Review: Precision medicine and driver mutations: Computational methods, functional assays and conformational principles for interpreting cancer drivers

Molecular and Genomic Determinants of Response to Immune Checkpoint Inhibition in Cancer

(2018) Russell W. Jenkins et al.   Annual Review of Medicine

Precision Medicine: Functional Advancements

(2018) Thomas Caskey   Annual Review of Medicine

Basket Studies: Redefining Clinical Trials in the Era of Genome-Driven Oncology

(2018) Jessica J. Tao et al.   Annual Review of Medicine

Systematic Functional Annotation of Somatic Mutations in Cancer

(2018) Patrick Kwok-Shing Ng et al.   CANCER CELL

Whole genome sequencing analysis for cancer genomics and precision medicine

(2018) Hidewaki Nakagawa et al.   CANCER SCIENCE

Comprehensive Characterization of Cancer Driver Genes and Mutations

(2018) Matthew H. Bailey et al.   CELL

A Map of Protein-Metabolite Interactions Reveals Principles of Chemical Communication

(2018) Ilaria Piazza et al.   CELL

ALLO: A tool to discriminate and prioritize allosteric pockets

(2018) Rahmad Akbar et al.   Chemical Biology & Drug Design

Structural fingerprints, interactions, and signaling networks of RAS family proteins beyond RAS isoforms

(2018) Saeideh Nakhaei-Rad et al.   CRITICAL REVIEWS IN BIOCHEMISTRY AND MOLECULAR BIOLOGY

Precision medicine in pediatric oncology

(2018) Suzanne J. Forrest et al.   CURRENT OPINION IN PEDIATRICS

Structure-based prediction of protein allostery

(2018) Joe G Greener et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Novel K-Ras G12C Switch-II Covalent Binders Destabilize Ras and Accelerate Nucleotide Exchange

(2018) Chimno I. Nnadi et al.   Journal of Chemical Information and Modeling

Genomic classifications of renal cell carcinoma: a critical step towards the future application of personalized kidney cancer care with pan-omics precision

(2018) James J Hsieh et al.   JOURNAL OF PATHOLOGY

PDK1: At the crossroad of cancer signaling pathways

(2018) Paolo Armando Gagliardi et al.   SEMINARS IN CANCER BIOLOGY

Exploiting Metabolic Vulnerabilities of Cancer with Precision and Accuracy

(2018) Adam J. Wolpaw et al.   TRENDS IN CELL BIOLOGY

Is It Our Duty To Hunt for Pathogenic Mutations?

(2018) Roel H.P. Wouters et al.   TRENDS IN MOLECULAR MEDICINE

Computational Approaches to Prioritize Cancer Driver Missense Mutations

(2018) Feiyang Zhao et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Rho GTPase effectors and NAD metabolism in cancer immune suppression

(2017) Mahmoud Chaker et al.   EXPERT OPINION ON THERAPEUTIC TARGETS

HIT'nDRIVE: patient-specific multidriver gene prioritization for precision oncology

(2017) Raunak Shrestha et al.   GENOME RESEARCH

Benchmarking predictions of allostery in liver pyruvate kinase in CAGI4

(2017) Qifang Xu et al.   HUMAN MUTATION

Allostery modulates the beat rate of a cardiac pacemaker

(2017) Chung-Jung Tsai et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

The small GTPases K-Ras, N-Ras, and H-Ras have distinct biochemical properties determined by allosteric effects

(2017) Christian W. Johnson et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Plasma membrane phosphatidylinositol 4-phosphate and 4,5-bisphosphate determine the distribution and function of K-Ras4B but not H-Ras proteins

(2017) Gergő Gulyás et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Conformational changes in the activation loop of mitochondrial glutaminase C: A direct fluorescence readout that distinguishes the binding of allosteric inhibitors from activators

(2017) Clint A. Stalnecker et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Next-generation sequencing: recent applications to the analysis of colorectal cancer

(2017) Filippo Del Vecchio et al.   Journal of Translational Medicine

Molecular testing for BRAF mutations to inform melanoma treatment decisions: a move toward precision medicine

(2017) Liang Cheng et al.   MODERN PATHOLOGY

Path toward Precision Oncology: Review of Targeted Therapy Studies and Tools to Aid in Defining “Actionability” of a Molecular Lesion and Patient Management Support

(2017) Young Kwang Chae et al.   MOLECULAR CANCER THERAPEUTICS

Programmable base editing of A•T to G•C in genomic DNA without DNA cleavage

(2017) Nicole M. Gaudelli et al.   NATURE

The evidence framework for precision cancer medicine

(2017) Jeffrey A. Moscow et al.   Nature Reviews Clinical Oncology

Precision medicine for urothelial bladder cancer: update on tumour genomics and immunotherapy

(2017) Kenneth M. Felsenstein et al.   Nature Reviews Urology

Dosing Three‐Drug Combinations That Include Targeted Anti‐Cancer Agents: Analysis of 37,763 Patients

(2017) Mina Nikanjam et al.   ONCOLOGIST

Clinical application of a cancer genomic profiling assay to guide precision medicine decisions

(2017) Cheryl Eifert et al.   Personalized Medicine

Evaluation of the selectivity and sensitivity of isoform- and mutation-specific RAS antibodies

(2017) Andrew M. Waters et al.   Science Signaling

Moral Duties of Genomics Researchers: Why Personalized Medicine Requires a Collective Approach

(2017) Shoko Vos et al.   TRENDS IN GENETICS

Precision Oncology: The Road Ahead

(2017) Daniela Senft et al.   TRENDS IN MOLECULAR MEDICINE

An Interview with Eric Lai

(2017)   TRENDS IN PHARMACOLOGICAL SCIENCES

What Precisely Is Precision Medicine?

(2017) Joanna Schaffhausen   TRENDS IN PHARMACOLOGICAL SCIENCES

A New View of Pathway-Driven Drug Resistance in Tumor Proliferation

(2017) Ruth Nussinov et al.   TRENDS IN PHARMACOLOGICAL SCIENCES

Evidence-Based Precision Oncology with the Cancer Targetome

(2017) Aurora S. Blucher et al.   TRENDS IN PHARMACOLOGICAL SCIENCES

Modeling of RAS complexes supports roles in cancer for less studied partners

(2017) H. Billur Engin et al.   BMC Biophysics

Mapping genetic variations to three-dimensional protein structures to enhance variant interpretation: a proposed framework

(2017) Gustavo Glusman et al.   Genome Medicine

3D clusters of somatic mutations in cancer reveal numerous rare mutations as functional targets

(2017) Jianjiong Gao et al.   Genome Medicine

Analysis of 100,000 human cancer genomes reveals the landscape of tumor mutational burden

(2017) Zachary R. Chalmers et al.   Genome Medicine

Unmet needs for analyzing biological big data: A survey of 704 NSF principal investigators

(2017) Lindsay Barone et al.   PLoS Computational Biology

Evaluation of the selectivity and sensitivity of isoform- and mutation-specific RAS antibodies

(2017) Andrew M. Waters et al.   Science Signaling

Resources for Interpreting Variants in Precision Genomic Oncology Applications

(2017) Hsinyi Tsang et al.   Frontiers in Oncology

Nucleotide based covalent inhibitors of KRas can only be efficient in vivo if they bind reversibly with GTP-like affinity

(2017) Matthias P. Müller et al.   Scientific Reports

An engineered protein antagonist of K-Ras/B-Raf interaction

(2017) Monique J. Kauke et al.   Scientific Reports

Membrane-associated Ras dimers are isoform-specific: K-Ras dimers differ from H-Ras dimers

(2016) H. Jang et al.   BIOCHEMICAL JOURNAL

Regulation of K-Ras4B Membrane Binding by Calmodulin

(2016) Benjamin Sperlich et al.   BIOPHYSICAL JOURNAL

Leveraging protein quaternary structure to identify oncogenic driver mutations

(2016) Gregory A. Ryslik et al.   BMC BIOINFORMATICS

Integrated Proteogenomic Characterization of Human High-Grade Serous Ovarian Cancer

(2016) Hui Zhang et al.   CELL

Environment Impacts the Metabolic Dependencies of Ras-Driven Non-Small Cell Lung Cancer

(2016) Shawn M. Davidson et al.   Cell Metabolism

Ras Conformational Ensembles, Allostery, and Signaling

(2016) Shaoyong Lu et al.   CHEMICAL REVIEWS

Protein Ensembles: How Does Nature Harness Thermodynamic Fluctuations for Life? The Diverse Functional Roles of Conformational Ensembles in the Cell

(2016) Guanghong Wei et al.   CHEMICAL REVIEWS

Emerging Computational Methods for the Rational Discovery of Allosteric Drugs

(2016) Jeffrey R. Wagner et al.   CHEMICAL REVIEWS

Drugging Ras GTPase: a comprehensive mechanistic and signaling structural view

(2016) Shaoyong Lu et al.   CHEMICAL SOCIETY REVIEWS

RASSF5: An MST activator and tumor suppressor in vivo but opposite in vitro

(2016) Tsung-Jen Liao et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Allosteric sites: remote control in regulation of protein activity

(2016) Enrico Guarnera et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

The disordered hypervariable region and the folded catalytic domain of oncogenic K-Ras4B partner in phospholipid binding

(2016) Avik Banerjee et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

OTUB1 triggers lung cancer development by inhibiting RAS monoubiquitination

(2016) M. F. Baietti et al.   EMBO Molecular Medicine

K-Ras4B/calmodulin/PI3Kα: A promising new adenocarcinoma-specific drug target?

(2016) Ruth Nussinov et al.   EXPERT OPINION ON THERAPEUTIC TARGETS

Independent and core pathways in oncogenic KRAS signaling

(2016) Ruth Nussinov et al.   Expert Review of Proteomics

The higher level of complexity of K-Ras4B activation at the membrane

(2016) Hyunbum Jang et al.   FASEB JOURNAL

CryptoSite: Expanding the Druggable Proteome by Characterization and Prediction of Cryptic Binding Sites

(2016) Peter Cimermancic et al.   JOURNAL OF MOLECULAR BIOLOGY

K-Ras protein as a drug target

(2016) Frank McCormick   JOURNAL OF MOLECULAR MEDICINE-JMM

Moving Beyond Active-Site Detection: MixMD Applied to Allosteric Systems

(2016) Phani Ghanakota et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Understanding Cryptic Pocket Formation in Protein Targets by Enhanced Sampling Simulations

(2016) Vladimiras Oleinikovas et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Inactivation of Cancer Mutations Utilizing CRISPR/Cas9

(2016) Christina Gebler et al.   JNCI-Journal of the National Cancer Institute

Precision oncology: origins, optimism, and potential

(2016) Vinay Prasad et al.   LANCET ONCOLOGY

Direct Inhibitors of Ras-Effector Protein Interactions

(2016) Punit Upadhyaya et al.   MINI-REVIEWS IN MEDICINAL CHEMISTRY

A Random Forest Model for Predicting Allosteric and Functional Sites on Proteins

(2016) Ava S.-Y. Chen et al.   Molecular Informatics

Pharmacogenetics: The right drug for you

(2016) Liam Drew   NATURE

Perspective: The precision-oncology illusion

(2016) Vinay Prasad   NATURE

Proteogenomics connects somatic mutations to signalling in breast cancer

(2016) Philipp Mertins et al.   NATURE

Functional characterization of somatic mutations in cancer using network-based inference of protein activity

(2016) Mariano J Alvarez et al.   NATURE GENETICS

Unsupervised detection of cancer driver mutations with parsimony-guided learning

(2016) Runjun D Kumar et al.   NATURE GENETICS

Protein-structure-guided discovery of functional mutations across 19 cancer types

(2016) Beifang Niu et al.   NATURE GENETICS

Direct small-molecule inhibitors of KRAS: from structural insights to mechanism-based design

(2016) Jonathan M. L. Ostrem et al.   NATURE REVIEWS DRUG DISCOVERY

Limits to Personalized Cancer Medicine

(2016) Ian F. Tannock et al.   NEW ENGLAND JOURNAL OF MEDICINE

MutaBind estimates and interprets the effects of sequence variants on protein–protein interactions

(2016) Minghui Li et al.   NUCLEIC ACIDS RESEARCH

Big data need big theory too

(2016) Peter V. Coveney et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY A-MATHEMATICAL PHYSICAL AND ENGINEERING SCIENCES

Evaluating the evaluation of cancer driver genes

(2016) Collin J. Tokheim et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Conformational dynamics of cancer-associated MyD88-TIR domain mutant L252P (L265P) allosterically tilts the landscape toward homo-dimerization

(2016) Chendi Zhan et al.   PROTEIN ENGINEERING DESIGN & SELECTION

Allele-specific inhibitors inactivate mutant KRAS G12C by a trapping mechanism

(2016) P. Lito et al.   SCIENCE

Oncogenic KRAS signaling and YAP1/β-catenin: Similar cell cycle control in tumor initiation

(2016) Ruth Nussinov et al.   SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY

Covalent Guanosine Mimetic Inhibitors of G12C KRAS

(2016) Yuan Xiong et al.   ACS Medicinal Chemistry Letters

Prediction of allosteric sites and mediating interactions through bond-to-bond propensities

(2016) B. R. C. Amor et al.   Nature Communications

DNA-Guided Precision Medicine for Cancer: A Case of Irrational Exuberance?

(2016) E. E. Voest et al.   Cancer Discovery

The Structural Basis of Oncogenic Mutations G12, G13 and Q61 in Small GTPase K-Ras4B

(2016) Shaoyong Lu et al.   Scientific Reports

Quantifying Clonal and Subclonal Passenger Mutations in Cancer Evolution

(2016) Ivana Bozic et al.   PLoS Computational Biology

Allostery: An Overview of Its History, Concepts, Methods, and Applications

(2016) Jin Liu et al.   PLoS Computational Biology

Inactivation of Cancer Mutations Utilizing CRISPR/Cas9

(2016) Christina Gebler et al.   JNCI-Journal of the National Cancer Institute

Metabolic Alterations Caused by KRAS Mutations in Colorectal Cancer Contribute to Cell Adaptation to Glutamine Depletion by Upregulation of Asparagine Synthetase

(2016) Kosuke Toda et al.   NEOPLASIA

Inhibition of Ras Signaling by Blocking Ras-Effector Interactions with Cyclic Peptides

(2015) Punit Upadhyaya et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

The Design of Covalent Allosteric Drugs

(2015) Ruth Nussinov et al.   Annual Review of Pharmacology and Toxicology

MADGiC: a model-based approach for identifying driver genes in cancer

(2015) Keegan D. Korthauer et al.   BIOINFORMATICS

ASBench: benchmarking sets for allosteric discovery: Fig. 1.

(2015) Wenkang Huang et al.   BIOINFORMATICS

A Structural View of Negative Regulation of the Toll-like Receptor-Mediated Inflammatory Pathway

(2015) Emine Guven-Maiorov et al.   BIOPHYSICAL JOURNAL

The Role of Conformational Dynamics and Allostery in the Disease Development of Human Ferritin

(2015) Avishek Kumar et al.   BIOPHYSICAL JOURNAL

AlloPred: prediction of allosteric pockets on proteins using normal mode perturbation analysis

(2015) Joe G Greener et al.   BMC BIOINFORMATICS

Redundancy: A Critical Obstacle to Improving Cancer Therapy

(2015) O. Lavi   CANCER RESEARCH

A New View of Ras Isoforms in Cancers

(2015) R. Nussinov et al.   CANCER RESEARCH

Balancing Protein Stability and Activity in Cancer: A New Approach for Identifying Driver Mutations Affecting CBL Ubiquitin Ligase Activation

(2015) M. Li et al.   CANCER RESEARCH

Kinome-wide Decoding of Network-Attacking Mutations Rewiring Cancer Signaling

(2015) Pau Creixell et al.   CELL

Widespread Macromolecular Interaction Perturbations in Human Genetic Disorders

(2015) Nidhi Sahni et al.   CELL

YAP in MAPK pathway targeted therapy resistance

(2015) Keith T Flaherty et al.   CELL CYCLE

Inhibitors of Ras-SOS Interactions

(2015) Shaoyong Lu et al.   ChemMedChem

Structural and physico-chemical effects of disease and non-disease nsSNPs on proteins

(2015) Tugba G Kucukkal et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Allostery without a conformational change? Revisiting the paradigm

(2015) Ruth Nussinov et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

‘Latent drivers’ expand the cancer mutational landscape

(2015) Ruth Nussinov et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Principles of K-Ras effector organization and the role of oncogenic K-Ras in cancer initiation through G1 cell cycle deregulation

(2015) Ruth Nussinov et al.   Expert Review of Proteomics

On Human Disease-Causing Amino Acid Variants: Statistical Study of Sequence and Structural Patterns

(2015) Marharyta Petukh et al.   HUMAN MUTATION

GTP Binding and Oncogenic Mutations May Attenuate Hypervariable Region (HVR)-Catalytic Domain Interactions in Small GTPase K-Ras4B, Exposing the Effector Binding Site

(2015) Shaoyong Lu et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Feasibility of Large-Scale Genomic Testing to Facilitate Enrollment Onto Genomically Matched Clinical Trials

(2015) Funda Meric-Bernstam et al.   JOURNAL OF CLINICAL ONCOLOGY

Molecularly targeted therapy based on tumour molecular profiling versus conventional therapy for advanced cancer (SHIVA): a multicentre, open-label, proof-of-concept, randomised, controlled phase 2 trial

(2015) Christophe Le Tourneau et al.   LANCET ONCOLOGY

Systematic Prioritization of Druggable Mutations in ∼5000 Genomes Across 16 Cancer Types Using a Structural Genomics-based Approach

(2015) Junfei Zhao et al.   MOLECULAR & CELLULAR PROTEOMICS

The Key Role of Calmodulin in KRAS-Driven Adenocarcinomas

(2015) R. Nussinov et al.   MOLECULAR CANCER RESEARCH

Discrimination of driver and passenger mutations in epidermal growth factor receptor in cancer

(2015) P. Anoosha et al.   MUTATION RESEARCH-FUNDAMENTAL AND MOLECULAR MECHANISMS OF MUTAGENESIS

YAP and the drug resistance highway

(2015) Alona Keren-Paz et al.   NATURE GENETICS

The Hippo effector YAP promotes resistance to RAF- and MEK-targeted cancer therapies

(2015) Luping Lin et al.   NATURE GENETICS

A New Initiative on Precision Medicine

(2015) Francis S. Collins et al.   NEW ENGLAND JOURNAL OF MEDICINE

ASD v3.0: unraveling allosteric regulation with structural mechanisms and biological networks

(2015) Qiancheng Shen et al.   NUCLEIC ACIDS RESEARCH

Using large-scale genomics data to identify driver mutations in lung cancer: methods and challenges

(2015) Andrew M Hudson et al.   PHARMACOGENOMICS

Direct inhibition of oncogenic KRAS by hydrocarbon-stapled SOS1 helices

(2015) Elizaveta S. Leshchiner et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The butterfly effect in cancer: A single base mutation can remodel the cell

(2015) Jonathan R. Hart et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Comprehensive assessment of cancer missense mutation clustering in protein structures

(2015) Atanas Kamburov et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Differential dynamics of RAS isoforms in GDP- and GTP-bound states

(2015) Abhijeet Kapoor et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Modeling metabolism: A window toward a comprehensive interpretation of networks in cancer

(2015) Osbaldo Resendis-Antonio et al.   SEMINARS IN CANCER BIOLOGY

The Mechanism of ATP-Dependent Allosteric Protection of Akt Kinase Phosphorylation

(2015) Shaoyong Lu et al.   STRUCTURE

GTP-Dependent K-Ras Dimerization

(2015) Serena Muratcioglu et al.   STRUCTURE

Allosteric Effects of the Oncogenic RasQ61L Mutant on Raf-RBD

(2015) Susan K. Fetics et al.   STRUCTURE

PI3K/AKT/mTOR and sonic hedgehog pathways cooperate together to inhibit human pancreatic cancer stem cell characteristics and tumor growth

(2015) Narinder Sharma et al.   Oncotarget

Revealing the favorable dissociation pathway of type II kinase inhibitors via enhanced sampling simulations and two-end-state calculations

(2015) Huiyong Sun et al.   Scientific Reports

Insights into the key interactions between human protein phosphatase 5 and cantharidin using molecular dynamics and site-directed mutagenesis bioassays

(2015) Ji-Yuan Liu et al.   Scientific Reports

Identification of Constrained Cancer Driver Genes Based on Mutation Timing

(2015) Thomas Sakoparnig et al.   PLoS Computational Biology

Mapping the Conformation Space of Wildtype and Mutant H-Ras with a Memetic, Cellular, and Multiscale Evolutionary Algorithm

(2015) Rudy Clausen et al.   PLoS Computational Biology

A Pan-Cancer Catalogue of Cancer Driver Protein Interaction Interfaces

(2015) Eduard Porta-Pardo et al.   PLoS Computational Biology

A Gene Gravity Model for the Evolution of Cancer Genomes: A Study of 3,000 Cancer Genomes across 9 Cancer Types

(2015) Feixiong Cheng et al.   PLoS Computational Biology

Systematic identification of cancer driving signaling pathways based on mutual exclusivity of genomic alterations

(2015) Özgün Babur et al.   GENOME BIOLOGY

Mapping of actionable mutations to histological subtype domains in lung adenocarcinoma: implications for precision medicine

(2015) Gavin M. Wright et al.   Oncotarget

Hypomethylation of the CTCFL/BORIS promoter and aberrant expression during endometrial cancer progression suggests a role as an Epi-driver gene

(2015) Erling A. Hoivik et al.   Oncotarget

Histone deacetylase 2 and N-Myc reduce p53 protein phosphorylation at serine 46 by repressing gene transcription of tumor protein 53-induced nuclear protein 1

(2015) Jeyran Shahbazi et al.   Oncotarget

The structural basis for cancer treatment decisions

(2015) Ruth Nussinov et al.   Oncotarget

ROS-mediated EB1 phosphorylation through Akt/GSK3β pathway: implication in cancer cell response to microtubule-targeting agents

(2015) Marion Le Grand et al.   Oncotarget

TFF1 activates p53 through down-regulation of miR-504 in gastric cancer

(2015) Mohammed Soutto et al.   Oncotarget

Caspase-8-mediated PAR-4 cleavage is required for TNFα-induced apoptosis

(2015) Fabian Treude et al.   Oncotarget

Structural basis of nSH2 regulation and lipid binding in PI3Kα

(2015) Michelle S. Miller et al.   Oncotarget

Translating Genomics for Precision Cancer Medicine

(2014) Roychowdhury Sameek et al.   Annual Review of Genomics and Human Genetics

Modeling the Role of G12V and G13V Ras Mutations in the Ras-GAP-Catalyzed Hydrolysis Reaction of Guanosine Triphosphate

(2014) Maria G. Khrenova et al.   BIOCHEMISTRY

Interpreting the language of histone and DNA modifications

(2014) Scott B. Rothbart et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

Macromolecular transport between the nucleus and the cytoplasm: Advances in mechanism and emerging links to disease

(2014) Elizabeth J. Tran et al.   BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH

PARS: a web server for the prediction of Protein Allosteric and Regulatory Sites

(2014) Alejandro Panjkovich et al.   BIOINFORMATICS

Kinesin-5 Allosteric Inhibitors Uncouple the Dynamics of Nucleotide, Microtubule, and Neck-Linker Binding Sites

(2014) Guido Scarabelli et al.   BIOPHYSICAL JOURNAL

How will B-cell-receptor-targeted therapies change future CLL therapy?

(2014) J. A. Jones et al.   BLOOD

Distinguishing between driver and passenger mutations in individual cancer genomes by network enrichment analysis

(2014) Simon Merid et al.   BMC BIOINFORMATICS

Pegasus: a comprehensive annotation and prediction tool for detection of driver gene fusions in cancer

(2014) Francesco Abate et al.   BMC Systems Biology

Yap1 Activation Enables Bypass of Oncogenic Kras Addiction in Pancreatic Cancer

(2014) Avnish Kapoor et al.   CELL

KRAS and YAP1 Converge to Regulate EMT and Tumor Survival

(2014) Diane D. Shao et al.   CELL

CRISPR-Cas9 Knockin Mice for Genome Editing and Cancer Modeling

(2014) Randall J. Platt et al.   CELL

Free Energy Diagrams for Protein Function

(2014) Ruth Nussinov et al.   CHEMISTRY & BIOLOGY

New Strategies in Lung Cancer: Epigenetic Therapy for Non-Small Cell Lung Cancer

(2014) P. M. Forde et al.   CLINICAL CANCER RESEARCH

Circadian control of tissue homeostasis and adult stem cells

(2014) Peggy Janich et al.   CURRENT OPINION IN CELL BIOLOGY

Computational approaches to mapping allosteric pathways

(2014) Victoria A Feher et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Acute myeloid leukaemia: a paradigm for the clonal evolution of cancer?

(2014) C. S. Grove et al.   Disease Models & Mechanisms

Recent computational advances in the identification of allosteric sites in proteins

(2014) Shaoyong Lu et al.   DRUG DISCOVERY TODAY

Stability of Iowa mutant and wild type Aβ-peptide aggregates

(2014) Erik J. Alred et al.   JOURNAL OF CHEMICAL PHYSICS

Trastuzumab Plus Adjuvant Chemotherapy for Human Epidermal Growth Factor Receptor 2–Positive Breast Cancer: Planned Joint Analysis of Overall Survival From NSABP B-31 and NCCTG N9831

(2014) Edith A. Perez et al.   JOURNAL OF CLINICAL ONCOLOGY

Harnessing Allostery: A Novel Approach to Drug Discovery

(2014) Shaoyong Lu et al.   MEDICINAL RESEARCH REVIEWS

Studying Tumorigenesis through Network Evolution and Somatic Mutational Perturbations in the Cancer Interactome

(2014) Feixiong Cheng et al.   MOLECULAR BIOLOGY AND EVOLUTION

Proteogenomic characterization of human colon and rectal cancer

(2014) Bing Zhang et al.   NATURE

Discovery and saturation analysis of cancer genes across 21 tumour types

(2014) Michael S. Lawrence et al.   NATURE

A general framework for estimating the relative pathogenicity of human genetic variants

(2014) Martin Kircher et al.   NATURE GENETICS

Pan-cancer network analysis identifies combinations of rare somatic mutations across pathways and protein complexes

(2014) Mark D M Leiserson et al.   NATURE GENETICS

Proteogenomics: concepts, applications and computational strategies

(2014) Alexey I Nesvizhskii   NATURE METHODS

Drugging the undruggable RAS: Mission Possible?

(2014) Adrienne D. Cox et al.   NATURE REVIEWS DRUG DISCOVERY

Expanding the computational toolbox for mining cancer genomes

(2014) Li Ding et al.   NATURE REVIEWS GENETICS

Cancer3D: understanding cancer mutations through protein structures

(2014) Eduard Porta-Pardo et al.   NUCLEIC ACIDS RESEARCH

A second molecular biology revolution? The energy landscapes of biomolecular function

(2014) Ruth Nussinov et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

The free energy landscape in translational science: how can somatic mutations result in constitutive oncogenic activation?

(2014) Chung-Jung Tsai et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Only three driver gene mutations are required for the development of lung and colorectal cancers

(2014) Cristian Tomasetti et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Contact inhibition and high cell density deactivate the mammalian target of rapamycin pathway, thus suppressing the senescence program

(2014) O. V. Leontieva et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

In situ selectivity profiling and crystal structure of SML-8-73-1, an active site inhibitor of oncogenic K-Ras G12C

(2014) J. C. Hunter et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

KRAS: feeding pancreatic cancer proliferation

(2014) Kirsten L. Bryant et al.   TRENDS IN BIOCHEMICAL SCIENCES

Simplifying the complexity of resistance heterogeneity in metastasis

(2014) Orit Lavi et al.   TRENDS IN MOLECULAR MEDICINE

Unraveling structural mechanisms of allosteric drug action

(2014) Ruth Nussinov et al.   TRENDS IN PHARMACOLOGICAL SCIENCES

DawnRank: discovering personalized driver genes in cancer

(2014) Jack P Hou et al.   Genome Medicine

Identifying driver mutations in sequenced cancer genomes: computational approaches to enable precision medicine

(2014) Benjamin J Raphael et al.   Genome Medicine

Biomolecular Events in Cancer Revealed by Attractor Metagenes

(2014) Wei-Yi Cheng et al.   PLoS Computational Biology

Robustness of DNA Repair through Collective Rate Control

(2014) Paul Verbruggen et al.   PLoS Computational Biology

Communication Routes in ARID Domains between Distal Residues in Helix 5 and the DNA-Binding Loops

(2014) Gaetano Invernizzi et al.   PLoS Computational Biology

VarWalker: Personalized Mutation Network Analysis of Putative Cancer Genes from Next-Generation Sequencing Data

(2014) Peilin Jia et al.   PLoS Computational Biology

A Unified View of “How Allostery Works”

(2014) Chung-Jung Tsai et al.   PLoS Computational Biology

P-loop Conformation Governed Crizotinib Resistance in G2032R-Mutated ROS1 Tyrosine Kinase: Clues from Free Energy Landscape

(2014) Huiyong Sun et al.   PLoS Computational Biology

Investigating the Structure and Dynamics of the PIK3CA Wild-Type and H1047R Oncogenic Mutant

(2014) Paraskevi Gkeka et al.   PLoS Computational Biology

Computational Modeling of Allosteric Regulation in the Hsp90 Chaperones: A Statistical Ensemble Analysis of Protein Structure Networks and Allosteric Communications

(2014) Kristin Blacklock et al.   PLoS Computational Biology

An emerging role for long non-coding RNAs in cancer metastasis

(2014) Jason T. Serviss et al.   Frontiers in Genetics

Therapeutic Targeting of Oncogenic K-Ras by a Covalent Catalytic Site Inhibitor

(2013) Sang Min Lim et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

The Underappreciated Role of Allostery in the Cellular Network

(2013) Ruth Nussinov et al.   Annual Review of Biophysics

Emerging computational approaches for the study of protein allostery

(2013) Galen Collier et al.   ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS

Allosite: a method for predicting allosteric sites

(2013) Wenkang Huang et al.   BIOINFORMATICS

OncodriveCLUST: exploiting the positional clustering of somatic mutations to identify cancer genes

(2013) David Tamborero et al.   BIOINFORMATICS

Discovering causal pathways linking genomic events to transcriptional states using Tied Diffusion Through Interacting Events (TieDIE)

(2013) Evan O. Paull et al.   BIOINFORMATICS

 -Catenin activation synergizes with Pten loss and Myc overexpression in Notch-independent T-ALL

(2013) D. Kaveri et al.   BLOOD

Utilizing protein structure to identify non-random somatic mutations

(2013) Gregory A Ryslik et al.   BMC BIOINFORMATICS

Revealing selection in cancer using the predicted functional impact of cancer mutations. Application to nomination of cancer drivers

(2013) B Reva   BMC GENOMICS

Advances for studying clonal evolution in cancer

(2013) Li Ding et al.   CANCER LETTERS

Allostery in Disease and in Drug Discovery

(2013) Ruth Nussinov et al.   CELL

Cumulative Haploinsufficiency and Triplosensitivity Drive Aneuploidy Patterns and Shape the Cancer Genome

(2013) Teresa Davoli et al.   CELL

Emerging pathways as individualized therapeutic target of multiple myeloma

(2013) Gabriella Misso et al.   EXPERT OPINION ON BIOLOGICAL THERAPY

Epigenetics of melanoma: implications for immune-based therapies

(2013) Elisabetta Fratta et al.   Immunotherapy

Development of Therapeutic Combinations Targeting Major Cancer Signaling Pathways

(2013) Timothy A. Yap et al.   JOURNAL OF CLINICAL ONCOLOGY

Genomics-Driven Oncology: Framework for an Emerging Paradigm

(2013) Levi A. Garraway   JOURNAL OF CLINICAL ONCOLOGY

Molecular Mechanisms of Disease-Causing Missense Mutations

(2013) Shannon Stefl et al.   JOURNAL OF MOLECULAR BIOLOGY

Systematic analysis of somatic mutations in phosphorylation signaling predicts novel cancer drivers

(2013) J. Reimand et al.   Molecular Systems Biology

K-Ras(G12C) inhibitors allosterically control GTP affinity and effector interactions

(2013) Jonathan M. Ostrem et al.   NATURE

Mutational heterogeneity in cancer and the search for new cancer-associated genes

(2013) Michael S. Lawrence et al.   NATURE

Mutational landscape and significance across 12 major cancer types

(2013) Cyriac Kandoth et al.   NATURE

Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples

(2013) Kristian Cibulskis et al.   NATURE BIOTECHNOLOGY

Allosteric inhibition through suppression of transient conformational states

(2013) Shiou-Ru Tzeng et al.   Nature Chemical Biology

Emerging landscape of oncogenic signatures across human cancers

(2013) Giovanni Ciriello et al.   NATURE GENETICS

US National Cancer Institute's new Ras project targets an old foe

(2013) Helen Thompson   NATURE MEDICINE

Network-based stratification of tumor mutations

(2013) Matan Hofree et al.   NATURE METHODS

MCPath: Monte Carlo path generation approach to predict likely allosteric pathways and functional residues

(2013) Cihan Kaya et al.   NUCLEIC ACIDS RESEARCH

Clinical impact of genetic variants of drug transporters in different ethnic groups within and across regions

(2013) Chiho Ono et al.   PHARMACOGENOMICS

Regulation of Small GTPases by GEFs, GAPs, and GDIs

(2013) Jacqueline Cherfils et al.   PHYSIOLOGICAL REVIEWS

Cancer Missense Mutations Alter Binding Properties of Proteins and Their Interaction Networks

(2013) Hafumi Nishi et al.   PLoS One

CanDrA: Cancer-Specific Driver Missense Mutation Annotation with Optimized Features

(2013) Yong Mao et al.   PLoS One

In silico discovery of small-molecule Ras inhibitors that display antitumor activity by blocking the Ras-effector interaction

(2013) F. Shima et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Cancer Genome Landscapes

(2013) B. Vogelstein et al.   SCIENCE

Oncogenic Driver Mutations: Neither Tissue-Specific nor Independent

(2013) A. A. Margolin   Science Translational Medicine

The molecular basis of targeting protein kinases in cancer therapeutics

(2013) Chung-Jung Tsai et al.   SEMINARS IN CANCER BIOLOGY

Antigen selection in B-cell lymphomas—Tracing the evidence

(2013) Lesley-Ann Sutton et al.   SEMINARS IN CANCER BIOLOGY

Allosteric Conformational Barcodes Direct Signaling in the Cell

(2013) Ruth Nussinov et al.   STRUCTURE

‘Pathway drug cocktail’: targeting Ras signaling based on structural pathways

(2013) Ruth Nussinov et al.   TRENDS IN MOLECULAR MEDICINE

Molecular Mechanisms of SH2- and PTB-Domain-Containing Proteins in Receptor Tyrosine Kinase Signaling

(2013) M. J. Wagner et al.   Cold Spring Harbor Perspectives in Biology

Comprehensive identification of mutational cancer driver genes across 12 tumor types

(2013) David Tamborero et al.   Scientific Reports

Distinct Types of Disorder in the Human Proteome: Functional Implications for Alternative Splicing

(2013) Recep Colak et al.   PLoS Computational Biology

Improving Breast Cancer Survival Analysis through Competition-Based Multidimensional Modeling

(2013) Erhan Bilal et al.   PLoS Computational Biology

Synthetic Lethality between Gene Defects Affecting a Single Non-essential Molecular Pathway with Reversible Steps

(2013) Andrei Zinovyev et al.   PLoS Computational Biology

Simultaneous Identification of Multiple Driver Pathways in Cancer

(2013) Mark D. M. Leiserson et al.   PLoS Computational Biology

DriverNet: uncovering the impact of somatic driver mutations on transcriptional networks in cancer

(2013) Ali Bashashati et al.   GENOME BIOLOGY

Discovery of Small Molecules that Bind to K-Ras and Inhibit Sos-Mediated Activation

(2012) Qi Sun et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Strelka: accurate somatic small-variant calling from sequenced tumor–normal sample pairs

(2012) Christopher T. Saunders et al.   BIOINFORMATICS

The metastatic niche and stromal progression

(2012) Jonathan P. Sleeman   CANCER AND METASTASIS REVIEWS

Intratumor Heterogeneity: Evolution through Space and Time

(2012) C. Swanton   CANCER RESEARCH

A Comprehensive Survey of Ras Mutations in Cancer

(2012) I. A. Prior et al.   CANCER RESEARCH

Hedgehog Signaling Is a Novel Therapeutic Target in Tamoxifen-Resistant Breast Cancer Aberrantly Activated by PI3K/AKT Pathway

(2012) B. Ramaswamy et al.   CANCER RESEARCH

Oncogenic Mutations Counteract Intrinsic Disorder in the EGFR Kinase and Promote Receptor Dimerization

(2012) Yibing Shan et al.   CELL

The Different Ways through Which Specificity Works in Orthosteric and Allosteric Drugs

(2012) Ruth Nussinov et al.   CURRENT PHARMACEUTICAL DESIGN

Colorectal Cancer Microenvironment: Among Nutrition, Gut Microbiota, Inflammation and Epigenetics

(2012) Paolo Garagnani et al.   CURRENT PHARMACEUTICAL DESIGN

MuSiC: Identifying mutational significance in cancer genomes

(2012) N. D. Dees et al.   GENOME RESEARCH

VarScan 2: Somatic mutation and copy number alteration discovery in cancer by exome sequencing

(2012) D. C. Koboldt et al.   GENOME RESEARCH

Dabrafenib in BRAF-mutated metastatic melanoma: a multicentre, open-label, phase 3 randomised controlled trial

(2012) Axel Hauschild et al.   LANCET

Erlotinib versus standard chemotherapy as first-line treatment for European patients with advanced EGFR mutation-positive non-small-cell lung cancer (EURTAC): a multicentre, open-label, randomised phase 3 trial

(2012) Rafael Rosell et al.   LANCET ONCOLOGY

Proteomic Analyses Reveal Divergent Ubiquitylation Site Patterns in Murine Tissues

(2012) Sebastian A. Wagner et al.   MOLECULAR & CELLULAR PROTEOMICS

Driver mutations in histone H3.3 and chromatin remodelling genes in paediatric glioblastoma

(2012) Jeremy Schwartzentruber et al.   NATURE

Functional impact bias reveals cancer drivers

(2012) Abel Gonzalez-Perez et al.   NUCLEIC ACIDS RESEARCH

Structure-based model of allostery predicts coupling between distant sites

(2012) P. Weinkam et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Disruption of PH-kinase domain interactions leads to oncogenic activation of AKT in human cancers

(2012) C. Parikh et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Allosteric post-translational modification codes

(2012) Ruth Nussinov et al.   TRENDS IN BIOCHEMICAL SCIENCES

Avogadro: an advanced semantic chemical editor, visualization, and analysis platform

(2012) Marcus D Hanwell et al.   Journal of Cheminformatics

Predicting cancer drivers: are we there yet?

(2012) Vidhya G Krishnan et al.   Genome Medicine

Chapter 1: Biomedical Knowledge Integration

(2012) Philip R. O. Payne   PLoS Computational Biology

Chapter 6: Structural Variation and Medical Genomics

(2012) Benjamin J. Raphael   PLoS Computational Biology

Single Nucleotide Polymorphisms Can Create Alternative Polyadenylation Signals and Affect Gene Expression through Loss of MicroRNA-Regulation

(2012) Laurent F. Thomas et al.   PLoS Computational Biology

Google Goes Cancer: Improving Outcome Prediction for Cancer Patients by Network-Based Ranking of Marker Genes

(2012) Christof Winter et al.   PLoS Computational Biology

CHASM and SNVBox: toolkit for detecting biologically important single nucleotide mutations in cancer

(2011) Wing Chung Wong et al.   BIOINFORMATICS

Cancer computational biology

(2011) Zohar Yakhini et al.   BMC BIOINFORMATICS

Regulation of the catalytic activity of the EGF receptor

(2011) Nicholas F Endres et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Oncogene addiction as a foundational rationale for targeted anti-cancer therapy: promises and perils

(2011) Davide Torti et al.   EMBO Molecular Medicine

Biomarker Analyses and Final Overall Survival Results From a Phase III, Randomized, Open-Label, First-Line Study of Gefitinib Versus Carboplatin/Paclitaxel in Clinically Selected Patients With Advanced Non–Small-Cell Lung Cancer in Asia (IPASS)

(2011) Masahiro Fukuoka et al.   JOURNAL OF CLINICAL ONCOLOGY

Four-Year Follow-Up of Trastuzumab Plus Adjuvant Chemotherapy for Operable Human Epidermal Growth Factor Receptor 2–Positive Breast Cancer: Joint Analysis of Data From NCCTG N9831 and NSABP B-31

(2011) Edith A. Perez et al.   JOURNAL OF CLINICAL ONCOLOGY

Catalytic Control in the EGF Receptor and Its Connection to General Kinase Regulatory Mechanisms

(2011) Natalia Jura et al.   MOLECULAR CELL

Molecular Tumor Clocks To Study the Evolution of Drug Resistance

(2011) Darryl Shibata   MOLECULAR PHARMACEUTICS

An orthosteric inhibitor of the Ras-Sos interaction

(2011) Anupam Patgiri et al.   Nature Chemical Biology

Simultaneous visualization of the extracellular and cytoplasmic domains of the epidermal growth factor receptor

(2011) Li-Zhi Mi et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Mechanistic insights into the activation of oncogenic forms of EGF receptor

(2011) Zhihong Wang et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Temozolomide in the treatment of high-grade gliomas in children: a report from the Children's Oncology Group

(2011) K. J. Cohen et al.   NEURO-ONCOLOGY

Predicting the functional impact of protein mutations: application to cancer genomics

(2011) Boris Reva et al.   NUCLEIC ACIDS RESEARCH

PI3K-targeted therapy can be evaded by gene amplification along the MYC-eukaryotic translation initiation factor 4E (eIF4E) axis

(2011) N. Ilic et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Inhibition of PI3K binding to activators by serine phosphorylation of PI3K regulatory subunit p85  Src homology-2 domains

(2011) J. Y. Lee et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Allo-network drugs: harnessing allostery in cellular networks

(2011) Ruth Nussinov et al.   TRENDS IN PHARMACOLOGICAL SCIENCES

The Roots of Bioinformatics in Theoretical Biology

(2011) Paulien Hogeweg   PLoS Computational Biology

Nucleotide Binding Switches the Information Flow in Ras GTPases

(2011) Francesco Raimondi et al.   PLoS Computational Biology

Statistical method on nonrandom clustering with application to somatic mutations in cancer

(2010) Jingjing Ye et al.   BMC BIOINFORMATICS

Activating K-Ras mutations outwith ‘hotspot’ codons in sporadic colorectal tumours – implications for personalised cancer medicine

(2010) G Smith et al.   BRITISH JOURNAL OF CANCER

An Integrated Approach to Uncover Drivers of Cancer

(2010) Uri David Akavia et al.   CELL

Cell Signaling by Receptor Tyrosine Kinases

(2010) Mark A. Lemmon et al.   CELL

The Src, Syk, and Tec family kinases: Distinct types of molecular switches

(2010) J. Michael Bradshaw   CELLULAR SIGNALLING

The Mdm2-p53 relationship evolves: Mdm2 swings both ways as an oncogene and a tumor suppressor

(2010) J. J. Manfredi   GENES & DEVELOPMENT

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

(2010) A. McKenna et al.   GENOME RESEARCH

Integrated Molecular Genetic Profiling of Pediatric High-Grade Gliomas Reveals Key Differences With the Adult Disease

(2010) Barbara S. Paugh et al.   JOURNAL OF CLINICAL ONCOLOGY

Spatial control of EGF receptor activation by reversible dimerization on living cells

(2010) Inhee Chung et al.   NATURE

A method and server for predicting damaging missense mutations

(2010) Ivan A Adzhubei et al.   NATURE METHODS

ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data

(2010) K. Wang et al.   NUCLEIC ACIDS RESEARCH

Folding and binding cascades: Dynamic landscapes and population shifts

(2010) Sandeep Kumar et al.   PROTEIN SCIENCE

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

The Distinct Conformational Dynamics of K-Ras and H-Ras A59G

(2010) Suryani Lukman et al.   PLoS Computational Biology

Cancer-Specific High-Throughput Annotation of Somatic Mutations: Computational Prediction of Driver Missense Mutations

(2009) H. Carter et al.   CANCER RESEARCH

Mechanism for Activation of the EGF Receptor Catalytic Domain by the Juxtamembrane Segment

(2009) Natalia Jura et al.   CELL

ErbB receptors and signaling pathways in cancer

(2009) Nancy E Hynes et al.   CURRENT OPINION IN CELL BIOLOGY

Towards inferring time dimensionality in protein–protein interaction networks by integrating structures: the p53 example

(2009) Nurcan Tuncbag et al.   Molecular BioSystems

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

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

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

(2009) Monica Red Brewer et al.   MOLECULAR CELL

The role of dynamic conformational ensembles in biomolecular recognition

(2009) David D Boehr et al.   Nature Chemical Biology

Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm

(2009) Prateek Kumar et al.   Nature Protocols

Sequence and Structure Signatures of Cancer Mutation Hotspots in Protein Kinases

(2009) Anshuman Dixit et al.   PLoS One

Cancer attractors: A systems view of tumors from a gene network dynamics and developmental perspective

(2009) Sui Huang et al.   SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY

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

(2009) Antonio del Sol et al.   STRUCTURE

Protein–protein interaction networks: how can a hub protein bind so many different partners?

(2009) Chung-Jung Tsai et al.   TRENDS IN BIOCHEMICAL SCIENCES

Modeling Signal Propagation Mechanisms and Ligand-Based Conformational Dynamics of the Hsp90 Molecular Chaperone Full-Length Dimer

(2009) Giulia Morra et al.   PLoS Computational Biology

Principles of Protein−Protein Interactions: What are the Preferred Ways For Proteins To Interact?

(2008) Ozlem Keskin et al.   CHEMICAL REVIEWS

Allostery Wiring Diagrams in the Transitions that Drive the GroEL Reaction Cycle

(2008) Riina Tehver et al.   JOURNAL OF MOLECULAR BIOLOGY

Somatic mutations affect key pathways in lung adenocarcinoma

(2008) Li Ding et al.   NATURE

Allosteric effects in the marginally stable von Hippel-Lindau tumor suppressor protein and allostery-based rescue mutant design

(2008) J. Liu 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

The T790M mutation in EGFR kinase causes drug resistance by increasing the affinity for ATP

(2008) C.-H. Yun et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Core Signaling Pathways in Human Pancreatic Cancers Revealed by Global Genomic Analyses

(2008) S. Jones et al.   SCIENCE

Mapping the Nucleotide and Isoform-Dependent Structural and Dynamical Features of Ras Proteins

(2008) Alemayehu A. Gorfe et al.   STRUCTURE

Multiple diverse ligands binding at a single protein site: A matter of pre-existing populations

(2002) Buyong Ma et al.   PROTEIN SCIENCE