Publications by authors named "Jonathan D Tyzack"

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EzMechanism: an automated tool to propose catalytic mechanisms of enzyme reactions.
Antonio J M Ribeiro, Ioannis G Riziotis, Jonathan D Tyzack, Neera Borkakoti, Janet M Thornton

Nat Methods· October 2023

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Using mechanism similarity to understand enzyme evolution.
António J M Ribeiro, Ioannis G Riziotis, Jonathan D Tyzack, Neera Borkakoti, Janet M Thornton

Biophys Rev· December 2022

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The Enzyme Portal: an integrative tool for enzyme information and analysis.
Rossana Zaru, Joseph Onwubiko, Antonio J M Ribeiro, Keeva Cochrane, Jonathan D Tyzack

FEBS J· October 2022

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GRaSP-web: a machine learning strategy to predict binding sites based on residue neighborhood graphs.
Charles A Santana, Sandro C Izidoro, Raquel C de Melo-Minardi, Jonathan D Tyzack, António J M Ribeiro

Nucleic Acids Res· July 2022

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Structure-Guided Engineering of a Family IV Cold-Adapted Esterase Expands Its Substrate Range.
Nehad Noby, Rachel L Johnson, Jonathan D Tyzack, Amira M Embaby, Hesham Saeed

Int J Mol Sci· April 2022

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GRaSP: a graph-based residue neighborhood strategy to predict binding sites.
Charles A Santana, Sabrina de A Silveira, João P A Moraes, Sandro C Izidoro, Raquel C de Melo-Minardi, Jonathan D Tyzack

Bioinformatics· December 2020

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Identifying pseudoenzymes using functional annotation: pitfalls of common practice.
Antonio J M Ribeiro, Jonathan D Tyzack, Neera Borkakoti, Janet M Thornton

FEBS J· October 2020

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A global analysis of function and conservation of catalytic residues in enzymes.
António J M Ribeiro, Jonathan D Tyzack, Neera Borkakoti, Gemma L Holliday, Janet M Thornton

J Biol Chem· January 2020

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Exploring Chemical Biosynthetic Design Space with Transform-MinER.
Jonathan D Tyzack, Antonio J M Ribeiro, Neera Borkakoti, Janet M Thornton

ACS Synth Biol· November 2019

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Finding enzyme cofactors in Protein Data Bank.
Abhik Mukhopadhyay, Neera Borkakoti, Lukáš Pravda, Jonathan D Tyzack, Janet M Thornton

Bioinformatics· September 2019

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Exploring Enzyme Evolution from Changes in Sequence, Structure, and Function.
Jonathan D Tyzack, Nicholas Furnham, Ian Sillitoe, Christine M Orengo, Janet M Thornton

Methods Mol Biol· May 2019

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Computational methods and tools to predict cytochrome P450 metabolism for drug discovery.
Jonathan D Tyzack, Johannes Kirchmair

Chem Biol Drug Des· April 2019

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Transform-MinER: transforming molecules in enzyme reactions.
Jonathan D Tyzack, Antonio J M Ribeiro, Neera Borkakoti, Janet M Thornton

Bioinformatics· October 2018

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Can the inhibition of cytochrome P450 in aquatic invertebrates due to azole fungicides be estimated with in silico and in vitro models and extrapolated between species?
Michele Gottardi, Jonathan D Tyzack, Andreas Bender, Nina Cedergreen

Aquat Toxicol· August 2018

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WhichP450: a multi-class categorical model to predict the major metabolising CYP450 isoform for a compound.
Peter A Hunt, Matthew D Segall, Jonathan D Tyzack

J Comput Aided Mol Des· April 2018

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Ranking Enzyme Structures in the PDB by Bound Ligand Similarity to Biological Substrates.
Jonathan D Tyzack, Laurent Fernando, Antonio J M Ribeiro, Neera Borkakoti, Janet M Thornton

Structure· April 2018

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Mechanism and Catalytic Site Atlas (M-CSA): a database of enzyme reaction mechanisms and active sites.
António J M Ribeiro, Gemma L Holliday, Nicholas Furnham, Jonathan D Tyzack, Katherine Ferris

Nucleic Acids Res· January 2018

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Understanding enzyme function evolution from a computational perspective.
Jonathan D Tyzack, Nicholas Furnham, Ian Sillitoe, Christine M Orengo, Janet M Thornton

Curr Opin Struct Biol· December 2017

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Predicting Regioselectivity and Lability of Cytochrome P450 Metabolism Using Quantum Mechanical Simulations.
Jonathan D Tyzack, Peter A Hunt, Matthew D Segall

J Chem Inf Model· November 2016

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Investigating and Predicting how Biology Changes Molecules and Their Properties.
Jonathan D Tyzack, Robert C Glen

Mol Inform· June 2014

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Cytochrome P450 site of metabolism prediction from 2D topological fingerprints using GPU accelerated probabilistic classifiers.
Jonathan D Tyzack, Hamse Y Mussa, Mark J Williamson, Johannes Kirchmair, Robert C Glen

J Cheminform· June 2014

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FAst MEtabolizer (FAME): A rapid and accurate predictor of sites of metabolism in multiple species by endogenous enzymes.
Johannes Kirchmair, Mark J Williamson, Avid M Afzal, Jonathan D Tyzack, Alison P K Choy

J Chem Inf Model· November 2013

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Prediction of cytochrome P450 xenobiotic metabolism: tethered docking and reactivity derived from ligand molecular orbital analysis.
Jonathan D Tyzack, Mark J Williamson, Rubben Torella, Robert C Glen

J Chem Inf Model· June 2013

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Computational prediction of metabolism: sites, products, SAR, P450 enzyme dynamics, and mechanisms.
Johannes Kirchmair, Mark J Williamson, Jonathan D Tyzack, Lu Tan, Peter J Bond

J Chem Inf Model· March 2012

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