(Q21562146)

2 September 2022

Sandro Bottaro

8

Sandro

Bottaro

1 reference

2 September 2022

Wouter Boomsma

7

Wouter

Boomsma

1 reference

2 September 2022

Mikael Borg

2

Mikael

Borg

1 reference

2 September 2022

Thomas Hamelryck

1

Thomas

Hamelryck

1 reference

2 September 2022

Jesper Ferkinghoff-Borg

series ordinal

9

object named as

Jesper Ferkinghoff-Borg

author given names

Jesper

author last names

Ferkinghoff-Borg

1 reference

2 September 2022

Martin Paluszewski

3

Martin

Paluszewski

1 reference

2 September 2022

Jonas Paulsen

series ordinal

4

author given names

Jonas

author last names

Paulsen

1 reference

2 September 2022

Christian Andreetta

series ordinal

6

author given names

Christian

author last names

Andreetta

1 reference

Creative Commons Attribution 4.0 International

2 September 2022

language of work or name

English

0 references

publication date

2010

0 references

published in

PLOS One

0 references

volume

5

0 references

issue

11

0 references

page(s)

e13714

0 references

copyright license

start time

10 November 2010

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

cites work

A generative, probabilistic model of local protein structure

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2978081

Sampling realistic protein conformations using local structural bias

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2978081

A composite score for predicting errors in protein structure models

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2978081

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

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2978081

19 March 2017

PMF scoring revisited

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2978081

From Levinthal to pathways to funnels

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2978081

Recognition of errors in three-dimensional structures of proteins

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2978081

Principles that govern the folding of protein chains

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2978081

A Method to Identify Protein Sequences That Fold into a Known Three-Dimensional Structure

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2978081

A new approach to protein fold recognition

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2978081

Assessment of protein models with three-dimensional profiles

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2978081

A probabilistic and continuous model of protein conformational space for template-free modeling

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2978081

Statistical potential for assessment and prediction of protein structures

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2978081

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

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2978081

New statistical potential for quality assessment of protein models and a survey of energy functions

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2978081

Quantitative prediction of protein-protein binding affinity with a potential of mean force considering volume correction.

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2978081

Generalized ensemble methods for de novo structure prediction.

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2978081

Probabilistic models and machine learning in structural bioinformatics.

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2978081

Simulated tempering yields insight into the low-resolution Rosetta scoring functions

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2978081

A free-rotating and self-avoiding chain model for deriving statistical potentials based on protein structures

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2978081

Minimalist representations and the importance of nearest neighbor effects in protein folding simulations

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2978081

Interfaces and the driving force of hydrophobic assembly

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2978081

Development of novel statistical potentials for protein fold recognition

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2978081

Funnel sculpting for in silico assembly of secondary structure elements of proteins

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2978081

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

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2978081

Effective energy functions for protein structure prediction.

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2978081

Knowledge-based potentials--back to the roots

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2978081

An all-atom distance-dependent conditional probability discriminatory function for protein structure prediction

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2978081

An iterative method for extracting energy-like quantities from protein structures.

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2978081

Are database-derived potentials valid for scoring both forward and inverted protein folding?

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2978081

Spin glasses and the statistical mechanics of protein folding

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2978081

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

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2978081

A generalized knowledge-based discriminatory function for biomolecular interactions

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2978081

Comparison of database potentials and molecular mechanics force fields

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2978081

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

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2978081

An accurate, residue-level, pair potential of mean force for folding and binding based on the distance-scaled, ideal-gas reference state.

30 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2978081

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

30 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2978081

Prediction of protein backbone conformation based on seven structure assignments. Influence of local interactions

30 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2978081

Assembly of polypeptide and protein backbone conformations from low energy ensembles of short fragments: Development of strategies and construction of models for myoglobin, lysozyme, and thymosin β4

30 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2978081

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

30 May 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0013714

Propensities, probabilities, and the Boltzmann hypothesis

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0013714

Knowledge-based scoring function to predict protein-ligand interactions.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0013714

PoPMuSiC, an algorithm for predicting protein mutant stability changes: application to prion proteins.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0013714

Deriving effective mesoscale potentials from atomistic simulations.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0013714

Effects of amino acid composition, finite size of proteins, and sparse statistics on distance-dependent statistical pair potentials

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0013714

On Information and Sufficiency

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0013714

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0013714

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0013714

Predicting protein stability changes upon mutation using database-derived potentials: solvent accessibility determines the importance of local versus non-local interactions along the sequence

21 January 2018

1 reference

12 December 2020

An empirical energy potential with a reference state for protein fold and sequence recognition

1 reference

12 December 2020

Why do protein architectures have Boltzmann-like statistics?

1 reference

12 December 2020

Monte Carlo simulation and global optimization without parameters

1 reference

12 December 2020

Helmholtz free energies of atom pair interactions in proteins

1 reference

12 December 2020

Improved recognition of native-like protein structures using a combination of sequence-dependent and sequence-independent features of proteins

1 reference

12 December 2020

10.1371/JOURNAL.PONE.0013714

Identifiers

DOI

1 reference

0 references

0 references

3091014

1 reference

1 reference

3091014

1 reference