On the public citation graph

Quantifying the topography of the intrinsic energy landscape of flexible biomolecular recognition

https://doi.org/10.1073/pnas.1220699110

0 signed · 140 inferred · view as graph

Inferred edges come from two machine sources: sweeps of open repository metadata (mostly SSRN and Zenodo), and a bulk OpenAlex citation snapshot. Every row below is labelled with the one it came from. Neither is a complete citation index — absence here is not evidence of absence.

Is this your work? Sign in with ORCID and put your name on the claims that are yours.

Claim with ORCID

Reference health. See whether every reference in this work resolves to a known work and none has been retracted — and get a dated CiteStamped badge you can embed.

See reference health

What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

inferredcites →https://doi.org/10.1002/(sici)1097-0134(199608)25:4<438::aid-prot4>3.3.co;2-1openalex-snapshot

Quantifying biological specificity: The statistical mechanics of molecular recognition

inferredcites →https://doi.org/10.1002/bip.10286openalex-snapshot

The physics and bioinformatics of binding and folding—an energy landscape perspective

inferredcites →https://doi.org/10.1002/cber.18940270364openalex-snapshot

Einfluss der Configuration auf die Wirkung der Enzyme

inferredcites →https://doi.org/10.1002/jcc.540130812openalex-snapshot

THE weighted histogram analysis method for free‐energy calculations on biomolecules. I. The method

inferredcites →https://doi.org/10.1002/jmr.747openalex-snapshot

Showing your ID: intrinsic disorder as an ID for recognition, regulation and cell signaling

inferredcites →https://doi.org/10.1002/pro.5560031202openalex-snapshot

Conformational stability of dimeric proteins: Quantitative studies by equilibrium denaturation

inferredcites →https://doi.org/10.1002/pro.5560070117openalex-snapshot

The response of T4 lysozyme to large‐to‐small substitutions within the core and its relation to the hydrophobic effect

inferredcites →https://doi.org/10.1002/pro.5560070301openalex-snapshot

Mechanism and evolution of protein dimerization

inferredcites →https://doi.org/10.1002/prot.340210302openalex-snapshot

Funnels, pathways, and the energy landscape of protein folding: A synthesis

inferredcites →https://doi.org/10.1002/prot.4openalex-snapshot

Quantifying biological specificity: The statistical mechanics of molecular recognition

inferredcites →https://doi.org/10.1006/jmbi.1999.3110openalex-snapshot

Intrinsically unstructured proteins: re-assessing the protein structure-function paradigm

inferredcites →https://doi.org/10.1007/978-1-4612-4380-9_25openalex-snapshot

Nonparametric Estimation from Incomplete Observations

inferredcites →https://doi.org/10.1007/s002140050198openalex-snapshot

Kinetic partitioning mechanism as a unifying theme in the folding of biomolecules

inferredcites →https://doi.org/10.1016/b978-0-12-374984-0.01698-3openalex-snapshot

Intrinsically Disordered Proteins

inferredcites →https://doi.org/10.1016/j.bpj.2010.12.278openalex-snapshot

Charge Interactions Can Dominate the Dimensions of Intrinsically Disordered Proteins

inferredcites →https://doi.org/10.1016/j.chemphys.2005.04.045openalex-snapshot

The cooperative nature of hydrophobic forces and protein folding kinetics

inferredcites →https://doi.org/10.1016/j.coph.2010.09.012openalex-snapshot

From protein folding to protein function and biomolecular binding by energy landscape theory

inferredcites →https://doi.org/10.1016/j.cplett.2005.11.016openalex-snapshot

Diffusion and single molecule dynamics on biomolecular interface binding energy landscape

inferredcites →https://doi.org/10.1016/j.jmb.2004.07.002openalex-snapshot

Analysis of Ordered and Disordered Protein Complexes Reveals Structural Features Discriminating Between Stable and Unstable Monomers

inferredcites →https://doi.org/10.1016/j.jmb.2004.12.021openalex-snapshot

A Survey of Flexible Protein Binding Mechanisms and their Transition States Using Native Topology Based Energy Landscapes

inferredcites →https://doi.org/10.1016/j.jmb.2009.09.005openalex-snapshot

Non-Sequence-Specific Interactions Can Account for the Compaction of Proteins Unfolded under “Native” Conditions

inferredcites →https://doi.org/10.1016/j.pbiomolbio.2008.05.004openalex-snapshot

Conformational stability and folding mechanisms of dimeric proteins

inferredcites →https://doi.org/10.1016/j.sbi.2004.01.009openalex-snapshot

Theory of protein folding

inferredcites →https://doi.org/10.1016/j.sbi.2008.12.003openalex-snapshot

Linking folding and binding

inferredcites →https://doi.org/10.1016/j.sbi.2011.10.005openalex-snapshot

How, when and why proteins collapse: the relation to folding

inferredcites →https://doi.org/10.1016/s0009-2614(99)01123-9openalex-snapshot

Replica-exchange molecular dynamics method for protein folding

inferredcites →https://doi.org/10.1016/s1074-5521(96)90090-3openalex-snapshot

Fast-folding eriments and the topography of protein folding energy landscapes

inferredcites →https://doi.org/10.1016/s1093-3263(00)00138-8openalex-snapshot

Intrinsically disordered protein

inferredcites →https://doi.org/10.1016/s1359-0278(97)00002-3openalex-snapshot

Protein folding kinetics: timescales, pathways and energy landscapes in terms of sequence-dependent properties

inferredcites →https://doi.org/10.1017/s0033583502003761openalex-snapshot

Understanding protein folding with energy landscape theory Part I: Basic concepts

inferredcites →https://doi.org/10.1017/s0033583505004075openalex-snapshot

Recent successes of the energy landscape theory of protein folding and function

inferredcites →https://doi.org/10.1017/s0033583506004185openalex-snapshot

The experimental survey of protein-folding energy landscapes

inferredcites →https://doi.org/10.1021/bi00695a021openalex-snapshot

Dynamics of ligand binding to myoglobin

inferredcites →https://doi.org/10.1021/bi982828sopenalex-snapshot

Thermal Stability and Mode of Oligomerization of the Tetrameric Peanut Agglutinin: A Differential Scanning Calorimetry Study

inferredcites →https://doi.org/10.1021/j100356a007openalex-snapshot

Intermediates and barrier crossing in a random energy model (with applications to protein folding)

inferredcites →https://doi.org/10.1021/ja3045663openalex-snapshot

Multidomain Protein Solves the Folding Problem by Multifunnel Combined Landscape: Theoretical Investigation of a Y-Family DNA Polymerase

inferredcites →https://doi.org/10.1038/nrm1589openalex-snapshot

Intrinsically unstructured proteins and their functions

inferredcites →https://doi.org/10.1038/nsb0197-10openalex-snapshot

From Levinthal to pathways to funnels

inferredcites →https://doi.org/10.1063/1.1527633openalex-snapshot

Statistics, pathways and dynamics of single molecule protein folding

inferredcites →https://doi.org/10.1063/1.473355openalex-snapshot

Statistical mechanics of a correlated energy landscape model for protein folding funnels

inferredcites →https://doi.org/10.1073/pnas.0409471102openalex-snapshot

Balancing energy and entropy: A minimalist model for the characterization of protein folding landscapes

inferredcites →https://doi.org/10.1073/pnas.0813120106openalex-snapshot

Electrostatic effects on funneled landscapes and structural diversity in denatured protein ensembles

inferredcites →https://doi.org/10.1073/pnas.0911107107openalex-snapshot

Net charge per residue modulates conformational ensembles of intrinsically disordered proteins

inferredcites →https://doi.org/10.1073/pnas.0914727107openalex-snapshot

Capillarity theory for the fly-casting mechanism

inferredcites →https://doi.org/10.1073/pnas.1001743107openalex-snapshot

Charge interactions can dominate the dimensions of intrinsically disordered proteins

inferredcites →https://doi.org/10.1073/pnas.1212842109openalex-snapshot

Topography of funneled landscapes determines the thermodynamics and kinetics of protein folding

inferredcites →https://doi.org/10.1073/pnas.1216215109openalex-snapshot

Predictive energy landscapes for protein–protein association

inferredcites →https://doi.org/10.1073/pnas.160259697openalex-snapshot

Speeding molecular recognition by using the folding funnel: The fly-casting mechanism

inferredcites →https://doi.org/10.1073/pnas.2534828100openalex-snapshot

Protein topology determines binding mechanism

inferredcites →https://doi.org/10.1073/pnas.44.2.98openalex-snapshot

Application of a Theory of Enzyme Specificity to Protein Synthesis

inferredcites →https://doi.org/10.1073/pnas.84.21.7524openalex-snapshot

Spin glasses and the statistical mechanics of protein folding.

inferredcites →https://doi.org/10.1073/pnas.89.18.8721openalex-snapshot

Protein folding funnels: a kinetic approach to the sequence-structure relationship.

inferredcites →https://doi.org/10.1073/pnas.90.15.7195openalex-snapshot

Engineering of stable and fast-folding sequences of model proteins.

inferredcites →https://doi.org/10.1073/pnas.92.8.3626openalex-snapshot

Toward an outline of the topography of a realistic protein-folding funnel.

inferredcites →https://doi.org/10.1073/pnas.94.12.6170openalex-snapshot

Folding funnels and energy landscapes of larger proteins within the capillarity approximation

inferredcites →https://doi.org/10.1073/pnas.95.9.4970openalex-snapshot

Dynamics of different functional parts of bacteriorhodopsin: H- 2 H labeling and neutron scattering

inferredcites →https://doi.org/10.1080/01621459.1958.10501452openalex-snapshot

Nonparametric Estimation from Incomplete Observations

inferredcites →https://doi.org/10.1093/nar/gkq498openalex-snapshot

SMOG@ctbp: simplified deployment of structure-based models in GROMACS

inferredcites →https://doi.org/10.1103/physreva.35.3072openalex-snapshot

Connections between some kinetic and equilibrium theories of the glass transition

inferredcites →https://doi.org/10.1103/physrevb.24.2613openalex-snapshot

Random-energy model: An exactly solvable model of disordered systems

inferredcites →https://doi.org/10.1103/physrevb.36.8552openalex-snapshot

Stable and metastable states in mean-field Potts and structural glasses

inferredcites →https://doi.org/10.1103/physrevlett.62.1916openalex-snapshot

Glassy behavior of a protein

inferredcites →https://doi.org/10.1103/physrevlett.76.4861openalex-snapshot

Statistics of Kinetic Pathways on Biased Rough Energy Landscapes with Applications to Protein Folding

inferredcites →https://doi.org/10.1103/physrevlett.90.188101openalex-snapshot

Energy Landscape Theory, Funnels, Specificity, and Optimal Criterion of Biomolecular Binding

inferredcites →https://doi.org/10.1103/physrevlett.99.198101openalex-snapshot

Quantifying Intrinsic Specificity: A Potential Complement to Affinity in Drug Screening

inferredcites →https://doi.org/10.1110/ps.4210102openalex-snapshot

Natively unfolded proteins: A point where biology waits for physics

inferredcites →https://doi.org/10.1110/ps.8.6.1181openalex-snapshot

Folding funnels, binding funnels, and protein function

inferredcites →https://doi.org/10.1110/ps.9.1.10openalex-snapshot

Folding and binding cascades: Dynamic landscapes and population shifts

inferredcites →https://doi.org/10.1126/science.1062559openalex-snapshot

Taking a Walk on a Landscape

inferredcites →https://doi.org/10.1126/science.1749933openalex-snapshot

The Energy Landscapes and Motions of Proteins

inferredcites →https://doi.org/10.1126/science.7886447openalex-snapshot

Navigating the Folding Routes

inferredcites →https://doi.org/10.1146/annurev.physchem.48.1.545openalex-snapshot

THEORY OF PROTEIN FOLDING: The Energy Landscape Perspective

inferredcites →https://doi.org/10.1152/physiologyonline.2001.16.4.171openalex-snapshot

Molecular Recognition by Induced Fit: How Fit is the Concept?

inferredcites →https://doi.org/10.1371/journal.pcbi.1001118openalex-snapshot

Multi-Scaled Explorations of Binding-Induced Folding of Intrinsically Disordered Protein Inhibitor IA3 to its Target Enzyme

inferredcites →https://doi.org/10.1371/journal.pcbi.1002608openalex-snapshot

Importance of Electrostatic Interactions in the Association of Intrinsically Disordered Histone Chaperone Chz1 and Histone H2A.Z-H2B

inferredcites →https://doi.org/10.1529/biophysj.106.094045openalex-snapshot

Intrinsic Disorder and Functional Proteomics

inferredcites →https://doi.org/10.1529/biophysj.107.105551openalex-snapshot

Optimal Specificity and Function for Flexible Biomolecular Recognition

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.2139/ssrn.3213915openalex-extracted

inferred← citeshttps://doi.org/10.1002/jcc.24004openalex-snapshot

Coupled folding and binding with 2D Window‐Exchange Umbrella Sampling

inferred← citeshttps://doi.org/10.1002/jmr.2413openalex-snapshot

Conformational frustration in calmodulin–target recognition

inferred← citeshttps://doi.org/10.1002/prot.24848openalex-snapshot

Optimizing the affinity and specificity of ligand binding with the inclusion of solvation effect

inferred← citeshttps://doi.org/10.1007/978-1-0716-1716-8_19openalex-snapshot

Molecular Simulations of Intrinsically Disordered Proteins and Their Binding Mechanisms

inferred← citeshttps://doi.org/10.1007/s10867-021-09586-5openalex-snapshot

Perspectives on the landscape and flux theory for describing emergent behaviors of the biological systems

inferred← citeshttps://doi.org/10.1016/j.bpj.2014.08.033openalex-snapshot

Protein-Protein Docking: From Interaction to Interactome

inferred← citeshttps://doi.org/10.1016/j.bpj.2016.05.041openalex-snapshot

Quantifying Nonnative Interactions in the Protein-Folding Free-Energy Landscape

inferred← citeshttps://doi.org/10.1016/j.bpj.2017.01.020openalex-snapshot

Opposing Intermolecular Tuning of Ca2+ Affinity for Calmodulin by Neurogranin and CaMKII Peptides

inferred← citeshttps://doi.org/10.1016/j.bpj.2022.11.2947openalex-snapshot

Learning continuous potentials from smFRET

inferred← citeshttps://doi.org/10.1016/j.isci.2022.104731openalex-snapshot

Inferring potential landscapes from noisy trajectories of particles within an optical feedback trap

inferred← citeshttps://doi.org/10.1016/j.nbd.2026.107536openalex-snapshot

Dual-tasking reveals severity-dependent reorganization of cortical beta energy landscapes in Parkinson's disease

inferred← citeshttps://doi.org/10.1016/j.physa.2017.10.021openalex-snapshot

Supersymmetric quantum mechanics method for the Fokker–Planck equation with applications to protein folding dynamics

inferred← citeshttps://doi.org/10.1016/j.sbi.2014.11.006openalex-snapshot

Molecular simulations of metal-coupled protein folding

inferred← citeshttps://doi.org/10.1016/j.str.2019.03.018openalex-snapshot

Coupling Molecular Dynamics and Deep Learning to Mine Protein Conformational Space

inferred← citeshttps://doi.org/10.1021/acs.biochem.4c00645openalex-snapshot

Dissecting the Roles of Electrostatic Interactions in Modulating the Folding Stability and Cooperativity of Engrailed Homeodomain

inferred← citeshttps://doi.org/10.1021/acs.chemrev.1c00044openalex-snapshot

Nonspecific Binding—Fundamental Concepts and Consequences for Biosensing Applications

inferred← citeshttps://doi.org/10.1021/acs.chemrev.5b00562openalex-snapshot

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

inferred← citeshttps://doi.org/10.1021/acs.jcim.0c01320openalex-snapshot

Shedding Light on the Inhibitory Mechanisms of SARS-CoV-1/CoV-2 Spike Proteins by ACE2-Designed Peptides

inferred← citeshttps://doi.org/10.1021/acs.jcim.4c00877openalex-snapshot

Unraveling the Interplay between Stability and Flexibility in the Design of Polyethylene Terephthalate (PET) Hydrolases

inferred← citeshttps://doi.org/10.1021/acs.jpcb.2c08877openalex-snapshot

Exploring the Folding Mechanism of Dimeric Superoxide Dismutase

inferred← citeshttps://doi.org/10.1021/acs.jpcb.7b06919openalex-snapshot

Consequences of Energetic Frustration on the Ligand-Coupled Folding/Dimerization Dynamics of Allosteric Protein S100A12

inferred← citeshttps://doi.org/10.1021/acs.jpcb.9b09640openalex-snapshot

Exploring Folding Aspects of Monomeric Superoxide Dismutase

inferred← citeshttps://doi.org/10.1021/acs.jpclett.5b00524openalex-snapshot

Neither Two-State nor Three-State: Dimerization of Lambda Cro Repressor

inferred← citeshttps://doi.org/10.1021/acscentsci.8b00274openalex-snapshot

Quantifying the Intrinsic Conformation Energy Landscape Topography of Proteins with Large-Scale Open–Closed Transition

inferred← citeshttps://doi.org/10.1021/acscentsci.9b00200openalex-snapshot

Explicit Characterization of the Free Energy Landscape of pKID–KIX Coupled Folding and Binding

inferred← citeshttps://doi.org/10.1021/acschembio.3c00649openalex-snapshot

Uncovering the Association Mechanism between Two Intrinsically Flexible Proteins

inferred← citeshttps://doi.org/10.1021/acsnano.6c06876openalex-snapshot

Nanowrinkled Interface-Coupled Metaphase Chromosome Spreading and Nanoscale Conformability

inferred← citeshttps://doi.org/10.1021/cr400514hopenalex-snapshot

Introducing Protein Intrinsic Disorder

inferred← citeshttps://doi.org/10.1021/jacsau.1c00368openalex-snapshot

Investigating the Conformational Dynamics of a Y-Family DNA Polymerase during Its Folding and Binding to DNA and a Nucleotide

inferred← citeshttps://doi.org/10.1039/c3cp54253jopenalex-snapshot

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

inferred← citeshttps://doi.org/10.1039/c4cp01454eopenalex-snapshot

Manipulating and probing enzymatic conformational fluctuations and enzyme–substrate interactions by single-molecule FRET-magnetic tweezers microscopy

inferred← citeshttps://doi.org/10.1039/c5cp06416copenalex-snapshot

Universal statistical fluctuations in thermodynamics and kinetics of single molecular recognition

inferred← citeshttps://doi.org/10.1039/c6cp02272copenalex-snapshot

Molecular dynamics simulations and CD spectroscopy reveal hydration-induced unfolding of the intrinsically disordered LEA proteins COR15A and COR15B from Arabidopsis thaliana

inferred← citeshttps://doi.org/10.1039/c7mb00103gopenalex-snapshot

Effects of flexibility and electrostatic interactions on the coupled binding–folding mechanisms of Chz.core and H2A.z–H2B

inferred← citeshttps://doi.org/10.1039/c7ra04133kopenalex-snapshot

Conformation dynamics of the intrinsically disordered protein c-Myb with the ff99IDPs force field

inferred← citeshttps://doi.org/10.1039/c8cp06803hopenalex-snapshot

Position-, disorder-, and salt-dependent diffusion in binding-coupled-folding of intrinsically disordered proteins

inferred← citeshttps://doi.org/10.1063/1.4995362openalex-snapshot

Manipulating motions of targeted single cells in solution by an integrated double-ring magnetic tweezers imaging microscope

inferred← citeshttps://doi.org/10.1063/5.0007316openalex-snapshot

Conformational state switching and pathways of chromosome dynamics in cell cycle

inferred← citeshttps://doi.org/10.1063/5.0220861openalex-snapshot

Balancing thermodynamic stability, dynamics, and kinetics in phase separation of intrinsically disordered proteins

inferred← citeshttps://doi.org/10.1063/5.0295393openalex-snapshot

Contact networks encode the ATP-induced dynamic structural asymmetry of condensin head domains

inferred← citeshttps://doi.org/10.1063/5.0322746openalex-snapshot

Quantifying the free energy landscapes of biomolecular condensation reveals the underlying physical mechanisms of phase separation

inferred← citeshttps://doi.org/10.1073/pnas.1312788110openalex-snapshot

Protein recognition and selection through conformational and mutually induced fit

inferred← citeshttps://doi.org/10.1073/pnas.1506405112openalex-snapshot

Interrogating the activities of conformational deformed enzyme by single-molecule fluorescence-magnetic tweezers microscopy

inferred← citeshttps://doi.org/10.1073/pnas.1615949114openalex-snapshot

Molecular mechanism of multispecific recognition of Calmodulin through conformational changes

inferred← citeshttps://doi.org/10.1073/pnas.1915333117openalex-snapshot

Investigations of the underlying mechanisms of HIF-1α and CITED2 binding to TAZ1

inferred← citeshttps://doi.org/10.1080/07391102.2018.1472669openalex-snapshot

Composition-related structural transition of random peptides: insight into the boundary between intrinsically disordered proteins and folded proteins

inferred← citeshttps://doi.org/10.1080/21690707.2016.1248273openalex-snapshot

Understanding the roles of intrinsic disorder in subunits of hemoglobin and the disease process of sickle cell anemia

inferred← citeshttps://doi.org/10.1088/1361-6633/ac3800openalex-snapshot

Physics of biomolecular recognition and conformational dynamics

inferred← citeshttps://doi.org/10.1093/bioinformatics/bty355openalex-snapshot

Efficient flexible backbone protein–protein docking for challenging targets

inferred← citeshttps://doi.org/10.1093/nar/gkx255openalex-snapshot

SPA-LN: a scoring function of ligand–nucleic acid interactions via optimizing both specificity and affinity

inferred← citeshttps://doi.org/10.1101/2024.01.05.574441openalex-snapshot

Balancing stability, dynamics and kinetics in phase separation of intrinsically disordered proteins

inferred← citeshttps://doi.org/10.1371/journal.pcbi.1003239openalex-snapshot

Polycation-π Interactions Are a Driving Force for Molecular Recognition by an Intrinsically Disordered Oncoprotein Family

inferred← citeshttps://doi.org/10.1371/journal.pcbi.1003562openalex-snapshot

Atomistic Picture for the Folding Pathway of a Hybrid-1 Type Human Telomeric DNA G-quadruplex

inferred← citeshttps://doi.org/10.1371/journal.pcbi.1003691openalex-snapshot

PolyUbiquitin Chain Linkage Topology Selects the Functions from the Underlying Binding Landscape

inferred← citeshttps://doi.org/10.1371/journal.pcbi.1003782openalex-snapshot

Specificity and Affinity Quantification of Flexible Recognition from Underlying Energy Landscape Topography

inferred← citeshttps://doi.org/10.1371/journal.pcbi.1006768openalex-snapshot

Structure, stability and specificity of the binding of ssDNA and ssRNA with proteins

inferred← citeshttps://doi.org/10.1371/journal.pone.0178405openalex-snapshot

Electrostatic forces govern the binding mechanism of intrinsically disordered histone chaperones

inferred← citeshttps://doi.org/10.17760/d20317952openalex-snapshot

Preparation of nanoparticles by green synthesis and a study on their antibacterial and anticancer properties

inferred← citeshttps://doi.org/10.3389/fimmu.2025.1657633openalex-snapshot

Application of the Richards function to serum antibody titration

inferred← citeshttps://doi.org/10.4161/idp.27454openalex-snapshot

Digested disorder

inferred← citeshttps://doi.org/10.7498/aps.72.20231060openalex-snapshot

Exploring proten’s conformational space by using encoding layer supervised auto-encoder

inferred← citeshttps://doi.org/10.7554/elife.60434openalex-snapshot

Investigating the trade-off between folding and function in a multidomain Y-family DNA polymerase

Editorial review for independent work. ICSAC — the Institute for Complexity Science and Advanced Computing — runs a structured editorial panel for researchers publishing outside journals, and publishes on CiteStamp rails. Submission is free and goes through ORCID: icsacinstitute.org/submit.