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Lista de obras de Paul A. Bates

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

artículo científico publicado en 2013

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

artículo científico publicado en 2009

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

artículo científico publicado en 2004

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

artículo científico publicado en 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

artículo científico publicado en 1989

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

artículo científico publicado en 2001

A simple biophysical model emulates budding yeast chromosome condensation

artículo científico publicado en 2015

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

artículo científico publicado en 2012

A structure-based benchmark for protein-protein binding affinity

artículo científico publicado en 2011

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

artículo científico publicado en 2008

Alternating evolutionary pressure in a genetic algorithm facilitates protein model selection

artículo científico publicado en 2008

An automated classification of the structure of protein loops

artículo científico publicado en 1997

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

artículo científico publicado en 2011

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

artículo científico publicado en 1995

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

artículo científico publicado en 1998

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

artículo científico publicado en 2013

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

artículo científico publicado en 2020

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

artículo científico publicado en 2006

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

artículo científico publicado en 2013

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

artículo científico publicado en 1995

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

artículo científico publicado en 2013

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

artículo científico publicado en 2006

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

artículo científico publicado en 2011

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

artículo científico publicado en 2013

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

artículo científico publicado en 2002

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

artículo científico publicado en 1998

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

artículo científico publicado en 2015

Crystallization of an antitumour antibody SM3 complexed with a peptide epitope

artículo científico publicado en 1997

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

artículo científico publicado en 1997

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

artículo científico publicado en 2016

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

artículo científico publicado en 2010

Developing a move-set for protein model refinement

artículo científico publicado en 2006

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

artículo científico publicado en 2014

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

artículo científico publicado en 2002

Domain fishing: a first step in protein comparative modelling

artículo científico publicado en 2002

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

artículo científico publicado en 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.

artículo científico publicado en 2001

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

artículo científico publicado en 2018

Flexible relaxation of rigid-body docking solutions

artículo científico publicado en 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

artículo científico publicado en 2003

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

artículo científico publicado en 2000

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

artículo científico publicado en 2014

Global topological features of cancer proteins in the human interactome

artículo científico publicado en 2006

Guided docking: first step to locate potential binding sites

artículo científico publicado en 2003

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

artículo científico publicado en 2001

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

artículo científico publicado en 2017

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

artículo científico publicado en 2007

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

artículo científico publicado en 2003

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

artículo científico publicado en 2005

Kinetic Rate Constant Prediction Supports the Conformational Selection Mechanism of Protein Binding ⬇️

artículo científico publicado el 12 de enero de 2012

Macroscopic pKa Calculations for Fluorescein and Its Derivatives

artículo científico publicado en 2006

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

artículo científico publicado en 2008

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

artículo científico publicado en 2013

Mechanism of cohesin loading onto chromosomes: a conformational dynamics study

artículo científico publicado en 2010

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

artículo científico publicado en 1997

Modeling protein association mechanisms and kinetics

artículo científico publicado en 2013

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

artículo científico publicado en 2003

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

artículo científico publicado en 2003

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

artículo científico publicado en 2016

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

artículo científico publicado en 1995

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

artículo científico publicado en 2011

Predicting improved protein conformations with a temporal deep recurrent neural network

artículo científico publicado en 2018

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

artículo científico publicado en 2016

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

artículo científico publicado en 2006

Protein determinants for specific polysialylation of the neural cell adhesion molecule

artículo científico publicado en 1995

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

artículo científico publicado en 2011

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

artículo científico publicado en 2013

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

artículo científico publicado en 2010

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

artículo científico publicado en 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

artículo científico publicado en 2004

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

artículo científico publicado en 2018

Relapse models for clear cell renal carcinoma

artículo científico publicado en 2015

Repair of alkylated DNA: recent advances

artículo científico publicado en 2006

Reversal of DNA alkylation damage by two human dioxygenases

artículo científico publicado en 2002

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

artículo científico publicado en 2015

STRIPAK components determine mode of cancer cell migration and metastasis.

artículo científico publicado en 2014

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

artículo científico publicado en 2003

Structure and function of intercellular adhesion molecule-1.

artículo científico publicado en 1991

SwarmDock and the Use of Normal Modes in Protein-Protein Docking ⬇️

artículo científico publicado el 28 de septiembre de 2010

SwarmDock: a server for flexible protein-protein docking

artículo científico publicado en 2013

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

artículo científico publicado en 2014

The BRCA1 C-terminal domain: structure and function.

artículo científico publicado en 2000

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)

artículo científico publicado en 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

artículo científico publicado en 2013

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

artículo científico publicado en 2000

The sticking point: How integrins bind to their ligands

artículo científico publicado en 1994

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

artículo científico publicado en 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

artículo científico publicado en 2009

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

artículo científico publicado en 2021

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

artículo científico publicado el 1 de junio de 1992

Understanding cancer mechanisms through network dynamics

artículo científico publicado en 2012

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

artículo científico publicado en 2015

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

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