Finding the needle in the haystack: towards solving the protein-folding problem computationally. (Q47567885)

PubMed publication ID

28976219

4 February 2018

http://europepmc.org/abstract/MED/28976219

title

Finding the needle in the haystack: towards solving the protein-folding problem computationally (English)

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=PMCID:PMC6790072&resulttype=core&format=json

12 May 2020

main subject

protein folding

0 references

computational biology

1 reference

4

Jens Meiler

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=PMCID:PMC6790072&resulttype=core&format=json

12 May 2020

author name string

Bian Li

series ordinal

1

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=PMCID:PMC6790072&resulttype=core&format=json

12 May 2020

Michaela Fooksa

series ordinal

2

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=PMCID:PMC6790072&resulttype=core&format=json

12 May 2020

Sten Heinze

series ordinal

3

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=PMCID:PMC6790072&resulttype=core&format=json

12 May 2020

publication date

4 October 2017

1 reference

PubMed publication ID

28976219

4 February 2018

http://europepmc.org/abstract/MED/28976219

published in

Critical Reviews in Biochemistry and Molecular Biology

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=PMCID:PMC6790072&resulttype=core&format=json

12 May 2020

volume

53

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=PMCID:PMC6790072&resulttype=core&format=json

12 May 2020

issue

1

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=PMCID:PMC6790072&resulttype=core&format=json

12 May 2020

page(s)

1-28

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=PMCID:PMC6790072&resulttype=core&format=json

describes a project that uses

12 May 2020

Bayes' theorem

1 reference

18 June 2022

https://europepmc.org/article/PMC/6790072

inferred from PubMed Central ID database lookup

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21 January 2018

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Progress in predicting inter-residue contacts of proteins with neural networks and correlated mutations.

21 January 2018

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Nucleation mechanisms in protein folding

21 January 2018

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BCL::MP-fold: Membrane protein structure prediction guided by EPR restraints

21 January 2018

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CASP11--An Evaluation of a Modular BCL::Fold-Based Protein Structure Prediction Pipeline.

21 January 2018

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21 January 2018

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The Energy Landscapes and Motions of Proteins

21 January 2018

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Side-chain torsional potentials: effect of dipeptide, protein, and solvent environment

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21 January 2018

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21 January 2018

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Multiple contact network is a key determinant to protein folding rates

21 January 2018

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21 January 2018

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21 January 2018

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21 January 2018

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21 January 2018

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An iterative knowledge-based scoring function to predict protein-ligand interactions: I. Derivation of interaction potentials.

21 January 2018

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21 January 2018

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21 January 2018

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pH replica‐exchange method based on discrete protonation states

21 January 2018

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https://api.crossref.org/works/10.1080/10409238.2017.1380596

Prediction of protein folding rates from the amino acid sequence-predicted secondary structure.

21 January 2018

1 reference

https://api.crossref.org/works/10.1080/10409238.2017.1380596

Structure and dynamics of dark-state bovine rhodopsin revealed by chemical cross-linking and high-resolution mass spectrometry.

21 January 2018

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https://api.crossref.org/works/10.1080/10409238.2017.1380596

Assessment of CASP7 structure predictions for template free targets

21 January 2018

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https://api.crossref.org/works/10.1080/10409238.2017.1380596

Bridging the information gap: computational tools for intermediate resolution structure interpretation

21 January 2018

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https://api.crossref.org/works/10.1080/10409238.2017.1380596

Progress in protein structure prediction

21 January 2018

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https://api.crossref.org/works/10.1080/10409238.2017.1380596

Protein secondary structure prediction based on position-specific scoring matrices

21 January 2018

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https://api.crossref.org/works/10.1080/10409238.2017.1380596

Predicting novel protein folds by using FRAGFOLD.

21 January 2018

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https://api.crossref.org/works/10.1080/10409238.2017.1380596

PSICOV: precise structural contact prediction using sparse inverse covariance estimation on large multiple sequence alignments

21 January 2018

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MetaPSICOV: combining coevolution methods for accurate prediction of contacts and long range hydrogen bonding in proteins.

21 January 2018

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21 January 2018

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Assessing the utility of coevolution-based residue-residue contact predictions in a sequence- and structure-rich era.

21 January 2018

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BCL::Fold--de novo prediction of complex and large protein topologies by assembly of secondary structure elements

21 January 2018

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Behind the folding funnel diagram

21 January 2018

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Molecular dynamics and protein function

21 January 2018

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Molecular dynamics simulations of biomolecules

21 January 2018

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Molecular dynamics simulations in biology

21 January 2018

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Protein folding dynamics: the diffusion-collision model and experimental data

21 January 2018

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Sampling bottlenecks in de novo protein structure prediction

21 January 2018

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One contact for every twelve residues allows robust and accurate topology-level protein structure modeling

21 January 2018

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Specific intermediates in the folding reactions of small proteins and the mechanism of protein folding

21 January 2018

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Intermediates in the folding reactions of small proteins

21 January 2018

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Statistical torsion angle potential energy functions for protein structure modeling: a bicubic interpolation approach

21 January 2018

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CASP9 assessment of free modeling target predictions

21 January 2018

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Evaluation of free modeling targets in CASP11 and ROLL.

21 January 2018

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Optimization by Simulated Annealing

21 January 2018

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21 January 2018

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Long-timescale molecular dynamics simulations of protein structure and function.

21 January 2018

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Coarse-Grained Protein Models and Their Applications

21 January 2018

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Factors influencing the ability of knowledge-based potentials to identify native sequence-structure matches

21 January 2018

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A structural-informatics approach for mining beta-sheets: locating sheets in intermediate-resolution density maps

21 January 2018

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A Structural-informatics approach for tracing beta-sheets: building pseudo-C(alpha) traces for beta-strands in intermediate-resolution density maps

21 January 2018

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An orientation-dependent hydrogen bonding potential improves prediction of specificity and structure for proteins and protein-protein complexes

21 January 2018

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https://api.crossref.org/works/10.1080/10409238.2017.1380596

De novo structure prediction of globular proteins aided by sequence variation-derived contacts

21 January 2018

1 reference

https://api.crossref.org/works/10.1080/10409238.2017.1380596

Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes

21 January 2018

1 reference

https://api.crossref.org/works/10.1080/10409238.2017.1380596

Improving the quality of NMR and crystallographic protein structures by means of a conformational database potential derived from structure databases

21 January 2018

1 reference

https://api.crossref.org/works/10.1080/10409238.2017.1380596

Escaping free-energy minima

21 January 2018

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https://api.crossref.org/works/10.1080/10409238.2017.1380596

Markov state model reveals folding and functional dynamics in ultra-long MD trajectories

21 January 2018

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https://api.crossref.org/works/10.1080/10409238.2017.1380596

To milliseconds and beyond: challenges in the simulation of protein folding

21 January 2018

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https://api.crossref.org/works/10.1080/10409238.2017.1380596

Molecular architecture of the 26S proteasome holocomplex determined by an integrative approach

21 January 2018

1 reference

https://api.crossref.org/works/10.1080/10409238.2017.1380596

Protein structure prediction: combining de novo modeling with sparse experimental data.

21 January 2018

1 reference

https://api.crossref.org/works/10.1080/10409238.2017.1380596

Effective energy function for proteins in solution

21 January 2018

1 reference

https://api.crossref.org/works/10.1080/10409238.2017.1380596

Effective energy functions for protein structure prediction.

21 January 2018

1 reference

https://api.crossref.org/works/10.1080/10409238.2017.1380596

Thermodynamics of protein folding: a microscopic view

21 January 2018

1 reference

https://api.crossref.org/works/10.1080/10409238.2017.1380596

Simultaneous prediction of protein secondary structure and transmembrane spans

21 January 2018

1 reference

https://api.crossref.org/works/10.1080/10409238.2017.1380596

Molecular insights into the D1R agonist and D2R/D3R antagonist effects of the natural product (-)-stepholidine: molecular modeling and dynamics simulations

21 January 2018

1 reference

https://api.crossref.org/works/10.1080/10409238.2017.1380596

Accurate Prediction of Contact Numbers for Multi-Spanning Helical Membrane Proteins.

21 January 2018

1 reference

https://api.crossref.org/works/10.1080/10409238.2017.1380596

Improving prediction of helix-helix packing in membrane proteins using predicted contact numbers as restraints

21 January 2018

1 reference

https://api.crossref.org/works/10.1080/10409238.2017.1380596

Predicting residue–residue contacts using random forest models

21 January 2018

1 reference

https://api.crossref.org/works/10.1080/10409238.2017.1380596

Consistent Force Field for Calculations of Conformations, Vibrational Spectra, and Enthalpies of Cycloalkane and n‐Alkane Molecules

21 January 2018

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Membrane proteins: molecular dynamics simulations.

21 January 2018

1 reference

https://api.crossref.org/works/10.1080/10409238.2017.1380596

EM-fold: de novo atomic-detail protein structure determination from medium-resolution density maps

21 January 2018

1 reference

https://api.crossref.org/works/10.1080/10409238.2017.1380596

Ab initio protein modeling into CryoEM density maps using EM-Fold

21 January 2018

1 reference

https://api.crossref.org/works/10.1080/10409238.2017.1380596

EM-fold: De novo folding of alpha-helical proteins guided by intermediate-resolution electron microscopy density maps.

21 January 2018

1 reference

https://api.crossref.org/works/10.1080/10409238.2017.1380596

Hybrid approaches: applying computational methods in cryo-electron microscopy

21 January 2018

1 reference

https://api.crossref.org/works/10.1080/10409238.2017.1380596

Systematic validation of protein force fields against experimental data

21 January 2018

1 reference

https://api.crossref.org/works/10.1080/10409238.2017.1380596

How fast-folding proteins fold

21 January 2018

1 reference

https://api.crossref.org/works/10.1080/10409238.2017.1380596

Prediction of protein beta-residue contacts by Markov logic networks with grounding-specific weights.

21 January 2018

1 reference

https://api.crossref.org/works/10.1080/10409238.2017.1380596

Current status of protein force fields for molecular dynamics simulations

21 January 2018

1 reference

https://api.crossref.org/works/10.1080/10409238.2017.1380596

A distance-dependent atomic knowledge-based potential for improved protein structure selection.

21 January 2018

1 reference

https://api.crossref.org/works/10.1080/10409238.2017.1380596

Protein threading using context-specific alignment potential

21 January 2018

1 reference

https://api.crossref.org/works/10.1080/10409238.2017.1380596

All-atom empirical potential for molecular modeling and dynamics studies of proteins

21 January 2018

1 reference

https://api.crossref.org/works/10.1080/10409238.2017.1380596

Empirical force fields for biological macromolecules: overview and issues.

21 January 2018

1 reference

https://api.crossref.org/works/10.1080/10409238.2017.1380596

Extending the treatment of backbone energetics in protein force fields: limitations of gas-phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations

21 January 2018

1 reference

https://api.crossref.org/works/10.1080/10409238.2017.1380596

A coarse-grained potential for fold recognition and molecular dynamics simulations of proteins

21 January 2018

1 reference

https://api.crossref.org/works/10.1080/10409238.2017.1380596

Protein 3D structure computed from evolutionary sequence variation

21 January 2018

1 reference

https://api.crossref.org/works/10.1080/10409238.2017.1380596

Protein structure prediction from sequence variation

21 January 2018

1 reference

https://api.crossref.org/works/10.1080/10409238.2017.1380596

The MARTINI force field: coarse grained model for biomolecular simulations

21 January 2018

1 reference

https://api.crossref.org/works/10.1080/10409238.2017.1380596

Perspective on the Martini model.

21 January 2018

1 reference

https://api.crossref.org/works/10.1080/10409238.2017.1380596

Principles and Overview of Sampling Methods for Modeling Macromolecular Structure and Dynamics

21 January 2018

1 reference

https://api.crossref.org/works/10.1080/10409238.2017.1380596

Dynamics of folded proteins

21 January 2018

1 reference

https://api.crossref.org/works/10.1080/10409238.2017.1380596

Equation of State Calculations by Fast Computing Machines

21 January 2018

1 reference

https://api.crossref.org/works/10.1080/10409238.2017.1380596

PconsFold: improved contact predictions improve protein models

21 January 2018

1 reference

https://api.crossref.org/works/10.1080/10409238.2017.1380596

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1080/10409238.2017.1380596

New encouraging developments in contact prediction: Assessment of the CASP11 results

21 January 2018

1 reference

https://api.crossref.org/works/10.1080/10409238.2017.1380596

The MARTINI Coarse-Grained Force Field: Extension to Proteins.

21 January 2018

1 reference

https://api.crossref.org/works/10.1080/10409238.2017.1380596

Direct-coupling analysis of residue coevolution captures native contacts across many protein families

21 January 2018

1 reference

https://api.crossref.org/works/10.1080/10409238.2017.1380596

Molecular dynamics simulations of biological membranes and membrane proteins using enhanced conformational sampling algorithms

21 January 2018

1 reference

https://api.crossref.org/works/10.1080/10409238.2017.1380596

Comparison of database potentials and molecular mechanics force fields

21 January 2018

1 reference

https://api.crossref.org/works/10.1080/10409238.2017.1380596

A decade of CASP: progress, bottlenecks and prognosis in protein structure prediction.

21 January 2018

1 reference

https://api.crossref.org/works/10.1080/10409238.2017.1380596

Critical assessment of methods of protein structure prediction: Progress and new directions in round XI.

21 January 2018

1 reference

https://api.crossref.org/works/10.1080/10409238.2017.1380596

A large-scale experiment to assess protein structure prediction methods.

21 January 2018

1 reference

https://api.crossref.org/works/10.1080/10409238.2017.1380596

How frequent are correlated changes in families of protein sequences?

21 January 2018

1 reference

https://api.crossref.org/works/10.1080/10409238.2017.1380596

Folding simulations for proteins with diverse topologies are accessible in days with a physics-based force field and implicit solvent

21 January 2018

1 reference

https://api.crossref.org/works/10.1080/10409238.2017.1380596

Transmembrane protein topology prediction using support vector machines

21 January 2018

1 reference

https://api.crossref.org/works/10.1080/10409238.2017.1380596

Generalized-ensemble algorithms: enhanced sampling techniques for Monte Carlo and molecular dynamics simulations

21 January 2018

1 reference

https://api.crossref.org/works/10.1080/10409238.2017.1380596

Theory of protein folding: the energy landscape perspective

21 January 2018

1 reference

https://api.crossref.org/works/10.1080/10409238.2017.1380596

Theory of protein folding

21 January 2018

1 reference

https://api.crossref.org/works/10.1080/10409238.2017.1380596

Predicting protein folding rates from geometric contact and amino acid sequence

21 January 2018

1 reference

https://api.crossref.org/works/10.1080/10409238.2017.1380596

Robust and accurate prediction of residue-residue interactions across protein interfaces using evolutionary information.

21 January 2018

1 reference

https://api.crossref.org/works/10.1080/10409238.2017.1380596

Protein structure determination using metagenome sequence data

21 January 2018

1 reference

https://api.crossref.org/works/10.1080/10409238.2017.1380596

Transition state contact orders correlate with protein folding rates

21 January 2018

1 reference

https://api.crossref.org/works/10.1080/10409238.2017.1380596

Atomistic protein folding simulations on the submillisecond time scale using worldwide distributed computing

21 January 2018

1 reference

https://api.crossref.org/works/10.1080/10409238.2017.1380596

Everything you wanted to know about Markov State Models but were afraid to ask

21 January 2018

1 reference

https://api.crossref.org/works/10.1080/10409238.2017.1380596

Energy functions that discriminate X-ray and near native folds from well-constructed decoys

21 January 2018

1 reference

https://api.crossref.org/works/10.1080/10409238.2017.1380596

Three force fields' views of the 3(10) helix.

21 January 2018

1 reference

https://api.crossref.org/works/10.1080/10409238.2017.1380596

Genetic algorithms for protein structure prediction

21 January 2018

1 reference

https://api.crossref.org/works/10.1080/10409238.2017.1380596

Interplay of G Protein-Coupled Receptors with the Membrane: Insights from Supra-Atomic Coarse Grain Molecular Dynamics Simulations.

21 January 2018

1 reference

https://api.crossref.org/works/10.1080/10409238.2017.1380596

Assessing the accuracy of physical models used in protein-folding simulations: quantitative evidence from long molecular dynamics simulations

21 January 2018

1 reference

https://api.crossref.org/works/10.1080/10409238.2017.1380596

A bias-exchange approach to protein folding

21 January 2018

1 reference

https://api.crossref.org/works/10.1080/10409238.2017.1380596

Protein folding kinetics and thermodynamics from atomistic simulation

21 January 2018

1 reference

https://api.crossref.org/works/10.1080/10409238.2017.1380596

Atomic-level description of ubiquitin folding

21 January 2018

1 reference

https://api.crossref.org/works/10.1080/10409238.2017.1380596

Recent improvements in prediction of protein structure by global optimization of a potential energy function.

21 January 2018

1 reference

https://api.crossref.org/works/10.1080/10409238.2017.1380596

Quantitative analysis of cryo-EM density map segmentation by watershed and scale-space filtering, and fitting of structures by alignment to regions

21 January 2018

1 reference

https://api.crossref.org/works/10.1080/10409238.2017.1380596

Understanding folding and design: replica-exchange simulations of "Trp-cage" miniproteins

21 January 2018

1 reference

https://api.crossref.org/works/10.1080/10409238.2017.1380596

Contact order, transition state placement and the refolding rates of single domain proteins.

21 January 2018

1 reference

https://api.crossref.org/works/10.1080/10409238.2017.1380596

Effectiveness of correlation analysis in identifying protein residues undergoing correlated evolution.

21 January 2018

1 reference

https://api.crossref.org/works/10.1080/10409238.2017.1380596

Force fields for protein simulations

21 January 2018

1 reference

https://api.crossref.org/works/10.1080/10409238.2017.1380596

Knowledge-based potentials in protein design.

21 January 2018

1 reference

https://api.crossref.org/works/10.1080/10409238.2017.1380596

Markov models of molecular kinetics: Generation and validation

21 January 2018

1 reference

https://api.crossref.org/works/10.1080/10409238.2017.1380596

Atomically detailed potentials to recognize native and approximate protein structures

21 January 2018

1 reference

https://api.crossref.org/works/10.1080/10409238.2017.1380596

Determination of the distance between two spin labels attached to a macromolecule

21 January 2018

1 reference

https://api.crossref.org/works/10.1080/10409238.2017.1380596

Protein folding: progress made and promises ahead

21 January 2018

1 reference

https://api.crossref.org/works/10.1080/10409238.2017.1380596

Stereochemical criteria for polypeptide and protein chain conformations. II. Allowed conformations for a pair of peptide units

21 January 2018

1 reference

https://api.crossref.org/works/10.1080/10409238.2017.1380596

Guided macro-mutation in a graded energy based genetic algorithm for protein structure prediction.

21 January 2018

1 reference

https://api.crossref.org/works/10.1080/10409238.2017.1380596

Residue-residue mean-force potentials for protein structure recognition.

21 January 2018

1 reference

https://api.crossref.org/works/10.1080/10409238.2017.1380596

Multiplexed-replica exchange molecular dynamics method for protein folding simulation

21 January 2018

1 reference

https://api.crossref.org/works/10.1080/10409238.2017.1380596

Improved Peptide and Protein Torsional Energetics with the OPLSAA Force Field

21 January 2018

1 reference

https://api.crossref.org/works/10.1080/10409238.2017.1380596

Protein structure prediction using Rosetta

21 January 2018

1 reference

https://api.crossref.org/works/10.1080/10409238.2017.1380596

Different derivations of knowledge-based potentials and analysis of their robustness and context-dependent predictive power

21 January 2018

1 reference

https://api.crossref.org/works/10.1080/10409238.2017.1380596

Prediction of protein secondary structure at better than 70% accuracy

21 January 2018

1 reference

https://api.crossref.org/works/10.1080/10409238.2017.1380596

Progress in protein structure prediction?

21 January 2018

1 reference

https://api.crossref.org/works/10.1080/10409238.2017.1380596

Error and efficiency of replica exchange molecular dynamics simulations

21 January 2018

1 reference

https://api.crossref.org/works/10.1080/10409238.2017.1380596

I-TASSER: a unified platform for automated protein structure and function prediction

21 January 2018

1 reference

https://api.crossref.org/works/10.1080/10409238.2017.1380596

An all-atom distance-dependent conditional probability discriminatory function for protein structure prediction 1 1Edited by F. Cohen

21 January 2018

1 reference

https://api.crossref.org/works/10.1080/10409238.2017.1380596

Genetic algorithms and protein folding

21 January 2018

1 reference

https://api.crossref.org/works/10.1080/10409238.2017.1380596

Contact prediction using mutual information and neural nets

21 January 2018

1 reference

https://api.crossref.org/works/10.1080/10409238.2017.1380596

Molecular basis for pseudokinase-dependent autoinhibition of JAK2 tyrosine kinase

21 January 2018

1 reference

https://api.crossref.org/works/10.1080/10409238.2017.1380596

How does a drug molecule find its target binding site?

21 January 2018

1 reference

https://api.crossref.org/works/10.1080/10409238.2017.1380596

Atomic-Level Characterization of the Structural Dynamics of Proteins

21 January 2018

1 reference

https://api.crossref.org/works/10.1080/10409238.2017.1380596

Statistical potential for assessment and prediction of protein structures

21 January 2018

1 reference

https://api.crossref.org/works/10.1080/10409238.2017.1380596

Propensities, probabilities, and the Boltzmann hypothesis

21 January 2018

1 reference

https://api.crossref.org/works/10.1080/10409238.2017.1380596

Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and Bayesian scoring functions

21 January 2018

1 reference

https://api.crossref.org/works/10.1080/10409238.2017.1380596

Chemical cross-linking and mass spectrometry for mapping three-dimensional structures of proteins and protein complexes

21 January 2018

1 reference

https://api.crossref.org/works/10.1080/10409238.2017.1380596

Calculation of conformational ensembles from potentials of mean force. An approach to the knowledge-based prediction of local structures in globular proteins.

21 January 2018

1 reference

https://api.crossref.org/works/10.1080/10409238.2017.1380596

Boltzmann's principle, knowledge-based mean fields and protein folding. An approach to the computational determination of protein structures

21 January 2018

1 reference

https://api.crossref.org/works/10.1080/10409238.2017.1380596

Knowledge-based potentials for proteins

21 January 2018

1 reference

https://api.crossref.org/works/10.1080/10409238.2017.1380596

In quest of an empirical potential for protein structure prediction.

21 January 2018

1 reference

https://api.crossref.org/works/10.1080/10409238.2017.1380596

Improved contact predictions using the recognition of protein like contact patterns

21 January 2018

1 reference

https://api.crossref.org/works/10.1080/10409238.2017.1380596

Replica-exchange molecular dynamics method for protein folding

21 January 2018

1 reference

https://api.crossref.org/works/10.1080/10409238.2017.1380596

Near-native structure refinement using in vacuo energy minimization.

21 January 2018

1 reference

https://api.crossref.org/works/10.1080/10409238.2017.1380596

An atomic environment potential for use in protein structure prediction.

21 January 2018

1 reference

https://api.crossref.org/works/10.1080/10409238.2017.1380596

Assessment of template-free modeling in CASP10 and ROLL.

21 January 2018

1 reference

https://api.crossref.org/works/10.1080/10409238.2017.1380596

Medium- and long-range interaction parameters between amino acids for predicting three-dimensional structures of proteins

21 January 2018

1 reference

https://api.crossref.org/works/10.1080/10409238.2017.1380596

NNcon: improved protein contact map prediction using 2D-recursive neural networks

21 January 2018

1 reference

https://api.crossref.org/works/10.1080/10409238.2017.1380596

Statistical potentials extracted from protein structures: how accurate are they?

21 January 2018

1 reference

https://api.crossref.org/works/10.1080/10409238.2017.1380596

Genetic algorithms for protein folding simulations.

21 January 2018

1 reference

https://api.crossref.org/works/10.1080/10409238.2017.1380596

Enhancing Important Fluctuations: Rare Events and Metadynamics from a Conceptual Viewpoint.

21 January 2018

1 reference

https://api.crossref.org/works/10.1080/10409238.2017.1380596

High-level 2H/13C/15N labeling of proteins for NMR studies

21 January 2018

1 reference

https://api.crossref.org/works/10.1080/10409238.2017.1380596

SPOCTOPUS: a combined predictor of signal peptides and membrane protein topology.

21 January 2018

1 reference

https://api.crossref.org/works/10.1080/10409238.2017.1380596

OCTOPUS: improving topology prediction by two-track ANN-based preference scores and an extended topological grammar

21 January 2018

1 reference

https://api.crossref.org/works/10.1080/10409238.2017.1380596

Methods for Monte Carlo simulations of biomacromolecules

21 January 2018

1 reference

https://api.crossref.org/works/10.1080/10409238.2017.1380596

Slow unfolded-state structuring in Acyl-CoA binding protein folding revealed by simulation and experiment

21 January 2018

1 reference

https://api.crossref.org/works/10.1080/10409238.2017.1380596

Identification of correct regions in protein models using structural, alignment, and consensus information

21 January 2018

1 reference

https://api.crossref.org/works/10.1080/10409238.2017.1380596

De novo protein structure determination from near-atomic-resolution cryo-EM maps

21 January 2018

1 reference

https://api.crossref.org/works/10.1080/10409238.2017.1380596

Biomolecular simulations: recent developments in force fields, simulations of enzyme catalysis, protein-ligand, protein-protein, and protein-nucleic acid noncovalent interactions

21 January 2018

1 reference

https://api.crossref.org/works/10.1080/10409238.2017.1380596

Characterization and rapid sampling of protein folding Markov state model topologies

21 January 2018

1 reference

https://api.crossref.org/works/10.1080/10409238.2017.1380596

BCL::Fold--protein topology determination from limited NMR restraints.

21 January 2018

1 reference

https://api.crossref.org/works/10.1080/10409238.2017.1380596

BCL::MP-fold: folding membrane proteins through assembly of transmembrane helices

21 January 2018

1 reference

https://api.crossref.org/works/10.1080/10409238.2017.1380596

AMBER: Assisted model building with energy refinement. A general program for modeling molecules and their interactions

21 January 2018

1 reference

https://api.crossref.org/works/10.1080/10409238.2017.1380596

Nucleation, rapid folding, and globular intrachain regions in proteins

21 January 2018

1 reference

https://api.crossref.org/works/10.1080/10409238.2017.1380596

BCL::Score--knowledge based energy potentials for ranking protein models represented by idealized secondary structure elements

21 January 2018

1 reference

https://api.crossref.org/works/10.1080/10409238.2017.1380596

BCL::EM-Fit: rigid body fitting of atomic structures into density maps using geometric hashing and real space refinement

21 January 2018

1 reference

https://api.crossref.org/works/10.1080/10409238.2017.1380596

Evolution, energy landscapes and the paradoxes of protein folding.

21 January 2018

1 reference

https://api.crossref.org/works/10.1080/10409238.2017.1380596

Ab initio modeling of small proteins by iterative TASSER simulations

21 January 2018

1 reference

https://api.crossref.org/works/10.1080/10409238.2017.1380596

A comprehensive assessment of sequence-based and template-based methods for protein contact prediction

21 January 2018

1 reference

https://api.crossref.org/works/10.1080/10409238.2017.1380596

Replica exchanging self-guided Langevin dynamics for efficient and accurate conformational sampling

21 January 2018

1 reference

https://api.crossref.org/works/10.1080/10409238.2017.1380596

Computational identification of self-inhibitory peptides from envelope proteins

21 January 2018

1 reference

https://api.crossref.org/works/10.1080/10409238.2017.1380596

Predicting residue-residue contact maps by a two-layer, integrated neural-network method

21 January 2018

1 reference

https://api.crossref.org/works/10.1080/10409238.2017.1380596

A comparative assessment and analysis of 20 representative sequence alignment methods for protein structure prediction.

21 January 2018

1 reference

https://api.crossref.org/works/10.1080/10409238.2017.1380596

The I-TASSER Suite: protein structure and function prediction.

21 January 2018

1 reference

https://api.crossref.org/works/10.1080/10409238.2017.1380596

STAP Refinement of the NMR database: a database of 2405 refined solution NMR structures

21 January 2018

1 reference

https://api.crossref.org/works/10.1080/10409238.2017.1380596

High throughput protein fold identification by using experimental constraints derived from intramolecular cross-links and mass spectrometry.

21 January 2018

1 reference

https://api.crossref.org/works/10.1080/10409238.2017.1380596

Simulation of folding of a small alpha-helical protein in atomistic detail using worldwide-distributed computing

21 January 2018

1 reference

https://api.crossref.org/works/10.1080/10409238.2017.1380596

A knowledge-based energy function for protein-ligand, protein-protein, and protein-DNA complexes

21 January 2018

1 reference

https://api.crossref.org/works/10.1080/10409238.2017.1380596

Integration of QUARK and I-TASSER for Ab Initio Protein Structure Prediction in CASP11.

21 January 2018

1 reference

https://api.crossref.org/works/10.1080/10409238.2017.1380596

3D protein structure prediction with genetic tabu search algorithm

21 January 2018

1 reference

https://api.crossref.org/works/10.1080/10409238.2017.1380596

Progress and challenges in protein structure prediction

21 January 2018

1 reference

https://api.crossref.org/works/10.1080/10409238.2017.1380596

I-TASSER: fully automated protein structure prediction in CASP8

21 January 2018

1 reference

https://api.crossref.org/works/10.1080/10409238.2017.1380596

TOUCHSTONE II: a new approach to ab initio protein structure prediction

21 January 2018

1 reference

https://api.crossref.org/works/10.1080/10409238.2017.1380596

Tertiary structure predictions on a comprehensive benchmark of medium to large size proteins

21 January 2018

1 reference

https://api.crossref.org/works/10.1080/10409238.2017.1380596

Distance-scaled, finite ideal-gas reference state improves structure-derived potentials of mean force for structure selection and stability prediction

21 January 2018

1 reference

https://api.crossref.org/works/10.1080/10409238.2017.1380596

Folding rate prediction using total contact distance

21 January 2018

1 reference

https://api.crossref.org/works/10.1080/10409238.2017.1380596

Striped sheets and protein contact prediction

21 January 2018

1 reference

https://api.crossref.org/works/10.1080/10409238.2017.1380596

Assembling novel protein folds from super-secondary structural fragments

21 January 2018

1 reference

https://api.crossref.org/works/10.1080/10409238.2017.1380596

Novel knowledge-based mean force potential at atomic level

21 January 2018

1 reference

https://api.crossref.org/works/10.1080/10409238.2017.1380596

PconsC: combination of direct information methods and alignments improves contact prediction

21 January 2018

1 reference

https://api.crossref.org/works/10.1080/10409238.2017.1380596

An iterative knowledge-based scoring function to predict protein-ligand interactions: II. Validation of the scoring function

21 January 2018

1 reference

12 December 2020

Configurational entropies of lipids in pure and mixed bilayers from atomic-level and coarse-grained molecular dynamics simulations

1 reference

12 December 2020

Identification of native protein folds amongst a large number of incorrect models. The calculation of low energy conformations from potentials of mean force

1 reference

12 December 2020

Successful ab initio prediction of the tertiary structure of NK‐lysin using multiple sequences and recognized supersecondary structural motifs

1 reference

12 December 2020

Micelle‐Based Brain‐Targeted Drug Delivery Enabled by a Nicotine Acetylcholine Receptor Ligand

1 reference

12 December 2020

Why do protein architectures have Boltzmann-like statistics?

1 reference

12 December 2020

Structural origin of slow diffusion in protein folding

1 reference

12 December 2020

Improving contact predictions by the combination of correlated mutations and other sources of sequence information

1 reference

12 December 2020

Statistical thermodynamics. Taking a walk on a landscape

1 reference

12 December 2020

The relation between the divergence of sequence and structure in proteins

1 reference

12 December 2020

Accurate contact predictions using covariation techniques and machine learning.

1 reference

12 December 2020

Local propensities and statistical potentials of backbone dihedral angles in proteins

1 reference

12 December 2020

Comparison of Thermodynamic Properties of Coarse-Grained and Atomic-Level Simulation Models

1 reference

12 December 2020

NMR-based protein potentials

1 reference

12 December 2020

Helmholtz free energy of peptide hydrogen bonds in proteins

1 reference

12 December 2020

Folding of fourteen small proteins with a residue-specific force field and replica-exchange molecular dynamics

1 reference

12 December 2020

Tests for comparing related amino-acid sequences. Cytochrome c and cytochrome c551

1 reference

12 December 2020

A consistent set of statistical potentials for quantifying local side-chain and backbone interactions

1 reference

12 December 2020

Factors affecting the ability of energy functions to discriminate correct from incorrect folds

1 reference

12 December 2020

Protein folding simulation with genetic algorithm and supersecondary structure constraints

1 reference

12 December 2020

Helmholtz free energies of atom pair interactions in proteins

1 reference

12 December 2020

A gradient-directed Monte Carlo approach for protein design

1 reference

12 December 2020

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

1 reference

12 December 2020

How molten is the molten globule?

1 reference

12 December 2020

Ab initio protein structure assembly using continuous structure fragments and optimized knowledge-based force field

1 reference

12 December 2020

10.1080/10409238.2017.1380596

Identifiers

DOI

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=PMCID:PMC6790072&resulttype=core&format=json

12 May 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=PMCID:PMC6790072&resulttype=core&format=json

12 May 2020

PubMed publication ID

28976219

1 reference