(Q30354195)

11 November 2017

Optimizing scoring function of protein-nucleic acid interactions with both affinity and specificity. (English)

1 reference

11 November 2017

Zhiqiang Yan

1

1 reference

11 November 2017

Jin Wang

series ordinal

2

1 reference

11 November 2017

language of work or name

English

0 references

publication date

30 September 2013

1 reference

11 November 2017

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11 November 2017

8

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11 November 2017

9

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11 November 2017

e74443

1 reference

Creative Commons Attribution 4.0 International

11 November 2017

start time

30 September 2013

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

cites work

Specificity and affinity quantification of protein-protein interactions

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NPIDB: Nucleic acid-Protein Interaction DataBase.

3 June 2018

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Role of the biomolecular energy gap in protein design, structure, and evolution.

3 June 2018

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A protein-RNA docking benchmark (II): extended set from experimental and homology modeling data

3 June 2018

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A protein-RNA docking benchmark (I): nonredundant cases.

3 June 2018

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Specificity quantification of biomolecular recognition and its implication for drug discovery

3 June 2018

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Benchmarking and analysis of protein docking performance in Rosetta v3.2.

3 June 2018

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Computational protein design: engineering molecular diversity, nonnatural enzymes, nonbiological cofactor complexes, and membrane proteins

3 June 2018

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Revisiting the central dogma one molecule at a time

3 June 2018

1 reference

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The RCSB Protein Data Bank: redesigned web site and web services

3 June 2018

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Scoring functions and their evaluation methods for protein-ligand docking: recent advances and future directions.

3 June 2018

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The Protein-DNA Interface database

3 June 2018

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

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3787031

Design of protein-interaction specificity gives selective bZIP-binding peptides.

3 June 2018

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An all-atom knowledge-based energy function for protein-DNA threading, docking decoy discrimination, and prediction of transcription-factor binding profiles

3 June 2018

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3 June 2018

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A protein-DNA docking benchmark

3 June 2018

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Dissecting protein-RNA recognition sites

3 June 2018

1 reference

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Recent Progress and Future Directions in Protein-Protein Docking

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3787031

Energetics of protein-DNA interactions

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3787031

Computational redesign of endonuclease DNA binding and cleavage specificity

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3787031

The Blue Obelisk-interoperability in chemical informatics

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3787031

Thermodynamic and kinetic methods of analyses of protein-nucleic acid interactions. From simpler to more complex systems

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3787031

Structural biology of cellular machines

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3787031

Specificity versus stability in computational protein design

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3787031

Interfacial inhibitors of protein-nucleic acid interactions

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3787031

Highly efficient endogenous human gene correction using designed zinc-finger nucleases

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3787031

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

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3787031

Large macromolecular complexes in the Protein Data Bank: a status report

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3787031

Quantitative evaluation of protein-DNA interactions using an optimized knowledge-based potential

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3787031

Protein topology determines binding mechanism

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3787031

Optimization of specificity in a cellular protein interaction network by negative selection

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3787031

Exploring the origins of binding specificity through the computational redesign of calmodulin

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3787031

Therapeutic modulation of endogenous gene function by agents with designed DNA-sequence specificities

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3787031

Protein-protein docking with simultaneous optimization of rigid-body displacement and side-chain conformations

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3787031

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

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3787031

An overview of the structures of protein-DNA complexes

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3787031

Folding funnels, binding funnels, and protein function

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3787031

Knowledge-based potentials--back to the roots

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3787031

Ligand binding to proteins: the binding landscape model

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3787031

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

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3787031

Unraveling principles of lead discovery: from unfrustrated energy landscapes to novel molecular anchors.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3787031

Principles of protein-protein recognition from structure to thermodynamics

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3787031

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

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3787031

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

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3787031

Optimal protein-folding codes from spin-glass theory

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3787031

The targets of CAPRI Rounds 13-19.

3 June 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0074443

Automated design of specificity in molecular recognition

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0074443

Computational redesign of protein-protein interaction specificity

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0074443

Native atom types for knowledge-based potentials: application to binding energy prediction

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0074443

Structural mining: self-consistent design on flexible protein-peptide docking and transferable binding affinity potential

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0074443

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0074443

A general and fast scoring function for protein-ligand interactions: a simplified potential approach.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0074443

Potential of mean force for protein-protein interaction studies

21 January 2018

1 reference

12 December 2020

Energy landscape theory, funnels, specificity, and optimal criterion of biomolecular binding

1 reference

12 December 2020

Quantifying biological specificity: the statistical mechanics of molecular recognition

1 reference

12 December 2020

Exploring the mechanism of flexible biomolecular recognition with single molecule dynamics

1 reference

12 December 2020

NPIDB: a database of nucleic acids-protein interactions

1 reference

12 December 2020

Quantifying intrinsic specificity: a potential complement to affinity in drug screening

1 reference

12 December 2020

An iterative knowledge-based scoring function for protein-protein recognition

1 reference

12 December 2020

10.1371/JOURNAL.PONE.0074443

Identifiers

DOI

1 reference

11 November 2017

0 references

1 reference

11 November 2017

PubMed publication ID

24098651

1 reference