List of works - Paul A. Bates

A Markov-chain model description of binding funnels to enhance the ranking of docked solutions

scientific article published on 10 September 2013

A dyad of lymphoblastic lysosomal cysteine proteases degrades the antileukemic drug L-asparaginase

scientific article published on 08 June 2009

A link between sequence conservation and domain motion within the AAA+ family

scientific article published in April 2004

A machine learning approach for ranking clusters of docked protein-protein complexes by pairwise cluster comparison

scientific article published on 9 December 2016

A predicted three-dimensional structure for the carcinoembryonic antigen (CEA)

scientific article published on 01 April 1992

A predicted three-dimensional structure for the human immunodeficiency virus binding domains of CD4 antigen

scientific article published in October 1989

A region encompassing the FERM domain of Jak1 is necessary for binding to the cytokine receptor gp130

scientific article published on 01 September 2001

A simple biophysical model emulates budding yeast chromosome condensation

scientific article published in 2015

A structural systems biology approach for quantifying the systemic consequences of missense mutations in proteins.

scientific article

A structure-based benchmark for protein-protein binding affinity

scientific article

Agent-based simulation of notch-mediated tip cell selection in angiogenic sprout initialisation

scientific article published in January 2008

Alternating evolutionary pressure in a genetic algorithm facilitates protein model selection

scientific article

An automated classification of the structure of protein loops.

scientific article

An siRNA screen identifies RSK1 as a key modulator of lung cancer metastasis

scientific article

Analysis of the binding site on intercellular adhesion molecule 3 for the leukocyte integrin lymphocyte function-associated antigen 1.

scientific article

Automated classification of antibody complementarity determining region 3 of the heavy chain (H3) loops into canonical forms and its application to protein structure prediction.

scientific article

Blind prediction of homo- and hetero-protein complexes: The CASP13-CAPRI experiment

scientific article published on 25 October 2019

Blind prediction of interfacial water positions in CAPRI

scientific article

Butyrophilin-2A1 Directly Binds Germline-Encoded Regions of the Vγ9Vδ2 TCR and Is Essential for Phosphoantigen Sensing

scientific article published on 09 March 2020

Can MM-PBSA calculations predict the specificities of protein kinase inhibitors?

scientific article

Cancer networks and beyond: interpreting mutations using the human interactome and protein structure

scientific article

Characterisation of the single copy trefoil peptides intestinal trefoil factor and pS2 and their ability to form covalent dimers

scientific article published on 01 January 1995

Characterizing changes in the rate of protein-protein dissociation upon interface mutation using hotspot energy and organization

scientific article (publication date: 2013)

Cluster analysis of networks generated through homology: automatic identification of important protein communities involved in cancer metastasis

scientific article

Community-wide assessment of protein-interface modeling suggests improvements to design methodology

scientific article

Community-wide evaluation of methods for predicting the effect of mutations on protein-protein interactions

scientific article

Comparative modelling: an essential methodology for protein structure prediction in the post-genomic era.

scientific article

Conformational analysis of the first observed non-proline cis-peptide bond occurring within the complementarity determining region (CDR) of an antibody

scientific article published on 01 December 1998

Cost-benefit analysis of the mechanisms that enable migrating cells to sustain motility upon changes in matrix environments

scientific article

Crystallization of an antitumour antibody SM3 complexed with a peptide epitope

scientific article published on 01 November 1997

Crystallization of the Fab fragment of the tumour-specific antibody PR1A3.

scientific article published in July 1997

Ctf4 Links DNA Replication with Sister Chromatid Cohesion Establishment by Recruiting the Chl1 Helicase to the Replisome

scientific article published on 5 July 2016

Detection and refinement of encounter complexes for protein-protein docking: taking account of macromolecular crowding

scientific article published on 01 November 2010

Developing a move-set for protein model refinement

scientific article published on 16 May 2006

Development of synchronous VHL syndrome tumors reveals contingencies and constraints to tumor evolution

scientific article

Different Smad2 partners bind a common hydrophobic pocket in Smad2 via a defined proline-rich motif

scientific article

Domain fishing: a first step in protein comparative modelling

scientific article published in August 2002

Emergence of novel cephalopod gene regulation and expression through large-scale genome reorganization

scientific article published on 21 April 2022

Enhanced sampling of protein conformational states for dynamic cross-docking within the protein-protein docking server SwarmDock

scientific article published on 07 November 2019

Enhancement of protein modeling by human intervention in applying the automatic programs 3D-JIGSAW and 3D-PSSM.

scientific article

Extracellular matrix anisotropy is determined by TFAP2C-dependent regulation of cell collisions

scientific article published on 28 October 2019

Flexible Protein-Protein Docking with SwarmDock.

scientific article published in January 2018

Flexible relaxation of rigid-body docking solutions

scientific article published on 01 July 2007

Functional recycling of C2 domains throughout evolution: a comparative study of synaptotagmin, protein kinase C and phospholipase C by sequence, structural and modelling approaches

scientific article

Genetic analysis of integrin function in man: LAD-1 and other syndromes.

scientific article

Genomic architecture and evolution of clear cell renal cell carcinomas defined by multiregion sequencing

scientific article

Global topological features of cancer proteins in the human interactome

scientific article

Guided docking: first step to locate potential binding sites.

scientific article

Homophilic adhesion of human CEACAM1 involves N-terminal domain interactions: structural analysis of the binding site

scientific article published on 01 September 2001

IRaPPA: information retrieval based integration of biophysical models for protein assembly selection

scientific article published on 14 February 2017

Implicit flexibility in protein docking: cross-docking and local refinement.

scientific article published in December 2007

In silico protein recombination: enhancing template and sequence alignment selection for comparative protein modelling

scientific article

Incorporation of flexibility into rigid-body docking: applications in rounds 3-5 of CAPRI.

scientific article published in August 2005

Kinetic rate constant prediction supports the conformational selection mechanism of protein binding

scientific article

Macroscopic pKa Calculations for Fluorescein and Its Derivatives

scientific article published on 01 November 2006

Mathematical modeling identifies Smad nucleocytoplasmic shuttling as a dynamic signal-interpreting system

scholarly article

Matrix feedback enables diverse higher-order patterning of the extracellular matrix

scientific article published on 28 October 2019

Matrix geometry determines optimal cancer cell migration strategy and modulates response to interventions

scientific article published on 23 June 2013

Mechanism of cohesin loading onto chromosomes: a conformational dynamics study

scientific article published on August 2010

Model building by comparison: a combination of expert knowledge and computer automation.

scientific article

Modeling protein association mechanisms and kinetics

scientific article

Novel use of a genetic algorithm for protein structure prediction: searching template and sequence alignment space.

scientific article

OPCML at 11q25 is epigenetically inactivated and has tumor-suppressor function in epithelial ovarian cancer

scientific article

Opposing effects of Elk-1 multisite phosphorylation shape its response to ERK activation

scientific article published on October 2016

PECAM-1: its expression and function as a cell adhesion molecule on hemopoietic and endothelial cells.

scientific article published on April 1995

Planar polarization of the atypical myosin Dachs orients cell divisions in Drosophila

scientific article published on January 2011

Predicting improved protein conformations with a temporal deep recurrent neural network

scientific article published in PLoS ONE

Predicting the structure of protein-protein complexes using the SwarmDock Web Server

scientific article published on 01 January 2014

Prediction of homoprotein and heteroprotein complexes by protein docking and template-based modeling: A CASP-CAPRI experiment

scientific article

Probability-based model of protein-protein interactions on biological timescales

scientific article published on 11 December 2006

Protein determinants for specific polysialylation of the neural cell adhesion molecule

scientific article published on July 1995

Protein-protein binding affinity prediction on a diverse set of structures

scientific article

RaTrav: a tool for calculating mean first-passage times on biochemical networks.

scientific article

Rational engineering of L-asparaginase reveals importance of dual activity for cancer cell toxicity.

scientific article published on 24 November 2010

Recognition of analogous and homologous protein folds--assessment of prediction success and associated alignment accuracy using empirical substitution matrices.

scientific article published in January 1998

Recognition of analogous and homologous protein folds: analysis of sequence and structure conservation 1 1Edited by F. E. Cohen

article

Recognition of phosphorylated-Smad2-containing complexes by a novel Smad interaction motif

scientific article published on February 2004

Refinement of protein-protein complexes in contact map space with metadynamics simulations

scientific article published on 30 October 2018

Relapse models for clear cell renal carcinoma

scientific article published on 01 August 2015

Repair of alkylated DNA: recent advances

scientific article published on 16 November 2006

Reversal of DNA alkylation damage by two human dioxygenases

scientific article

SETD2 loss-of-function promotes renal cancer branched evolution through replication stress and impaired DNA repair

scientific article

STRIPAK components determine mode of cancer cell migration and metastasis.

scientific article published on 22 December 2014

Structural context of exons in protein domains: implications for protein modelling and design.

scientific article

Structure and function of intercellular adhesion molecule-1.

scientific article published on January 1991

SwarmDock and the use of normal modes in protein-protein docking

scientific article

SwarmDock: a server for flexible protein-protein docking

scientific article published on 23 January 2013

Systematic evaluation of the prognostic impact and intratumour heterogeneity of clear cell renal cell carcinoma biomarkers

scientific article published on 19 July 2014

The BRCA1 C-terminal domain: structure and function.

scientific article

The I domain of integrin leukocyte function-associated antigen-1 is involved in a conformational change leading to high affinity binding to ligand intercellular adhesion molecule 1 (ICAM-1)

scientific article published on 01 October 1998

The relationship between the flexibility of proteins and their conformational states on forming protein-protein complexes with an application to protein-protein docking

scientific article published on 01 April 2005

The scoring of poses in protein-protein docking: current capabilities and future directions

scientific article

The second domain of intercellular adhesion molecule-1 (ICAM-1) maintains the structural integrity of the leucocyte function-associated antigen-1 (LFA-1) ligand-binding site in the first domain

scientific article published in October 2000

The sticking point: How integrins bind to their ligands

scientific article published on 01 November 1994

The structural basis for enhancer-dependent assembly and activation of the AAA transcriptional activator NorR.

scientific article published on 24 November 2014

The γδTCR combines innate immunity with adaptive immunity by utilizing spatially distinct regions for agonist selection and antigen responsiveness

scientific article published on 12 November 2018

Tipping the balance: robustness of tip cell selection, migration and fusion in angiogenesis

scientific article

Toward Patient-Specific Prediction of Ablation Strategies for Atrial Fibrillation Using Deep Learning

scientific article published on 26 May 2021

Towards an automatic method of predicting protein structure by homology: an evaluation of suboptimal sequence alignments

scientific article published on June 1, 1992

Understanding cancer mechanisms through network dynamics

scientific article published on 18 July 2012

Updates to the Integrated Protein-Protein Interaction Benchmarks: Docking Benchmark Version 5 and Affinity Benchmark Version 2.

scientific article

X-ray structural studies of I. low valence gold complexes, II. transition metal complexes containing terminal organoimido ligands

1985 doctoral thesis by Paul Alan Bates at University of Auckland

List of works by Paul A. Bates

A Markov-chain model description of binding funnels to enhance the ranking of docked solutions

A dyad of lymphoblastic lysosomal cysteine proteases degrades the antileukemic drug L-asparaginase

A link between sequence conservation and domain motion within the AAA+ family

A machine learning approach for ranking clusters of docked protein-protein complexes by pairwise cluster comparison

A predicted three-dimensional structure for the carcinoembryonic antigen (CEA)

A predicted three-dimensional structure for the human immunodeficiency virus binding domains of CD4 antigen

A region encompassing the FERM domain of Jak1 is necessary for binding to the cytokine receptor gp130

A simple biophysical model emulates budding yeast chromosome condensation

A structural systems biology approach for quantifying the systemic consequences of missense mutations in proteins.

A structure-based benchmark for protein-protein binding affinity

Agent-based simulation of notch-mediated tip cell selection in angiogenic sprout initialisation

Alternating evolutionary pressure in a genetic algorithm facilitates protein model selection

An automated classification of the structure of protein loops.

An siRNA screen identifies RSK1 as a key modulator of lung cancer metastasis

Analysis of the binding site on intercellular adhesion molecule 3 for the leukocyte integrin lymphocyte function-associated antigen 1.

Automated classification of antibody complementarity determining region 3 of the heavy chain (H3) loops into canonical forms and its application to protein structure prediction.

Blind prediction of homo- and hetero-protein complexes: The CASP13-CAPRI experiment

Blind prediction of interfacial water positions in CAPRI

Butyrophilin-2A1 Directly Binds Germline-Encoded Regions of the Vγ9Vδ2 TCR and Is Essential for Phosphoantigen Sensing

Can MM-PBSA calculations predict the specificities of protein kinase inhibitors?

Cancer networks and beyond: interpreting mutations using the human interactome and protein structure

Characterisation of the single copy trefoil peptides intestinal trefoil factor and pS2 and their ability to form covalent dimers

Characterizing changes in the rate of protein-protein dissociation upon interface mutation using hotspot energy and organization

Cluster analysis of networks generated through homology: automatic identification of important protein communities involved in cancer metastasis

Community-wide assessment of protein-interface modeling suggests improvements to design methodology

Community-wide evaluation of methods for predicting the effect of mutations on protein-protein interactions

Comparative modelling: an essential methodology for protein structure prediction in the post-genomic era.

Conformational analysis of the first observed non-proline cis-peptide bond occurring within the complementarity determining region (CDR) of an antibody

Cost-benefit analysis of the mechanisms that enable migrating cells to sustain motility upon changes in matrix environments

Crystallization of an antitumour antibody SM3 complexed with a peptide epitope

Crystallization of the Fab fragment of the tumour-specific antibody PR1A3.

Ctf4 Links DNA Replication with Sister Chromatid Cohesion Establishment by Recruiting the Chl1 Helicase to the Replisome

Detection and refinement of encounter complexes for protein-protein docking: taking account of macromolecular crowding

Developing a move-set for protein model refinement

Development of synchronous VHL syndrome tumors reveals contingencies and constraints to tumor evolution

Different Smad2 partners bind a common hydrophobic pocket in Smad2 via a defined proline-rich motif

Domain fishing: a first step in protein comparative modelling

Emergence of novel cephalopod gene regulation and expression through large-scale genome reorganization

Enhanced sampling of protein conformational states for dynamic cross-docking within the protein-protein docking server SwarmDock

Enhancement of protein modeling by human intervention in applying the automatic programs 3D-JIGSAW and 3D-PSSM.

Extracellular matrix anisotropy is determined by TFAP2C-dependent regulation of cell collisions

Flexible Protein-Protein Docking with SwarmDock.

Flexible relaxation of rigid-body docking solutions

Functional recycling of C2 domains throughout evolution: a comparative study of synaptotagmin, protein kinase C and phospholipase C by sequence, structural and modelling approaches

Genetic analysis of integrin function in man: LAD-1 and other syndromes.

Genomic architecture and evolution of clear cell renal cell carcinomas defined by multiregion sequencing

Global topological features of cancer proteins in the human interactome

Guided docking: first step to locate potential binding sites.

Homophilic adhesion of human CEACAM1 involves N-terminal domain interactions: structural analysis of the binding site

IRaPPA: information retrieval based integration of biophysical models for protein assembly selection

Implicit flexibility in protein docking: cross-docking and local refinement.

In silico protein recombination: enhancing template and sequence alignment selection for comparative protein modelling

Incorporation of flexibility into rigid-body docking: applications in rounds 3-5 of CAPRI.

Kinetic rate constant prediction supports the conformational selection mechanism of protein binding

Macroscopic pKa Calculations for Fluorescein and Its Derivatives

Mathematical modeling identifies Smad nucleocytoplasmic shuttling as a dynamic signal-interpreting system

Matrix feedback enables diverse higher-order patterning of the extracellular matrix

Matrix geometry determines optimal cancer cell migration strategy and modulates response to interventions

Mechanism of cohesin loading onto chromosomes: a conformational dynamics study

Model building by comparison: a combination of expert knowledge and computer automation.

Modeling protein association mechanisms and kinetics

Novel use of a genetic algorithm for protein structure prediction: searching template and sequence alignment space.

OPCML at 11q25 is epigenetically inactivated and has tumor-suppressor function in epithelial ovarian cancer

Opposing effects of Elk-1 multisite phosphorylation shape its response to ERK activation

PECAM-1: its expression and function as a cell adhesion molecule on hemopoietic and endothelial cells.

Planar polarization of the atypical myosin Dachs orients cell divisions in Drosophila

Predicting improved protein conformations with a temporal deep recurrent neural network

Predicting the structure of protein-protein complexes using the SwarmDock Web Server

Prediction of homoprotein and heteroprotein complexes by protein docking and template-based modeling: A CASP-CAPRI experiment

Probability-based model of protein-protein interactions on biological timescales

Protein determinants for specific polysialylation of the neural cell adhesion molecule

Protein-protein binding affinity prediction on a diverse set of structures

RaTrav: a tool for calculating mean first-passage times on biochemical networks.

Rational engineering of L-asparaginase reveals importance of dual activity for cancer cell toxicity.

Recognition of analogous and homologous protein folds--assessment of prediction success and associated alignment accuracy using empirical substitution matrices.

Recognition of analogous and homologous protein folds: analysis of sequence and structure conservation 1 1Edited by F. E. Cohen

Recognition of phosphorylated-Smad2-containing complexes by a novel Smad interaction motif

Refinement of protein-protein complexes in contact map space with metadynamics simulations

Relapse models for clear cell renal carcinoma