of bovine nasal cartilage degradation by selective matrix metalloproteinase inhibitors.

N. Borkakoti, P. Eyers, T. Hallam, 1997, The Biochemical journal.

Collagenase and Family

N. Borkakoti, F. Winkler, A. D'arcy, 1998 .

Collagenase inhibitors: their design and potential therapeutic use.

N. Borkakoti, N. Roberts, W. Johnson, 1987, Journal of enzyme inhibition.

Targets for Drug Design

N. Borkakoti, F. Winkler, E. J. Lewis, 1998 .

EzMechanism: an automated tool to propose catalytic mechanisms of enzyme reactions

Jonathan D. Tyzack, António J. M. Ribeiro, J. Thornton, 2022, bioRxiv.

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

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

AlphaFold2 protein structure prediction: Implications for drug discovery.

J. Thornton, N. Borkakoti, 2023, Current opinion in structural biology.

Design and synthesis of potent hydroxyethylamine (HEA) BACE-1 inhibitors carrying prime side 4,5,6,7-tetrahydrobenzazole and 4,5,6,7-tetrahydropyridinoazole templates.

N. Borkakoti, Elizabeth Hamelink, L. Vrang, 2012, Bioorganic & medicinal chemistry letters.

Matrix metalloprotease inhibitors: design from structure.

N. Borkakoti, 2004, Biochemical Society transactions.

Design and synthesis of the cartilage protective agent (CPA, Ro32-3555)

N. Borkakoti, M. Cooper, E. J. Lewis, 1997 .

Synthesis of potent BACE-1 inhibitors incorporating a hydroxyethylene isostere as central core.

N. Borkakoti, B. Samuelsson, A. Hallberg, 2010, European journal of medicinal chemistry.

Design, synthesis and SAR of potent statine-based BACE-1 inhibitors: exploration of P1 phenoxy and benzyloxy residues.

N. Borkakoti, B. Samuelsson, A. Hallberg, 2008, Bioorganic & medicinal chemistry.

Design and synthesis of potent macrocyclic renin inhibitors.

N. Borkakoti, Elizabeth Hamelink, L. Vrang, 2011, Bioorganic & medicinal chemistry letters.

Structure of the catalytic domain of human fibroblast collagenase complexed with an inhibitor

N. Borkakoti, F. Winkler, A. D'arcy, 1994, Nature Structural Biology.

Design and synthesis of potent and selective BACE-1 inhibitors.

N. Borkakoti, L. Vrang, B. Samuelsson, 2010, Journal of medicinal chemistry.

A structural biology community assessment of AlphaFold2 applications

Douglas E. V. Pires, Norman E. Davey, Carlos H. M. Rodrigues, 2021, bioRxiv.

Using mechanism similarity to understand enzyme evolution

Jonathan D. Tyzack, António J. M. Ribeiro, J. Thornton, 2022, Biophysical Reviews.

AlphaFold heralds a data-driven revolution in biology and medicine

R. Laskowski, N. Borkakoti, Janet M Thornton, 2021, Nature Medicine.

Conformational Variation in Enzyme Catalysis: A Structural Study on Catalytic Residues

António J. M. Ribeiro, J. Thornton, N. Borkakoti, 2021, bioRxiv.

Tess: A geometric hashing algorithm for deriving 3D coordinate templates for searching structural databases. Application to enzyme active sites

J. Thornton, N. Borkakoti, A. C. Wallace, 1997, Protein science : a publication of the Protein Society.

Mutagenesis Studies of Interleukin-8

N. Borkakoti, Glyn Williams, P. Jones, 1996, The Journal of Biological Chemistry.

Structure-based design of peptidomimetic antagonists of p56lck SH2 domain

I. E. Smith, N. Borkakoti, D. Banner, 2002 .

Exploring Chemical Biosynthetic Design Space with Transform-MinER.

Neera Borkakoti, Janet M Thornton, Jonathan D. Tyzack, 2019, ACS synthetic biology.

Ranking Enzyme Structures in the PDB by Bound Ligand Similarity to Biological Substrates

Neera Borkakoti, Janet M. Thornton, Jonathan D. Tyzack, 2018, Structure.

Identifying pseudoenzymes using functional annotation: pitfalls of common practice

Jonathan D. Tyzack, António J. M. Ribeiro, J. Thornton, 2019, The FEBS journal.

Matrix metalloproteases: variations on a theme.

N. Borkakoti, 1998, Progress in biophysics and molecular biology.

Zinc Endoproteases: A Structural Superfamily

N. Borkakoti, 2008 .

Structural characteristics of the matrix metalloproteinases

N. Borkakoti, 1999 .

The 3D modules of enzyme catalysis: deconstructing active sites into distinct functional entities

António J. M. Ribeiro, J. Thornton, N. Borkakoti, 2023, bioRxiv.

Identification and characterisation of an inhibitor of interleukin-8: a receptor based approach

N. Borkakoti, F. Wilson, Glyn Williams, 1996 .

Mutagenesis Studies of Interleukin-8 IDENTIFICATION OF A SECOND EPITOPE INVOLVED IN RECEPTOR BINDING*

N. Borkakoti, S. Kirtland, G. Williams, 1996 .

Synthesis of potent BACE-1 inhibitors incorporating a hydroxyethylene isostere as central core.

N. Borkakoti, B. Samuelsson, A. Hallberg, 2010, European journal of medicinal chemistry.

Enzyme function and evolution through the lens of bioinformatics

António J. M. Ribeiro, N. Borkakoti, Ioannis G. Riziotis, 2023, The Biochemical journal.

Protein interactions in the herpes simplex virus type 1 VP16-induced complex: VP16 peptide inhibition and mutational analysis of host cell factor requirements

N. Borkakoti, N. Borkakoti, M. Robinson, 1997, Journal of virology.

Paradigms of convergent evolution in enzymes

António J. M. Ribeiro, N. Borkakoti, Ioannis G. Riziotis, 2024, bioRxiv.