Molecular Determinants Underlying Binding Specificities of the ABL Kinase Inhibitors: Combining Alanine Scanning of Binding Hot Spots with Network Analysis of Residue Interactions and Coevolution

Integrated Analysis of Residue Coevolution and Protein Structures Capture Key Protein Sectors in HIV-1 Proteins

(2015) Yuqi Zhao et al.   PLoS One

Improving the Robustness of Complex Networks with Preserving Community Structure

(2015) Yang Yang et al.   PLoS One

All tyrosine kinase inhibitor-resistant chronic myelogenous cells are highly sensitive to Ponatinib

(2015) Ophelie Cassuto et al.   Oncotarget

Evaluating the Promiscuous Nature of Tyrosine Kinase Inhibitors Assessed in A431 Epidermoid Carcinoma Cells by Both Chemical- and Phosphoproteomics

(2014) Piero Giansanti et al.   ACS Chemical Biology

Exploration of Type II Binding Mode: A Privileged Approach for Kinase Inhibitor Focused Drug Discovery?

(2014) Zheng Zhao et al.   ACS Chemical Biology

BCR-ABL1 Compound Mutations Combining Key Kinase Domain Positions Confer Clinical Resistance to Ponatinib in Ph Chromosome-Positive Leukemia

(2014) Matthew S. Zabriskie et al.   CANCER CELL

Novel approaches for targeting kinases: allosteric inhibition, allosteric activation and pseudokinases

(2014) Sandra W Cowan-Jacob et al.   Future Medicinal Chemistry

Computational Study of Gleevec and G6G Reveals Molecular Determinants of Kinase Inhibitor Selectivity

(2014) Yen-Lin Lin et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Systems Biology Brings New Dimensions for Structure-Based Drug Design

(2014) Jianfeng Pei et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

UniProt: a hub for protein information

(2014)   NUCLEIC ACIDS RESEARCH

Structure-Based Network Analysis of Activation Mechanisms in the ErbB Family of Receptor Tyrosine Kinases: The Regulatory Spine Residues Are Global Mediators of Structural Stability and Allosteric Interactions

(2014) Kevin A. James et al.   PLoS One

Molecular dynamics reveal BCR-ABL1 polymutants as a unique mechanism of resistance to PAN-BCR-ABL1 kinase inhibitor therapy

(2014) Don L. Gibbons et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Control of catalytic efficiency by a coevolving network of catalytic and noncatalytic residues

(2014) T. A. McMurrough et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Conformation-Selective Inhibitors Reveal Differences in the Activation and Phosphate-Binding Loops of the Tyrosine Kinases Abl and Src

(2013) Sanjay B. Hari et al.   ACS Chemical Biology

PKA: Lessons learned after twenty years

(2013) Susan S. Taylor et al.   BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS

Drug resistance and BCR-ABL kinase domain mutations in Philadelphia chromosome-positive acute lymphoblastic leukemia from the imatinib to the second-generation tyrosine kinase inhibitor era: The main changes are in the type of mutations, but not in the fr

(2013) Simona Soverini et al.   CANCER

Allo-Network Drugs: Extension of the Allosteric Drug Concept to Protein- Protein Interaction and Signaling Networks

(2013) Andras Szilagyi et al.   CURRENT TOPICS IN MEDICINAL CHEMISTRY

BCR-ABL residues interacting with ponatinib are critical to preserve the tumorigenic potential of the oncoprotein

(2013) Pietro Buffa et al.   FASEB JOURNAL

Structure and Dynamic Regulation of Abl Kinases

(2013) Shoghag Panjarian et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Grcarma: A fully automated task-oriented interface for the analysis of molecular dynamics trajectories

(2013) Panagiotis I. Koukos et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Rapid parameterization of small molecules using the force field toolkit

(2013) Christopher G. Mayne et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Buried and Accessible Surface Area Control Intrinsic Protein Flexibility

(2013) Joseph A. Marsh   JOURNAL OF MOLECULAR BIOLOGY

Computational Analysis of the Binding Specificity of Gleevec to Abl, c-Kit, Lck, and c-Src Tyrosine Kinases

(2013) Yen-Lin Lin et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Through the open door: Preferential binding of dasatinib to the active form of BCR-ABL unveiled by in silico experiments

(2013) Erik Laurini et al.   Molecular Oncology

A conserved water-mediated hydrogen bond network defines bosutinib's kinase selectivity

(2013) Nicholas M Levinson et al.   Nature Chemical Biology

Emerging methods in protein co-evolution

(2013) David de Juan et al.   NATURE REVIEWS GENETICS

iPfam: a database of protein family and domain interactions found in the Protein Data Bank

(2013) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

MISTIC: mutual information server to infer coevolution

(2013) Franco L. Simonetti et al.   NUCLEIC ACIDS RESEARCH

Pfam: the protein families database

(2013) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

The ErbB/HER family of protein-tyrosine kinases and cancer

(2013) Robert Roskoski   PHARMACOLOGICAL RESEARCH

Structure and dynamics of molecular networks: A novel paradigm of drug discovery

(2013) Peter Csermely et al.   PHARMACOLOGY & THERAPEUTICS

Ponatinib Is a Pan-BCR-ABL Kinase Inhibitor: MD Simulations and SIE Study

(2013) Karunakar Tanneeru et al.   PLoS One

Explaining why Gleevec is a specific and potent inhibitor of Abl kinase

(2013) Y.-L. Lin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Deciphering the Structural Basis of Eukaryotic Protein Kinase Regulation

(2013) Hiruy S. Meharena et al.   PLOS BIOLOGY

Three novel patient-derived BCR/ABL mutants show different sensitivity to second and third generation tyrosine kinase inhibitors

(2012) Sara Redaelli et al.   AMERICAN JOURNAL OF HEMATOLOGY

The Structural Basis for Control of Eukaryotic Protein Kinases

(2012) Jane A. Endicott et al.   Annual Review of Biochemistry

Assessing the range of kinase autoinhibition mechanisms in the insulin receptor family

(2012) Stephen C. Artim et al.   BIOCHEMICAL JOURNAL

Mechanisms of resistance to BCR-ABL and other kinase inhibitors

(2012) Allan Joaquim Lamontanara et al.   BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS

Disentangling evolutionary signals: conservation, specificity determining positions and coevolution. Implication for catalytic residue prediction

(2012) Elin Teppa et al.   BMC BIOINFORMATICS

The Growing Arsenal of ATP-Competitive and Allosteric Inhibitors of BCR-ABL

(2012) O. Hantschel et al.   CANCER RESEARCH

Molecular dynamics simulations and statistical coupling analysis reveal functional coevolution network of oncogenic mutations in the CDKN2A-CDK6 complex

(2012) Jingwen Wang et al.   FEBS LETTERS

Automation of the CHARMM General Force Field (CGenFF) II: Assignment of Bonded Parameters and Partial Atomic Charges

(2012) K. Vanommeslaeghe et al.   Journal of Chemical Information and Modeling

Automation of the CHARMM General Force Field (CGenFF) I: Bond Perception and Atom Typing

(2012) K. Vanommeslaeghe et al.   Journal of Chemical Information and Modeling

The Different Flexibility of c-Src and c-Abl Kinases Regulates the Accessibility of a Druggable Inactive Conformation

(2012) Silvia Lovera et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Sequence Evolution Correlates with Structural Dynamics

(2012) Ying Liu et al.   MOLECULAR BIOLOGY AND EVOLUTION

The spatial architecture of protein function and adaptation

(2012) Richard N. McLaughlin Jr et al.   NATURE

Assembly of allosteric macromolecular switches: lessons from PKA

(2012) Susan S. Taylor et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Design principles underpinning the regulatory diversity of protein kinases

(2012) K. Oruganty et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Evolution of the eukaryotic protein kinases as dynamic molecular switches

(2012) S. S. Taylor et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Structural and Spectroscopic Analysis of the Kinase Inhibitor Bosutinib and an Isomer of Bosutinib Binding to the Abl Tyrosine Kinase Domain

(2012) Nicholas M. Levinson et al.   PLoS One

Mapping the Mutual Information Network of Enzymatic Families in the Protein Structure to Unveil Functional Features

(2012) Daniel Aguilar et al.   PLoS One

The Evolution of Protein Kinase Inhibitors from Antagonists to Agonists of Cellular Signaling

(2011) Arvin C. Dar et al.   Annual Review of Biochemistry

Novel Computational Approaches to Polypharmacology as a Means to Define Responses to Individual Drugs

(2011) Lei Xie et al.   Annual Review of Pharmacology and Toxicology

BCR-ABL kinase domain mutation analysis in chronic myeloid leukemia patients treated with tyrosine kinase inhibitors: recommendations from an expert panel on behalf of European LeukemiaNet

(2011) S. Soverini et al.   BLOOD

X-Ray Crystal Structure of Bone Marrow Kinase in the X Chromosome: A Tec Family Kinase

(2011) Jodi Muckelbauer et al.   Chemical Biology & Drug Design

Crystal structure of the EphA4 protein tyrosine kinase domain in the apo- and dasatinib-bound state

(2011) Carine Farenc et al.   FEBS LETTERS

MATCH: An atom-typing toolset for molecular mechanics force fields

(2011) Joseph D. Yesselman et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Molecular Evolution of Protein Conformational Changes Revealed by a Network of Evolutionarily Coupled Residues

(2011) Jouhyun Jeon et al.   MOLECULAR BIOLOGY AND EVOLUTION

Comprehensive assay of kinase catalytic activity reveals features of kinase inhibitor selectivity

(2011) Theonie Anastassiadis et al.   NATURE BIOTECHNOLOGY

Comprehensive analysis of kinase inhibitor selectivity

(2011) Mindy I Davis et al.   NATURE BIOTECHNOLOGY

The Pfam protein families database

(2011) M. Punta et al.   NUCLEIC ACIDS RESEARCH

Choosing the Best Second-Line Tyrosine Kinase Inhibitor in Imatinib-Resistant Chronic Myeloid Leukemia Patients Harboring Bcr-Abl Kinase Domain Mutations: How Reliable Is the IC50?

(2011) S. Soverini et al.   ONCOLOGIST

Allosteric Interactions between the Myristate- and ATP-Site of the Abl Kinase

(2011) Roxana E. Iacob et al.   PLoS One

Direct-coupling analysis of residue coevolution captures native contacts across many protein families

(2011) F. Morcos et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Mitigation of malicious attacks on networks

(2011) C. M. Schneider et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Relative Solvent Accessible Surface Area Predicts Protein Conformational Changes upon Binding

(2011) Joseph A. Marsh et al.   STRUCTURE

Computational Modeling of Allosteric Communication Reveals Organizing Principles of Mutation-Induced Signaling in ABL and EGFR Kinases

(2011) Anshuman Dixit et al.   PLoS Computational Biology

Cell Signaling by Receptor Tyrosine Kinases

(2010) Mark A. Lemmon et al.   CELL

Structural Mechanism of the Pan-BCR-ABL Inhibitor Ponatinib (AP24534): Lessons for Overcoming Kinase Inhibitor Resistance

(2010) Tianjun Zhou et al.   Chemical Biology & Drug Design

Activation State-Dependent Binding of Small Molecule Kinase Inhibitors: Structural Insights from Biochemistry

(2010) Lisa M. Wodicka et al.   CHEMISTRY & BIOLOGY

Diseases as network perturbations

(2010) Antonio del Sol et al.   CURRENT OPINION IN BIOTECHNOLOGY

Molecular Dynamics Simulations Show That Conformational Selection Governs the Binding Preferences of Imatinib for Several Tyrosine Kinases

(2010) Alexey Aleksandrov et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Structural and Functional Roles of Coevolved Sites in Proteins

(2010) Saikat Chakrabarti et al.   PLoS One

Reciprocally Coupled Residues Crucial for Protein Kinase Pak2 Activity Calculated by Statistical Coupling Analysis

(2010) Yuan-Hao Hsu et al.   PLoS One

Induced fit, conformational selection and independent dynamic segments: an extended view of binding events

(2010) Peter Csermely et al.   TRENDS IN BIOCHEMICAL SCIENCES

Protein kinases: evolution of dynamic regulatory proteins

(2010) Susan S. Taylor et al.   TRENDS IN BIOCHEMICAL SCIENCES

Networks of High Mutual Information Define the Structural Proximity of Catalytic Sites: Implications for Catalytic Residue Identification

(2010) Cristina Marino Buslje et al.   PLoS Computational Biology

Correlated Mutations: A Hallmark of Phenotypic Amino Acid Substitutions

(2010) Andreas Kowarsch et al.   PLoS Computational Biology

Comparative Analysis of Mutant Tyrosine Kinase Chemical Rescue†‡

(2009) Kathryn E. Muratore et al.   BIOCHEMISTRY

Correction for phylogeny, small number of observations and data redundancy improves the identification of coevolving amino acid pairs using mutual information

(2009) C. M. Buslje et al.   BIOINFORMATICS

Dasatinib treatment of chronic-phase chronic myeloid leukemia: analysis of responses according to preexisting BCR-ABL mutations

(2009) M. C. Muller et al.   BLOOD

Long-term outcome of patients with chronic myeloid leukemia treated with second-generation tyrosine kinase inhibitors after imatinib failure is predicted by the in vitro sensitivity of BCR-ABL kinase domain mutations

(2009) E. Jabbour et al.   BLOOD

Selecting optimal second-line tyrosine kinase inhibitor therapy for chronic myeloid leukemia patients after imatinib failure: does the BCR-ABL mutation status really matter?

(2009) S. Branford et al.   BLOOD

AP24534, a Pan-BCR-ABL Inhibitor for Chronic Myeloid Leukemia, Potently Inhibits the T315I Mutant and Overcomes Mutation-Based Resistance

(2009) Thomas O'Hare et al.   CANCER CELL

Equally Potent Inhibition of c-Src and Abl by Compounds that Recognize Inactive Kinase Conformations

(2009) M. A. Seeliger et al.   CANCER RESEARCH

Protein Sectors: Evolutionary Units of Three-Dimensional Structure

(2009) Najeeb Halabi et al.   CELL

Impact of BaselineBCR-ABLMutations on Response to Nilotinib in Patients With Chronic Myeloid Leukemia in Chronic Phase

(2009) Timothy Hughes et al.   JOURNAL OF CLINICAL ONCOLOGY

Hybrid Compound Design To Overcome the Gatekeeper T338M Mutation in cSrc#

(2009) Matthäus Getlik et al.   JOURNAL OF MEDICINAL CHEMISTRY

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

(2009) Chung-Jung Tsai et al.   Molecular BioSystems

Correlated Mutation Analysis on the Catalytic Domains of Serine/Threonine Protein Kinases

(2009) Feng Xu et al.   PLoS One

Dynamical networks in tRNA:protein complexes

(2009) A. Sethi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Origin of Allosteric Functional Modulation: Multiple Pre-existing Pathways

(2009) Antonio del Sol et al.   STRUCTURE

Hierarchical Modeling of Activation Mechanisms in the ABL and EGFR Kinase Domains: Thermodynamic and Mechanistic Catalysts of Kinase Activation by Cancer Mutations

(2009) Anshuman Dixit et al.   PLoS Computational Biology

Molecular basis explanation for imatinib resistance of BCR-ABL due to T315I and P-loop mutations from molecular dynamics simulations

(2008) Tai-Sung Lee et al.   CANCER

Crystal Structures of the Lyn Protein Tyrosine Kinase Domain in Its Apo- and Inhibitor-bound State

(2008) Neal K. Williams et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Solution Conformations and Dynamics of ABL Kinase-Inhibitor Complexes Determined by NMR Substantiate the Different Binding Modes of Imatinib/Nilotinib and Dasatinib

(2008) Navratna Vajpai et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Activity of Bosutinib, Dasatinib, and Nilotinib Against 18 Imatinib-Resistant BCR/ABL Mutants

(2008) Sara Redaelli et al.   JOURNAL OF CLINICAL ONCOLOGY

A quantitative analysis of kinase inhibitor selectivity

(2008) Mazen W Karaman et al.   NATURE BIOTECHNOLOGY

Activation of tyrosine kinases by mutation of the gatekeeper threonine

(2008) Mohammad Azam et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

A helix scaffold for the assembly of active protein kinases

(2008) A. P. Kornev et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A conserved protonation-dependent switch controls drug binding in the Abl kinase

(2008) Y. Shan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Analysis of the residue-residue coevolution network and the functionally important residues in proteins

(2008) Byung-Chul Lee et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Coevolution in defining the functional specificity

(2008) Saikat Chakrabarti et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Conserved spatial patterns across the protein kinase family

(2007) Lynn F. Ten Eyck et al.   BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS