Protein ensembles link genotype to phenotype

Natural history and genotype-phenotype correlations in 72 individuals with SATB2 -associated syndrome

(2018) Yuri A. Zarate et al.   AMERICAN JOURNAL OF MEDICAL GENETICS PART A

Systems Approaches to Understanding and Designing Allosteric Proteins

(2018) Srivatsan Raman   BIOCHEMISTRY

ProteomeVis: a web app for exploration of protein properties from structure to sequence evolution across organisms’ proteomes

(2018) Rostam M Razban et al.   BIOINFORMATICS

Dependence of Chromatosome Structure on Linker Histone Sequence and Posttranslational Modification

(2018) Mehmet Ali Öztürk et al.   BIOPHYSICAL JOURNAL

Large scale analysis of protein conformational transitions from aqueous to non-aqueous media

(2018) Ana Julia Velez Rueda et al.   BMC BIOINFORMATICS

Enzyme intermediates captured “on the fly” by mix-and-inject serial crystallography

(2018) Jose L. Olmos et al.   BMC BIOLOGY

How structural elements evolving from bacterial to human SLC6 transporters enabled new functional properties

(2018) Asghar M. Razavi et al.   BMC BIOLOGY

Entering an era of dynamic structural biology…

(2018) Allen M. Orville   BMC BIOLOGY

Role of conformational dynamics in the evolution of novel enzyme function

(2018) Miguel A. Maria-Solano et al.   CHEMICAL COMMUNICATIONS

Bringing diffuse X-ray scattering into focus

(2018) Michael E Wall et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Structural heterogeneity and dynamics in protein evolution and design

(2018) Kristoffer E Johansson et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Recognition of the polycistronic nature of human genes is critical to understanding the genotype-phenotype relationship

(2018) Marie A. Brunet et al.   GENOME RESEARCH

Inference of developmental gene regulatory networks beyond classical model systems: new approaches in the post-genomic era

(2018) Selene L Fernandez-Valverde et al.   INTEGRATIVE AND COMPARATIVE BIOLOGY

Predicting the Conformational Variability of Abl Tyrosine Kinase using Molecular Dynamics Simulations and Markov State Models

(2018) Yilin Meng et al.   Journal of Chemical Theory and Computation

ClusPro FMFT-SAXS: Ultra-fast Filtering Using Small-Angle X-ray Scattering Data in Protein Docking

(2018) Mikhail Ignatov et al.   JOURNAL OF MOLECULAR BIOLOGY

Fuzziness in Protein Interactions—A Historical Perspective

(2018) Monika Fuxreiter   JOURNAL OF MOLECULAR BIOLOGY

Transition-State Ensembles Navigate the Pathways of Enzyme Catalysis

(2018) Matthias J. Mickert et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Specific Substates of Ras To Interact with GAPs and Effectors: Revealed by Theoretical Simulations and FTIR Experiments

(2018) Yang Li et al.   Journal of Physical Chemistry Letters

Unraveling co-translational protein folding: Concepts and methods

(2018) Anton A. Komar   METHODS

Network Analysis of Protein Adaptation: Modeling the Functional Impact of Multiple Mutations

(2018) Violeta Beleva Guthrie et al.   MOLECULAR BIOLOGY AND EVOLUTION

Evolution on the biophysical fitness landscape of an RNA virus

(2018) Assaf Rotem et al.   MOLECULAR BIOLOGY AND EVOLUTION

How is structural divergence related to evolutionary information?

(2018) Diego Javier Zea et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Somatic Activating KRAS Mutations in Arteriovenous Malformations of the Brain

(2018) Sergey I. Nikolaev et al.   NEW ENGLAND JOURNAL OF MEDICINE

Ancient thioredoxins evolved to modern-day stability–function requirement by altering native state ensemble

(2018) Tushar Modi et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Extant fold-switching proteins are widespread

(2018) Lauren L. Porter et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Towards conformational fidelity of a quaternary HIV-1 epitope: computational design and directed evolution of a minimal V1V2 antigen

(2018) Jennifer I Lai et al.   PROTEIN ENGINEERING DESIGN & SELECTION

Structural effects of point mutations in proteins

(2018) Suvethigaa Shanthirabalan et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Phenotypic plasticity, canalization, and the origins of novelty: Evidence and mechanisms from amphibians

(2018) Nicholas A. Levis et al.   SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY

Structural and Dynamics Comparison of Thermostability in Ancient, Modern, and Consensus Elongation Factor Tus

(2018) C. Denise Okafor et al.   STRUCTURE

ZFR coordinates crosstalk between RNA decay and transcription in innate immunity

(2018) Nazmul Haque et al.   Nature Communications

Memory functions reveal structural properties of gene regulatory networks

(2018) Edgar Herrera-Delgado et al.   PLoS Computational Biology

Patterning mechanisms diversify neuroepithelial domains in the Drosophila optic placode

(2018) Abhishek Kumar Mishra et al.   PLoS Genetics

Non-equilibrium repressor binding kinetics link DNA damage dose to transcriptional timing within the SOS gene network

(2018) Matthew J. Culyba et al.   PLoS Genetics

Synergistic co-regulation and competition by a SOX9-GLI-FOXA phasic transcriptional network coordinate chondrocyte differentiation transitions

(2018) Zhijia Tan et al.   PLoS Genetics

Stability of the Influenza Virus Hemagglutinin Protein Correlates with Evolutionary Dynamics

(2018) Eili Y. Klein et al.   mSphere

Phenotypic Plasticity, Bet-Hedging, and Androgen Independence in Prostate Cancer: Role of Non-Genetic Heterogeneity

(2018) Mohit Kumar Jolly et al.   Frontiers in Oncology

Identification and characterization of a missense mutation in theO-linked β-N-acetylglucosamine (O-GlcNAc) transferase gene that segregates with X-linked intellectual disability

(2017) Krithika Vaidyanathan et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Regulatory network and genetic interactions established by OsMADS34 in rice inflorescence and spikelet morphogenesis

(2017) Qingcai Meng et al.   Journal of Integrative Plant Biology

Structure of Human M-type Phospholipase A2 Receptor Revealed by Cryo-Electron Microscopy

(2017) Yue Dong et al.   JOURNAL OF MOLECULAR BIOLOGY

Structural properties of genotype–phenotype maps

(2017) S. E. Ahnert   Journal of the Royal Society Interface

Mechanistic insights into thrombin's switch between “slow” and “fast” forms

(2017) Jiajie Xiao et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Evidence of evolutionary selection for cotranslational folding

(2017) William M. Jacobs et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Foldamer hypothesis for the growth and sequence differentiation of prebiotic polymers

(2017) Elizaveta Guseva et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Patterns of coevolving amino acids unveil structural and dynamical domains

(2017) Daniele Granata et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Molecular ensembles make evolution unpredictable

(2017) Zachary R. Sailer et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Combining protein sequence, structure, and dynamics: A novel approach for functional evolution analysis of PAS domain superfamily

(2017) Zheng Dong et al.   PROTEIN SCIENCE

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

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

Role of Conformational Dynamics in the Evolution of Retro-Aldolase Activity

(2017) Adrian Romero-Rivera et al.   ACS Catalysis

LASSIM—A network inference toolbox for genome-wide mechanistic modeling

(2017) Rasmus Magnusson et al.   PLoS Computational Biology

Diverse type 2 diabetes genetic risk factors functionally converge in a phenotype-focused gene network

(2017) Cynthia Sandor et al.   PLoS Computational Biology

BeWith: A Between-Within method to discover relationships between cancer modules via integrated analysis of mutual exclusivity, co-occurrence and functional interactions

(2017) Phuong Dao et al.   PLoS Computational Biology

Network perturbation by recurrent regulatory variants in cancer

(2017) Kiwon Jang et al.   PLoS Computational Biology

Transcriptional and Post-Transcriptional Regulation of Thrombospondin-1 Expression: A Computational Model

(2017) Chen Zhao et al.   PLoS Computational Biology

The genotype-phenotype map of an evolving digital organism

(2017) Miguel A. Fortuna et al.   PLoS Computational Biology

Computational Analysis of Residue Interaction Networks and Coevolutionary Relationships in the Hsp70 Chaperones: A Community-Hopping Model of Allosteric Regulation and Communication

(2017) Gabrielle Stetz et al.   PLoS Computational Biology

Evolutionary fine-tuning of conformational ensembles in FimH during host-pathogen interactions

(2017) Vasilios Kalas et al.   Science Advances

Edge-based sensitivity analysis of signaling networks by using Boolean dynamics

(2016) Hung-Cuong Trinh et al.   BIOINFORMATICS

The MC1R Gene and Youthful Looks

(2016) Fan Liu et al.   CURRENT BIOLOGY

De Novo Proteins with Life-Sustaining Functions Are Structurally Dynamic

(2016) Grant S. Murphy et al.   JOURNAL OF MOLECULAR BIOLOGY

Effects of Crowding and Environment on the Evolution of Conformational Ensembles of the Multi-Stimuli-Responsive Intrinsically Disordered Protein, Rec1-Resilin: A Small-Angle Scattering Investigation

(2016) Rajkamal Balu et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Structural and dynamic evolution of the amphipathic N-terminus diversifies enzyme thermostability in the glycoside hydrolase family 12

(2016) Xukai Jiang et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Drivers of structural features in gene regulatory networks: From biophysical constraints to biological function

(2016) O.C. Martin et al.   Physics of Life Reviews

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

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

The Gearbox of the Bacterial Flagellar Motor Switch

(2016) Alessandro Pandini et al.   STRUCTURE

Key Intermediates in Ribosome Recycling Visualized by Time-Resolved Cryoelectron Microscopy

(2016) Ziao Fu et al.   STRUCTURE

Evolutionary Conserved Positions Define Protein Conformational Diversity

(2016) Tadeo E. Saldaño et al.   PLoS Computational Biology

Theoretical Insights into the Biophysics of Protein Bi-stability and Evolutionary Switches

(2016) Tobias Sikosek et al.   PLoS Computational Biology

Understanding Genotype-Phenotype Effects in Cancer via Network Approaches

(2016) Yoo-Ah Kim et al.   PLoS Computational Biology

Translation of Genotype to Phenotype by a Hierarchy of Cell Subsystems

(2016) Michael Ku Yu et al.   Cell Systems

Nucleosome adaptability conferred by sequence and structural variations in histone H2A–H2B dimers

(2015) Alexey K Shaytan et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Conformational diversity and the emergence of sequence signatures during evolution

(2015) Gustavo Parisi et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Integration of structural dynamics and molecular evolution via protein interaction networks: a new era in genomic medicine

(2015) Avishek Kumar et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

‘Latent drivers’ expand the cancer mutational landscape

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

Target the More Druggable Protein States in a Highly Dynamic Protein–Protein Interaction System

(2015) Zuojun Guo et al.   Journal of Chemical Information and Modeling

A Genome-Wide Association Study Identifies the Skin Color Genes IRF4 , MC1R , ASIP , and BNC2 Influencing Facial Pigmented Spots

(2015) Leonie C. Jacobs et al.   JOURNAL OF INVESTIGATIVE DERMATOLOGY

Understanding multicellular function and disease with human tissue-specific networks

(2015) Casey S Greene et al.   NATURE GENETICS

From residue coevolution to protein conformational ensembles and functional dynamics

(2015) Ludovico Sutto et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Mapping the conformational landscape of a dynamic enzyme by multitemperature and XFEL crystallography

(2015) Daniel A Keedy et al.   eLife

Towards time-resolved serial crystallography in a microfluidic device

(2015) Ashtamurthy S. Pawate et al.   Acta Crystallographica Section F-Structural Biology Communications

The differential view of genotype–phenotype relationships

(2015) Virginie Orgogozo et al.   Frontiers in Genetics

The structural basis for cancer treatment decisions

(2015) Ruth Nussinov et al.   Oncotarget

PI3K/Akt-mediated regulation of p53 in cancer

(2014) Aswin G. Abraham et al.   BIOCHEMICAL SOCIETY TRANSACTIONS

Structure–activity relationships of oxysterol-derived pharmacological chaperones for Niemann–Pick type C1 protein

(2014) Kenji Ohgane et al.   BIOORGANIC & MEDICINAL CHEMISTRY LETTERS

MDM2-p53 Pathway in Hepatocellular Carcinoma

(2014) X. Meng et al.   CANCER RESEARCH

Free Energy Diagrams for Protein Function

(2014) Ruth Nussinov et al.   CHEMISTRY & BIOLOGY

Gain-of-Function Mutation in STIM1 (P.R304W) Is Associated with Stormorken Syndrome

(2014) Gilles Morin et al.   HUMAN MUTATION

Expanding the Proteome of an RNA Virus by Phosphorylation of an Intrinsically Disordered Viral Protein

(2014) Daniel G. Cordek et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Biophysics of protein evolution and evolutionary protein biophysics

(2014) T. Sikosek et al.   Journal of the Royal Society Interface

A multiscale statistical mechanical framework integrates biophysical and genomic data to assemble cancer networks

(2014) Mohammed AlQuraishi et al.   NATURE GENETICS

Crystal structure of a BRAF kinase domain monomer explains basis for allosteric regulation

(2014) Neroshan Thevakumaran et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Time-resolved crystallography and protein design: signalling photoreceptors and optogenetics

(2014) K. Moffat   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

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

Time-resolved serial crystallography captures high-resolution intermediates of photoactive yellow protein

(2014) Jason Tenboer et al.   SCIENCE

Mutation spectrum and genotype-phenotype correlations in a large French cohort of MYH9-Related Disorders

(2014) Béatrice Saposnik et al.   Molecular Genetics & Genomic Medicine

Protein energy landscapes determined by five-dimensional crystallography

(2013) Marius Schmidt et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

The Underappreciated Role of Allostery in the Cellular Network

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

Edgotype: a fundamental link between genotype and phenotype

(2013) Nidhi Sahni et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

A systematic review and meta-analysis of genotype–phenotype associations in patients with hypertrophic cardiomyopathy caused by sarcomeric protein mutations

(2013) Luís R Lopes et al.   HEART

Protein Conformational Diversity Correlates with Evolutionary Rate

(2013) Diego Javier Zea et al.   MOLECULAR BIOLOGY AND EVOLUTION

Pleiotropy in complex traits: challenges and strategies

(2013) Nadia Solovieff et al.   NATURE REVIEWS GENETICS

The spatial structure of cell signaling systems

(2013) Ruth Nussinov   PHYSICAL BIOLOGY

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

(2013) Hafumi Nishi et al.   PLoS One

Adaptive Evolution of Multiple Traits Through Multiple Mutations at a Single Gene

(2013) C. R. Linnen et al.   SCIENCE

The structural network of inflammation and cancer: Merits and challenges

(2013) Emine Guven Maiorov et al.   SEMINARS IN CANCER BIOLOGY

Allosteric Conformational Barcodes Direct Signaling in the Cell

(2013) Ruth Nussinov et al.   STRUCTURE

A Comprehensive Survey of Ras Mutations in Cancer

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

The Genetic Basis for Cancer Treatment Decisions

(2012) Janet E. Dancey et al.   CELL

Three-dimensional reconstruction of protein networks provides insight into human genetic disease

(2012) Xiujuan Wang et al.   NATURE BIOTECHNOLOGY

Leveraging models of cell regulation and GWAS data in integrative network-based association studies

(2012) Andrea Califano et al.   NATURE GENETICS

Protein frustratometer: a tool to localize energetic frustration in protein molecules

(2012) M. Jenik et al.   NUCLEIC ACIDS RESEARCH

Modeling and Molecular Dynamics of HPA-1a and -1b Polymorphisms: Effects on the Structure of the β3 Subunit of the αIIbβ3 Integrin

(2012) Vincent Jallu et al.   PLoS One

The mystery of missing heritability: Genetic interactions create phantom heritability

(2012) O. Zuk 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

Gene-specific transcription activation via long-range allosteric shape-shifting

(2011) Chung-Jung Tsai et al.   BIOCHEMICAL JOURNAL

Selective Molecular Recognition in Amyloid Growth and Transmission and Cross-Species Barriers

(2011) Buyong Ma et al.   JOURNAL OF MOLECULAR BIOLOGY

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

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

A drug-resistant duo

(2011) Hugo Lavoie et al.   NATURE

RAF inhibitor resistance is mediated by dimerization of aberrantly spliced BRAF(V600E)

(2011) Poulikos I. Poulikakos et al.   NATURE

The pleiotropic structure of the genotype–phenotype map: the evolvability of complex organisms

(2011) Günter P. Wagner et al.   NATURE REVIEWS GENETICS

Detecting Low Frequent Loss-of-Function Alleles in Genome Wide Association Studies with Red Hair Color as Example

(2011) Fan Liu et al.   PLoS One

Allo-network drugs: harnessing allostery in cellular networks

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

The Evolution of Protein Structures and Structural Ensembles Under Functional Constraint

(2011) Jessica Siltberg-Liberles et al.   Genes

Evolvability and Single-Genotype Fluctuation in Phenotypic Properties: A Simple Heteropolymer Model

(2010) Tao Chen et al.   BIOPHYSICAL JOURNAL

Polymorphism in Alzheimer Aβ Amyloid Organization Reflects Conformational Selection in a Rugged Energy Landscape

(2010) Yifat Miller et al.   CHEMICAL REVIEWS

Genotype-phenotype mapping and the end of the 'genes as blueprint' metaphor

(2010) M. Pigliucci   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Folding and binding cascades: Dynamic landscapes and population shifts

(2010) Sandeep Kumar et al.   PROTEIN SCIENCE

Genotype to Phenotype: A Complex Problem

(2010) R. D. Dowell et al.   SCIENCE

Edgetic perturbation models of human inherited disorders

(2009) Quan Zhong et al.   Molecular Systems Biology

Bet-hedging as an evolutionary game: the trade-off between egg size and number

(2009) M. Rees et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

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

Genome-wide association studies for complex traits: consensus, uncertainty and challenges

(2008) Mark I. McCarthy et al.   NATURE REVIEWS GENETICS