Network representation of conformational transitions between hidden intermediates of Rd-apocytochrome b562 (Q36117892)

12 August 2017

Network representation of conformational transitions between hidden intermediates of Rd-apocytochrome b562 (English)

1 reference

12 August 2017

Mojie Duan

1

1 reference

12 August 2017

Hanzhong Liu

series ordinal

2

1 reference

12 August 2017

Minghai Li

series ordinal

3

1 reference

12 August 2017

Shuanghong Huo

series ordinal

4

1 reference

12 August 2017

language of work or name

English

0 references

publication date

1 October 2015

1 reference

Journal of Chemical Physics

12 August 2017

1 reference

12 August 2017

143

1 reference

12 August 2017

13

1 reference

12 August 2017

135101

1 reference

On the Application of Molecular-Dynamics Based Markov State Models to Functional Proteins

12 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4592431

General mechanism of two-state protein folding kinetics

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4592431

Cloud-based simulations on Google Exacycle reveal ligand modulation of GPCR activation pathways

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4592431

Native contacts determine protein folding mechanisms in atomistic simulations

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4592431

Discrete kinetic models from funneled energy landscape simulations

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4592431

De novo prediction of protein folding pathways and structure using the principle of sequential stabilization

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4592431

Evaluation and optimization of discrete state models of protein folding

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4592431

Simple few-state models reveal hidden complexity in protein folding

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4592431

Transiently populated intermediate functions as a branching point of the FF domain folding pathway

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4592431

MSMBuilder2: Modeling Conformational Dynamics on the Picosecond to Millisecond Scale

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4592431

Observation of Two Families of Folding Pathways of BBL

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4592431

A Transient and Low-Populated Protein-Folding Intermediate at Atomic Resolution

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4592431

The folding transition-state ensemble of a four-helix bundle protein: helix propensity as a determinant and macromolecular crowding as a probe.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4592431

Improved side-chain torsion potentials for the Amber ff99SB protein force field

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4592431

Molecular simulation of ab initio protein folding for a millisecond folder NTL9(1-39)

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4592431

Constructing the equilibrium ensemble of folding pathways from short off-equilibrium simulations.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4592431

Using generalized ensemble simulations and Markov state models to identify conformational states

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4592431

Amyloid formation by globular proteins under native conditions

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4592431

Transition-path theory and path-finding algorithms for the study of rare events

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4592431

Protein folding and misfolding: mechanism and principles.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4592431

Probing invisible, low-populated States of protein molecules by relaxation dispersion NMR spectroscopy: an application to protein folding

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4592431

Probing the folding intermediate of Rd-apocyt b562 by protein engineering and infrared T-jump

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4592431

Exploring subdomain cooperativity in T4 lysozyme I: Structural and energetic studies of a circular permutant and protein fragment

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4592431

Exploring subdomain cooperativity in T4 lysozyme II: uncovering the C-terminal subdomain as a hidden intermediate in the kinetic folding pathway

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4592431

The folding pathway of T4 lysozyme: the high-resolution structure and folding of a hidden intermediate

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4592431

The folding pathway of T4 lysozyme: an on-pathway hidden folding intermediate

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4592431

Routes are trees: the parsing perspective on protein folding.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4592431

A protein folding pathway with multiple folding intermediates at atomic resolution

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4592431

Gaussian split Ewald: A fast Ewald mesh method for molecular simulation

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4592431

UCSF Chimera--a visualization system for exploratory research and analysis

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4592431

Specific non-native hydrophobic interactions in a hidden folding intermediate: implications for protein folding

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4592431

Hidden intermediates and levinthal paradox in the folding of small proteins

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4592431

Fast-folding protein kinetics, hidden intermediates, and the sequential stabilization model

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4592431

An amino acid code for protein folding

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4592431

From Levinthal to pathways to funnels

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4592431

Knowledge-based protein secondary structure assignment

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4592431

VMD: visual molecular dynamics

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4592431

Navigating the folding routes

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4592431

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

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4592431

The Sequential Unfolding of Ribonuclease A: Detection of a Fast Initial Phase in the Kinetics of Unfolding

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4592431

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

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4592431

NMR analysis of the conformational properties of the trapped on-pathway folding intermediate of the bacterial immunity protein Im7.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4592431

Populating partially unfolded forms by hydrogen exchange-directed protein engineering

2 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4592431

Relationship between the native-state hydrogen exchange and folding pathways of a four-helix bundle protein

2 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4592431

Protein folding intermediates: native-state hydrogen exchange

2 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4592431

Kinetic Evidence for Incorrectly Folded Intermediate States in the Refolding of Denatured Proteins

2 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4592431

Accurate and efficient integration for molecular dynamics simulations at constant temperature and pressure

2 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4592431

Markov models of molecular kinetics: Generation and validation

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4592431

Coarse master equations for peptide folding dynamics

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4592431

Unveiling a hidden folding intermediate in c-type cytochromes by protein engineering

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4592431

Solution structure of a protein denatured state and folding intermediate

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4592431

An on-pathway hidden intermediate and the early rate-limiting transition state of Rd-apocytochrome b562 characterized by protein engineering

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4592431

Detection of a hidden folding intermediate of the third domain of PDZ.

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4592431

Detection and structure determination of an equilibrium unfolding intermediate of Rd-apocytochrome b562: native fold with non-native hydrophobic interactions

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4592431

Explicit-chain model of native-state hydrogen exchange: implications for event ordering and cooperativity in protein folding

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4592431

Elucidating the folding problem of helical peptides using empirical parameters

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4592431

Comparison of simple potential functions for simulating liquid water

23 September 2018

1 reference

Crossref

https://api.crossref.org/works/10.1063/1.4931921

Molecular dynamics with coupling to an external bath

21 January 2018

1 reference

Crossref

https://api.crossref.org/works/10.1063/1.4931921

Two-state allosteric behavior in a single-domain signaling protein

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/26450332

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1063/1.4931921

1 reference

12 August 2017

1 reference

12 August 2017

PubMed publication ID

26450332

1 reference