(Q85857386)

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Investigating Molecular Mechanisms of Activation and Mutation of the HER2 Receptor Tyrosine Kinase through Computational Modeling and Simulation

scientific article published on 01 January 2011

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21 February 2020

Investigating Molecular Mechanisms of Activation and Mutation of the HER2 Receptor Tyrosine Kinase through Computational Modeling and Simulation (English)

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Europe PubMed Central

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21 February 2020

author name string

Shannon E Telesco

1

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21 February 2020

Andrew Shih

2

1 reference

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21 February 2020

Yingting Liu

3

1 reference

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21 February 2020

Ravi Radhakrishnan

4

1 reference

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21 February 2020

publication date

1 January 2011

1 reference

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21 February 2020

4

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21 February 2020

4

1 reference

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21 February 2020

1-35

1 reference

Europe PubMed Central

PMC publication ID

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21 February 2020

Mechanism of biological synergy between cellular Src and epidermal growth factor receptor

1 reference

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12 December 2020

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Cell signaling by receptor tyrosine kinases

1 reference

https://pubmed.ncbi.nlm.nih.gov/25346782

12 December 2020

based on heuristic

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Single mutation induced H3N2 hemagglutinin antibody neutralization: a free energy perturbation study

1 reference

https://pubmed.ncbi.nlm.nih.gov/25346782

12 December 2020

based on heuristic

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Progress in modeling of protein structures and interactions

1 reference

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12 December 2020

based on heuristic

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Large-scale protein structure modeling of the Saccharomyces cerevisiae genome

1 reference

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12 December 2020

based on heuristic

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Absence of autophosphorylation site Y882 in the p185neu oncogene product correlates with a reduction of transforming potential

1 reference

https://pubmed.ncbi.nlm.nih.gov/25346782

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Tertiary templates for proteins. Use of packing criteria in the enumeration of allowed sequences for different structural classes

1 reference

https://pubmed.ncbi.nlm.nih.gov/25346782

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

An efficient method for sampling the essential subspace of proteins.

1 reference

https://pubmed.ncbi.nlm.nih.gov/25346782

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

The Protein Data Bank

1 reference

https://pubmed.ncbi.nlm.nih.gov/25346782

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Molecular dynamics analysis of conserved hydrophobic and hydrophilic bond-interaction networks in ErbB family kinases

1 reference

https://pubmed.ncbi.nlm.nih.gov/25346782

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Molecular dynamics: applications to proteins

1 reference

https://pubmed.ncbi.nlm.nih.gov/25346782

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Protein structure prediction and model quality assessment

1 reference

https://pubmed.ncbi.nlm.nih.gov/25346782

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Hsp90 restrains ErbB-2/HER2 signalling by limiting heterodimer formation

1 reference

https://pubmed.ncbi.nlm.nih.gov/25346782

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Predicting for activity of second-line trastuzumab-based therapy in her2-positive advanced breast cancer

1 reference

https://pubmed.ncbi.nlm.nih.gov/25346782

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

c-Src modulates ErbB2 and ErbB3 heterocomplex formation and function

1 reference

https://pubmed.ncbi.nlm.nih.gov/25346782

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

The extracellular region of ErbB4 adopts a tethered conformation in the absence of ligand

1 reference

https://pubmed.ncbi.nlm.nih.gov/25346782

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Molecular systems biology of ErbB1 signaling: bridging the gap through multiscale modeling and high-performance computing

1 reference

https://pubmed.ncbi.nlm.nih.gov/25346782

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

EGF-ERBB signalling: towards the systems level

1 reference

https://pubmed.ncbi.nlm.nih.gov/25346782

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Phase II trial of pertuzumab and trastuzumab in patients with human epidermal growth factor receptor 2-positive metastatic breast cancer that progressed during prior trastuzumab therapy

1 reference

https://pubmed.ncbi.nlm.nih.gov/25346782

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Protein tyrosine kinase structure and function

1 reference

https://pubmed.ncbi.nlm.nih.gov/25346782

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

An automated method for modeling proteins on known templates using distance geometry

1 reference

https://pubmed.ncbi.nlm.nih.gov/25346782

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Computer simulations of protein folding by targeted molecular dynamics

1 reference

https://pubmed.ncbi.nlm.nih.gov/25346782

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Characterizing hydrophobicity of interfaces by using cavity formation, solute binding, and water correlations

1 reference

https://pubmed.ncbi.nlm.nih.gov/25346782

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

EGF-independent activation of cell-surface EGF receptors harboring mutations found in gefitinib-sensitive lung cancer

1 reference

https://pubmed.ncbi.nlm.nih.gov/25346782

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Atomistic insights into regulatory mechanisms of the HER2 tyrosine kinase domain: a molecular dynamics study

1 reference

https://pubmed.ncbi.nlm.nih.gov/25346782

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Modulation of erlotinib pharmacokinetics in mice by a novel cytochrome P450 3A4 inhibitor, BAS 100.

1 reference

https://pubmed.ncbi.nlm.nih.gov/25346782

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Studies of the HER-2/neu proto-oncogene in human breast and ovarian cancer

1 reference

https://pubmed.ncbi.nlm.nih.gov/25346782

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

The impact of human EGFR kinase domain mutations on lung tumorigenesis and in vivo sensitivity to EGFR-targeted therapies

1 reference

https://pubmed.ncbi.nlm.nih.gov/25346782

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Mapping hydrophobicity at the nanoscale: applications to heterogeneous surfaces and proteins

1 reference

https://pubmed.ncbi.nlm.nih.gov/25346782

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Gefitinib as first-line, compassionate use therapy in patients with advanced non-small-cell lung cancer

1 reference

https://pubmed.ncbi.nlm.nih.gov/25346782

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Absolute binding free energy calculations using molecular dynamics simulations with restraining potentials

1 reference

https://pubmed.ncbi.nlm.nih.gov/25346782

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Essential dynamics of proteins

1 reference

https://pubmed.ncbi.nlm.nih.gov/25346782

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Structure of the extracellular region of HER2 alone and in complex with the Herceptin Fab

1 reference

https://pubmed.ncbi.nlm.nih.gov/25346782

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

ERBB2 kinase domain mutation in the lung squamous cell carcinoma

1 reference

https://pubmed.ncbi.nlm.nih.gov/25346782

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Loss of Hsp90 association up-regulates Src-dependent ErbB2 activity

1 reference

https://pubmed.ncbi.nlm.nih.gov/25346782

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Erlotinib: small-molecule targeted therapy in the treatment of non-small-cell lung cancer

1 reference

https://pubmed.ncbi.nlm.nih.gov/25346782

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Gefitinib, a selective EGFR tyrosine kinase inhibitor, induces apoptosis through activation of Bax in human gallbladder adenocarcinoma cells

1 reference

https://pubmed.ncbi.nlm.nih.gov/25346782

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Structure of the epidermal growth factor receptor kinase domain alone and in complex with a 4-anilinoquinazoline inhibitor

1 reference

https://pubmed.ncbi.nlm.nih.gov/25346782

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Somatic mutations of the HER2 kinase domain in lung adenocarcinomas.

1 reference

https://pubmed.ncbi.nlm.nih.gov/25346782

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Detection of epidermal growth factor receptor and human epidermal growth factor receptor 2 activating mutations in lung adenocarcinoma by high-resolution melting amplicon analysis: correlation with gene copy number, protein expression, and hormone r

1 reference

https://pubmed.ncbi.nlm.nih.gov/25346782

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Computer simulation of the chemical catalysis of DNA polymerases: discriminating between alternative nucleotide insertion mechanisms for T7 DNA polymerase

1 reference

https://pubmed.ncbi.nlm.nih.gov/25346782

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

The crystal structure of a truncated ErbB2 ectodomain reveals an active conformation, poised to interact with other ErbB receptors

1 reference

https://pubmed.ncbi.nlm.nih.gov/25346782

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Phosphoproteomic analysis of Her2/neu signaling and inhibition

1 reference

https://pubmed.ncbi.nlm.nih.gov/25346782

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Modelling enzyme reaction mechanisms, specificity and catalysis.

1 reference

https://pubmed.ncbi.nlm.nih.gov/25346782

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Surface charge and hydrophobicity determine ErbB2 binding to the Hsp90 chaperone complex.

1 reference

https://pubmed.ncbi.nlm.nih.gov/25346782

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

A sequence alignment algorithm with an arbitrary gap penalty function

1 reference

https://pubmed.ncbi.nlm.nih.gov/25346782

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

The conformational plasticity of protein kinases

1 reference

https://pubmed.ncbi.nlm.nih.gov/25346782

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Mechanism for activation of the EGF receptor catalytic domain by the juxtamembrane segment

1 reference

https://pubmed.ncbi.nlm.nih.gov/25346782

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

A unique structure for epidermal growth factor receptor bound to GW572016 (Lapatinib): relationships among protein conformation, inhibitor off-rate, and receptor activity in tumor cells

1 reference

https://pubmed.ncbi.nlm.nih.gov/25346782

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Scalable molecular dynamics with NAMD

1 reference

https://pubmed.ncbi.nlm.nih.gov/25346782

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

ErbB3/HER3 intracellular domain is competent to bind ATP and catalyze autophosphorylation

1 reference

https://pubmed.ncbi.nlm.nih.gov/25346782

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Coupling of fast and slow modes in the reaction pathway of the minimal hammerhead ribozyme cleavage

1 reference

https://pubmed.ncbi.nlm.nih.gov/25346782

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Molecular dynamics and protein function

1 reference

https://pubmed.ncbi.nlm.nih.gov/25346782

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

EGFR mutations in lung cancer: correlation with clinical response to gefitinib therapy

1 reference

https://pubmed.ncbi.nlm.nih.gov/25346782

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

EGF receptor gene mutations are common in lung cancers from "never smokers" and are associated with sensitivity of tumors to gefitinib and erlotinib

1 reference

https://pubmed.ncbi.nlm.nih.gov/25346782

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Structure of the extracellular region of HER3 reveals an interdomain tether

1 reference

https://pubmed.ncbi.nlm.nih.gov/25346782

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Surface comparison of active and inactive protein kinases identifies a conserved activation mechanism

1 reference

https://pubmed.ncbi.nlm.nih.gov/25346782

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Comparative protein structure modeling of genes and genomes

1 reference

https://pubmed.ncbi.nlm.nih.gov/25346782

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Trastuzumab: mechanism of action, resistance and future perspectives in HER2-overexpressing breast cancer.

1 reference

https://pubmed.ncbi.nlm.nih.gov/25346782

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Mechanism of activation and inhibition of the HER4/ErbB4 kinase

1 reference

https://pubmed.ncbi.nlm.nih.gov/25346782

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Activating mutations in the epidermal growth factor receptor underlying responsiveness of non-small-cell lung cancer to gefitinib

1 reference

https://pubmed.ncbi.nlm.nih.gov/25346782

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Comparative Modeling in Structural Genomics

1 reference

https://pubmed.ncbi.nlm.nih.gov/25346782

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Somatic mutations of ERBB2 kinase domain in gastric, colorectal, and breast carcinomas.

1 reference

https://pubmed.ncbi.nlm.nih.gov/25346782

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Lapatinib: a small-molecule inhibitor of epidermal growth factor receptor and human epidermal growth factor receptor-2 tyrosine kinases used in the treatment of breast cancer

1 reference

https://pubmed.ncbi.nlm.nih.gov/25346782

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Software news and updates. Carma: a molecular dynamics analysis program

1 reference

https://pubmed.ncbi.nlm.nih.gov/25346782

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Untangling the ErbB signalling network

1 reference

https://pubmed.ncbi.nlm.nih.gov/25346782

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Phase I clinical study of pertuzumab, a novel HER dimerization inhibitor, in patients with advanced cancer

1 reference

https://pubmed.ncbi.nlm.nih.gov/25346782

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Detection of EGFR- and HER2-activating mutations in squamous cell carcinoma involving the head and neck

1 reference

https://pubmed.ncbi.nlm.nih.gov/25346782

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Crystal structure of a truncated epidermal growth factor receptor extracellular domain bound to transforming growth factor alpha

1 reference

https://pubmed.ncbi.nlm.nih.gov/25346782

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Modeller: generation and refinement of homology-based protein structure models

1 reference

https://pubmed.ncbi.nlm.nih.gov/25346782

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Protein allostery, signal transmission and dynamics: a classification scheme of allosteric mechanisms

1 reference

https://pubmed.ncbi.nlm.nih.gov/25346782

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

A helix scaffold for the assembly of active protein kinases

1 reference

https://pubmed.ncbi.nlm.nih.gov/25346782

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

ERBB2 kinase domain mutation in a gastric cancer metastasis.

1 reference

https://pubmed.ncbi.nlm.nih.gov/25346782

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

VMD: visual molecular dynamics

1 reference

https://pubmed.ncbi.nlm.nih.gov/25346782

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

All-atom empirical potential for molecular modeling and dynamics studies of proteins

1 reference

https://pubmed.ncbi.nlm.nih.gov/25346782

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

An allosteric mechanism for activation of the kinase domain of epidermal growth factor receptor

1 reference

https://pubmed.ncbi.nlm.nih.gov/25346782

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Resistance to Trastuzumab in Breast Cancer.

1 reference

https://pubmed.ncbi.nlm.nih.gov/25346782

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Structure/function correlations of proteins using MM, QM/MM, and related approaches: methods, concepts, pitfalls, and current progress

1 reference

https://pubmed.ncbi.nlm.nih.gov/25346782

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Phosphotyrosine interactome of the ErbB-receptor kinase family

1 reference

https://pubmed.ncbi.nlm.nih.gov/25346782

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Knowledge-based model building of proteins: concepts and examples

1 reference

https://pubmed.ncbi.nlm.nih.gov/25346782

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Efficacy and safety of lapatinib as first-line therapy for ErbB2-amplified locally advanced or metastatic breast cancer

1 reference

https://pubmed.ncbi.nlm.nih.gov/25346782

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

The Juxtamembrane Region of the EGF Receptor Functions as an Activation Domain

1 reference

https://pubmed.ncbi.nlm.nih.gov/25346782

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Dynamics of folded proteins

1 reference

https://pubmed.ncbi.nlm.nih.gov/25346782

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

A phase I and pharmacokinetic study of oral lapatinib administered once or twice daily in patients with solid malignancies

1 reference

https://pubmed.ncbi.nlm.nih.gov/25346782

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Trastuzumab prolongs overall survival in patients with brain metastases from Her2 positive breast cancer

1 reference

https://pubmed.ncbi.nlm.nih.gov/25346782

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

ErbB receptors: new insights on mechanisms and biology

1 reference

https://pubmed.ncbi.nlm.nih.gov/25346782

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Pairwise sequence alignment below the twilight zone

1 reference

https://pubmed.ncbi.nlm.nih.gov/25346782

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

HER2 kinase domain mutation results in constitutive phosphorylation and activation of HER2 and EGFR and resistance to EGFR tyrosine kinase inhibitors

1 reference

https://pubmed.ncbi.nlm.nih.gov/25346782

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Molecular dynamics simulations reveal that Tyr-317 phosphorylation reduces Shc binding affinity for phosphotyrosyl residues of epidermal growth factor receptor

1 reference

https://pubmed.ncbi.nlm.nih.gov/25346782

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Comparative modeling for protein structure prediction

1 reference

https://pubmed.ncbi.nlm.nih.gov/25346782

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Calculating structures and free energies of complex molecules: combining molecular mechanics and continuum models

1 reference

https://pubmed.ncbi.nlm.nih.gov/25346782

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Biomolecular simulations: recent developments in force fields, simulations of enzyme catalysis, protein-ligand, protein-protein, and protein-nucleic acid noncovalent interactions

1 reference

https://pubmed.ncbi.nlm.nih.gov/25346782

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Sequence comparison and protein structure prediction.

1 reference

https://pubmed.ncbi.nlm.nih.gov/25346782

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

In silico evidence for DNA polymerase-beta's substrate-induced conformational change

1 reference

https://pubmed.ncbi.nlm.nih.gov/25346782

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Homology modelling by distance geometry

1 reference

https://pubmed.ncbi.nlm.nih.gov/25346782

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

A new therapeutic antibody masks ErbB2 to its partners

1 reference

https://pubmed.ncbi.nlm.nih.gov/25346782

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

A new method for building protein conformations from sequence alignments with homologues of known structure

1 reference

https://pubmed.ncbi.nlm.nih.gov/25346782

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Advances in Homology Protein Structure Modeling

1 reference

https://pubmed.ncbi.nlm.nih.gov/25346782

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Mutational activation of ErbB2 reveals a new protein kinase autoinhibition mechanism

1 reference

https://pubmed.ncbi.nlm.nih.gov/25346782

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

EGF activates its receptor by removing interactions that autoinhibit ectodomain dimerization

1 reference

https://pubmed.ncbi.nlm.nih.gov/25346782

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Lung cancer: intragenic ERBB2 kinase mutations in tumours

1 reference

https://pubmed.ncbi.nlm.nih.gov/25346782

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Extending the accuracy limits of prediction for side-chain conformations

1 reference

https://pubmed.ncbi.nlm.nih.gov/25346782

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Dynamics of biochemical and biophysical reactions: insight from computer simulations

1 reference

https://pubmed.ncbi.nlm.nih.gov/25346782

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Structural analysis of the catalytically inactive kinase domain of the human EGF receptor 3

1 reference

https://pubmed.ncbi.nlm.nih.gov/25346782

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Free energy via molecular simulation: applications to chemical and biomolecular systems

1 reference

https://pubmed.ncbi.nlm.nih.gov/25346782

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Biomolecular free energy profiles by a shooting/umbrella sampling protocol, "BOLAS"

1 reference

https://pubmed.ncbi.nlm.nih.gov/25346782

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Identifiers

PMC publication ID

1 reference

Europe PubMed Central

PMC publication ID

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25346782%20AND%20SRC:MED&resulttype=core&format=json

21 February 2020

PubMed publication ID

1 reference

Europe PubMed Central

PMC publication ID

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25346782%20AND%20SRC:MED&resulttype=core&format=json

21 February 2020

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