(Q40191495)

18 September 2017

Inferring ideal amino acid interaction forms from statistical protein contact potentials (English)

1 reference

18 September 2017

0 references

3

Robert L Jernigan

1 reference

18 September 2017

2

Andrzej Kloczkowski

1 reference

18 September 2017

Andrzej Kolinski

6

0 references

Piotr Pokarowski

series ordinal

1

object named as

Piotr Pokarowski

1 reference

18 September 2017

5

Maria Pokarowska

1 reference

18 September 2017

Neha S Kothari

4

1 reference

PMCID

4417612

18 September 2017

language of work or name

English

0 references

publication date

1 April 2005

1 reference

18 September 2017

1 reference

18 September 2017

59

1 reference

18 September 2017

49-57

1 reference

18 September 2017

1

1 reference

Protein modeling and structure prediction with a reduced representation.

18 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4417612

Protein fragment reconstruction using various modeling techniques

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4417612

Orientational potentials extracted from protein structures improve native fold recognition

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4417612

Prediction of protein structure by emphasizing local side-chain/backbone interactions in ensembles of turn fragments

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4417612

TOUCHSTONE: a unified approach to protein structure prediction.

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4417612

Rosetta predictions in CASP5: successes, failures, and prospects for complete automation.

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4417612

Novel use of a genetic algorithm for protein structure prediction: searching template and sequence alignment space.

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4417612

Site-specific contributions to the pH dependence of protein stability

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4417612

A minimal physically realistic protein-like lattice model: designing an energy landscape that ensures all-or-none folding to a unique native state

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4417612

Combining conformational flexibility and continuum electrostatics for calculating pK(a)s in proteins

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4417612

How to guarantee optimal stability for most representative structures in the Protein Data Bank.

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4417612

Lattice protein folding with two and four-body statistical potentials.

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4417612

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

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4417612

Ab initio construction of protein tertiary structures using a hierarchical approach

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4417612

Environment-dependent residue contact energies for proteins.

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4417612

Designing potential energy functions for protein folding

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4417612

Pair potentials for protein folding: choice of reference states and sensitivity of predicted native states to variations in the interaction schemes

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4417612

Empirical solvent-mediated potentials hold for both intra-molecular and inter-molecular inter-residue interactions

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4417612

Statistical significance of hierarchical multi-body potentials based on Delaunay tessellation and their application in sequence-structure alignment

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4417612

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

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4417612

Derivation and testing of pair potentials for protein folding. When is the quasichemical approximation correct?

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4417612

How to derive a protein folding potential? A new approach to an old problem

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4417612

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

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4417612

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

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4417612

Are proteins ideal mixtures of amino acids? Analysis of energy parameter sets

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4417612

An empirical energy function for threading protein sequence through the folding motif

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4417612

Exploring conformational space with a simple lattice model for protein structure

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4417612

Knowledge-based potentials for proteins

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4417612

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

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4417612

Inter-residue potentials in globular proteins and the dominance of highly specific hydrophilic interactions at close separation.

25 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4417612

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

15 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4417612

Contact potential that recognizes the correct folding of globular proteins

15 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4417612

A minimal proteinlike lattice model: an alpha-helix motif.

15 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4417612

Charge-charge interactions are key determinants of the pK values of ionizable groups in ribonuclease Sa (pI=3.5) and a basic variant (pI=10.2).

20 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4417612

The role of hydrophobic microenvironments in modulating pKa shifts in proteins.

20 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4417612

Learning effective amino acid interactions through iterative stochastic techniques.

20 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4417612

Comparison of two optimization methods to derive energy parameters for protein folding: perceptron and Z score.

20 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4417612

On the design and analysis of protein folding potentials.

20 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4417612

Combination of threading potentials and sequence profiles improves fold recognition.

20 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4417612

A fast and simple method to calculate protonation states in proteins.

20 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4417612

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

20 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4417612

Assembling novel protein folds from super-secondary structural fragments

20 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4417612

Derivation of protein-specific pair potentials based on weak sequence fragment similarity

2 December 2018

1 reference

12 December 2020

Refined models for computer simulation of protein folding. Applications to the study of conserved secondary structure and flexible hinge points during the folding of pancreatic trypsin inhibitor

1 reference

12 December 2020

Predicting interresidue contacts using templates and pathways

1 reference

12 December 2020

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

1 reference

12 December 2020

Models of protein interactions: how to choose one

1 reference

12 December 2020

Self-consistent estimation of inter-residue protein contact energies based on an equilibrium mixture approximation of residues

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

Identifiers

DOI

10.1002/PROT.20380

1 reference

18 September 2017

1 reference

18 September 2017

1 reference

PMCID

4417612