Topology‐based modeling of intrinsically disordered proteins: Balancing intrinsic folding and intermolecular interactions (Q53079816)

11 May 2018

reason for preferred rank

title

Topology‐based modeling of intrinsically disordered proteins: Balancing intrinsic folding and intermolecular interactions (English)

1 reference

22 November 2024

Topology-based modeling of intrinsically disordered proteins: balancing intrinsic folding and intermolecular interactions (English)

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?resulttype=core&format=json&query=SRC%3AMED%20AND%20EXT_ID%3A21268115

molecular dynamics simulation

22 November 2024

main subject

protein folding

0 references

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?resulttype=core&format=json&query=SRC%3AMED%20AND%20EXT_ID%3A21268115

22 November 2024

Debabani Ganguly

1 reference

11 May 2018

Jianhan Chen

series ordinal

1 reference

11 May 2018

language of work or name

English

0 references

publication date

25 January 2011

1 reference

11 May 2018

full work available at URL

https://api.wiley.com/onlinelibrary/tdm/v1/articles/10.1002%2Fprot.22960

1 reference

https://onlinelibrary.wiley.com/doi/pdf/10.1002/prot.22960

22 November 2024

1 reference

22 November 2024

1 reference

11 May 2018

volume

1 reference

11 May 2018

issue

1 reference

11 May 2018

page(s)

1251-1266

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11 May 2018

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

cites work

1 reference

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Intrinsically unstructured proteins and their functions

21 January 2018

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Function and structure of inherently disordered proteins

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Intrinsic disorder and functional proteomics

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

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Regulation of cell division by intrinsically unstructured proteins: intrinsic flexibility, modularity, and signaling conduits

21 January 2018

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Intrinsic disorder in cell-signaling and cancer-associated proteins

21 January 2018

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Intrinsically Disordered Proteins in Human Diseases: Introducing the D 2 Concept

21 January 2018

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Flexible nets. The roles of intrinsic disorder in protein interaction networks.

21 January 2018

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Intrinsic disorder as a mechanism to optimize allosteric coupling in proteins

21 January 2018

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Linking folding and binding

21 January 2018

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Dynamic equilibrium engagement of a polyvalent ligand with a single-site receptor

21 January 2018

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Structure/function implications in a dynamic complex of the intrinsically disordered Sic1 with the Cdc4 subunit of an SCF ubiquitin ligase

21 January 2018

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Principles of protein-protein interactions: what are the preferred ways for proteins to interact?

21 January 2018

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Atomistic details of the disordered states of KID and pKID. Implications in coupled binding and folding

21 January 2018

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Intrinsically disordered p53 extreme C-terminus binds to S100B(betabeta) through "fly-casting".

21 January 2018

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Assessing protein disorder and induced folding

21 January 2018

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Preformed structural elements feature in partner recognition by intrinsically unstructured proteins

21 January 2018

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Roles of phosphorylation and helix propensity in the binding of the KIX domain of CREB-binding protein by constitutive (c-Myb) and inducible (CREB) activators

21 January 2018

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Functional consequences of preorganized helical structure in the intrinsically disordered cell-cycle inhibitor p27(Kip1).

21 January 2018

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The role of dynamic conformational ensembles in biomolecular recognition

21 January 2018

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Theoretical Studies of Protein Folding

21 January 2018

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Exploring the origins of topological frustration: design of a minimally frustrated model of fragment B of protein A.

21 January 2018

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How native-state topology affects the folding of dihydrofolate reductase and interleukin-1beta

21 January 2018

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Protein folding theory: from lattice to all-atom models

21 January 2018

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

21 January 2018

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Insights from coarse-grained Gō models for protein folding and dynamics

21 January 2018

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Folding funnels, binding funnels, and protein function

21 January 2018

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Folding and binding cascades: shifts in energy landscapes

21 January 2018

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Protein topology determines binding mechanism

21 January 2018

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A survey of flexible protein binding mechanisms and their transition states using native topology based energy landscapes

21 January 2018

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Mechanisms of protein assembly: lessons from minimalist models

21 January 2018

1 reference

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

21 January 2018

1 reference

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Simulations of beta-hairpin folding confined to spherical pores using distributed computing

21 January 2018

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Molecular crowding enhances native state stability and refolding rates of globular proteins

21 January 2018

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The origins of asymmetry in the folding transition states of protein L and protein G.

21 January 2018

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Residue-residue potentials with a favorable contact pair term and an unfavorable high packing density term, for simulation and threading.

21 January 2018

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The structural basis for biphasic kinetics in the folding of the WW domain from a formin-binding protein: lessons for protein design?

21 January 2018

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Integrating folding kinetics and protein function: biphasic kinetics and dual binding specificity in a WW domain

21 January 2018

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Subdomain competition, cooperativity, and topological frustration in the folding of CheY.

21 January 2018

1 reference

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Binding-induced folding of a natively unstructured transcription factor.

21 January 2018

1 reference

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Flexible nets: disorder and induced fit in the associations of p53 and 14-3-3 with their partners

21 January 2018

1 reference

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Intrinsically disordered protein

21 January 2018

1 reference

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Solution Structure of the KIX Domain of CBP Bound to the Transactivation Domain of CREB: A Model for Activator:Coactivator Interactions

21 January 2018

1 reference

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Structure of the negative regulatory domain of p53 bound to S100B(betabeta)

21 January 2018

1 reference

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Analysis of an activator:coactivator complex reveals an essential role for secondary structure in transcriptional activation

21 January 2018

1 reference

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Conformational preferences in the Ser133-phosphorylated and non-phosphorylated forms of the kinase inducible transactivation domain of CREB

21 January 2018

1 reference

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Mechanism of coupled folding and binding of an intrinsically disordered protein

21 January 2018

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Coarse-grained models of protein folding: toy models or predictive tools?

21 January 2018

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Replica-exchange molecular dynamics method for protein folding

21 January 2018

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MMTSB Tool Set: enhanced sampling and multiscale modeling methods for applications in structural biology.

21 January 2018

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CHARMM: A program for macromolecular energy, minimization, and dynamics calculations

21 January 2018

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CHARMM: the biomolecular simulation program

21 January 2018

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Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes

21 January 2018

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From transition paths to transition states and rate coefficients

21 January 2018

1 reference

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Reaction coordinates and rates from transition paths

21 January 2018

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P versus Q: structural reaction coordinates capture protein folding on smooth landscapes

21 January 2018

1 reference

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Quantitative criteria for native energetic heterogeneity influences in the prediction of protein folding kinetics

21 January 2018

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Kinetics of folding and binding of an intrinsically disordered protein: the inhibitor of yeast aspartic proteinase YPrA.

21 January 2018

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

21 January 2018

1 reference

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Capillarity theory for the fly-casting mechanism

21 January 2018

1 reference

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Complex network analysis of free-energy landscapes

21 January 2018

1 reference

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Hidden complexity of free energy surfaces for peptide (protein) folding

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.22960

Isotope labeling methods for studies of excited protein states by relaxation dispersion NMR spectroscopy

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.22960

Defining the role of active-site loop fluctuations in dihydrofolate reductase catalysis

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.22960

Kinetic advantage of intrinsically disordered proteins in coupled folding-binding process: a critical assessment of the "fly-casting" mechanism

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.22960

Simulating disorder-order transitions in molecular recognition of unstructured proteins: where folding meets binding

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.22960

Disordered p27Kip1 exhibits intrinsic structure resembling the Cdk2/cyclin A-bound conformation

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.22960

Intrinsically disordered -subunit of cGMP phosphodiesterase encodes functionally relevant transient secondary and tertiary structure

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.22960

From induced fit to conformational selection: a continuum of binding mechanism controlled by the timescale of conformational transitions

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.22960

Conformational selection or induced fit: a flux description of reaction mechanism

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.22960

Protein folding thermodynamics and dynamics: where physics, chemistry, and biology meet

21 January 2018

1 reference

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An all-atom structure-based potential for proteins: bridging minimal models with all-atom empirical forcefields

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.22960

Fly-casting in protein-DNA binding: frustration between protein folding and electrostatics facilitates target recognition

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.22960

Molecular Principles of the Interactions of Disordered Proteins

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.22960

Exploring the mechanism of flexible biomolecular recognition with single molecule dynamics

21 January 2018

1 reference

The Ca(2+)-dependent interaction of S100B(beta beta) with a peptide derived from p53

22 November 2024

1 reference

The protein folding network

22 November 2024

1 reference

Mechanism of induced folding: Both folding before binding and binding before folding can be realized in staphylococcal nuclease mutants

22 November 2024

1 reference

Nonnative electrostatic interactions can modulate protein folding: molecular dynamics with a grain of salt

22 November 2024

1 reference

22 November 2024

Identifiers

DOI

10.1002/PROT.22960

1 reference

11 May 2018

1 reference

11 May 2018