(Q37701287)

22 August 2017

A knowledge-based scoring function for protein-RNA interactions derived from a statistical mechanics-based iterative method (English)

1 reference

22 August 2017

0 references

Sheng-You Huang

1

1 reference

22 August 2017

Xiaoqin Zou

series ordinal

2

1 reference

22 August 2017

language of work or name

English

0 references

publication date

29 January 2014

1 reference

22 August 2017

Nucleic Acids Research

1 reference

22 August 2017

42

1 reference

22 August 2017

7

1 reference

22 August 2017

e55

1 reference

Creative Commons Attribution 3.0 Unported

22 August 2017

start time

10 November 2016

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

cites work

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

23 August 2017

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

23 August 2017

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Highly accurate and high-resolution function prediction of RNA binding proteins by fold recognition and binding affinity prediction

23 August 2017

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DARS-RNP and QUASI-RNP: new statistical potentials for protein-RNA docking

23 August 2017

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DECK: Distance and environment-dependent, coarse-grained, knowledge-based potentials for protein-protein docking

23 August 2017

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Statistical mechanics-based method to extract atomic distance-dependent potentials from protein structures

23 August 2017

1 reference

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Structure-based prediction of RNA-binding domains and RNA-binding sites and application to structural genomics targets.

23 August 2017

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Advances and challenges in protein-ligand docking

23 August 2017

1 reference

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MDockPP: A hierarchical approach for protein-protein docking and its application to CAPRI rounds 15-19

23 August 2017

1 reference

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Regulation of mRNA translation and stability by microRNAs

23 August 2017

1 reference

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RNA processing and its regulation: global insights into biological networks

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3985650

Dissecting the expression dynamics of RNA-binding proteins in posttranscriptional regulatory networks.

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3985650

Role of plant RNA-binding proteins in development, stress response and genome organization.

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3985650

Diverse RNA-binding proteins interact with functionally related sets of RNAs, suggesting an extensive regulatory system

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3985650

RNA-binding proteins in human genetic disease

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3985650

Tetrahymena ORC contains a ribosomal RNA fragment that participates in rDNA origin recognition.

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3985650

Docking and scoring protein complexes: CAPRI 3rd Edition

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3985650

RNA-binding proteins: modular design for efficient function

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3985650

High-resolution protein-protein docking

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3985650

Flexible protein-protein docking

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3985650

Protein-Protein Docking Benchmark 2.0: an update

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3985650

Assessment of CAPRI predictions in rounds 3-5 shows progress in docking procedures

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3985650

PatchDock and SymmDock: servers for rigid and symmetric docking

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3985650

A new hydrogen-bonding potential for the design of protein-RNA interactions predicts specific contacts and discriminates decoys

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3985650

Predicting molecular interactions in silico: II. Protein-protein and protein-drug docking

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3985650

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

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3985650

CAPRI: a Critical Assessment of PRedicted Interactions

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3985650

Class I tyrosyl-tRNA synthetase has a class II mode of cognate tRNA recognition

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3985650

Principles of docking: An overview of search algorithms and a guide to scoring functions

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3985650

Prediction of protein-protein interactions by docking methods.

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3985650

23 August 2017

The Protein Data Bank

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3985650

Evaluation of GRAMM low-resolution docking methodology on the hemagglutinin-antibody complex

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3985650

Modelling protein docking using shape complementarity, electrostatics and biochemical information

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3985650

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

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3985650

A geometric approach to macromolecule-ligand interactions

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3985650

Molecular surface recognition: determination of geometric fit between proteins and their ligands by correlation techniques

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3985650

Computer analysis of protein-protein interaction

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3985650

Electrostatics in protein-protein docking

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3985650

A coarse-grained force field for Protein-RNA docking

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3985650

Protein-protein docking with a reduced protein model accounting for side-chain flexibility

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3985650

How do potentials derived from structural databases relate to "true" potentials?

23 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3985650

Molecular surface recognition by a computer vision-based technique

23 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3985650

"Soft docking": matching of molecular surface cubes

23 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3985650

Protein docking and complementarity

23 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3985650

A nonredundant structure dataset for benchmarking protein-RNA computational docking

23 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3985650

A new residue-nucleotide propensity potential with structural information considered for discriminating protein-RNA docking decoys

1 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3985650

Blind predictions of protein interfaces by docking calculations in CAPRI

1 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3985650

Structural prediction of protein-RNA interaction by computational docking with propensity-based statistical potentials

1 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3985650

Optimal protein-RNA area, OPRA: a propensity-based method to identify RNA-binding sites on proteins

1 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3985650

A knowledge-based potential function predicts the specificity and relative binding energy of RNA-binding proteins.

1 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3985650

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

1 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3985650

A protein-protein docking benchmark.

1 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3985650

ZDOCK: an initial-stage protein-docking algorithm.

1 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3985650

A novel shape complementarity scoring function for protein‐protein docking

1 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3985650

Docking unbound proteins using shape complementarity, desolvation, and electrostatics.

1 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3985650

Protein docking using a genetic algorithm.

1 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3985650

BiGGER: a new (soft) docking algorithm for predicting protein interactions.

1 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3985650

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

1 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3985650

ICM?A new method for protein modeling and design: Applications to docking and structure prediction from the distorted native conformation

1 September 2018

1 reference

Crossref

https://api.crossref.org/works/10.1093%2FNAR%2FGKU077

A Simplex Method for Function Minimization

21 January 2018

1 reference

Crossref

https://api.crossref.org/works/10.1093%2FNAR%2FGKU077

Principles of docking: An overview of search algorithms and a guide to scoring functions

21 January 2018

1 reference

Crossref

https://api.crossref.org/works/10.1093%2FNAR%2FGKU077

Protein docking using continuum electrostatics and geometric fit

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/24476917

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

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

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/24476917

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

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

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/24476917

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1093/NAR/GKU077

1 reference

22 August 2017

1 reference

22 August 2017

PubMed publication ID

24476917

1 reference