(Q51900421)

17 April 2018

title

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

1 reference

17 April 2018

protein function prediction

main subject

0 references

author name string

Suxin Zheng

series ordinal

1

1 reference

17 April 2018

Timothy A Robertson

series ordinal

2

1 reference

17 April 2018

Gabriele Varani

series ordinal

3

1 reference

17 April 2018

language of work or name

English

0 references

publication date

12 November 2007

1 reference

17 April 2018

published in

FEBS Journal

1 reference

17 April 2018

volume

274

1 reference

17 April 2018

issue

24

1 reference

17 April 2018

page(s)

6378-6391

1 reference

17 April 2018

Alanine-scanning mutagenesis of the predicted rRNA-binding domain of ErmC' redefines the substrate-binding site and suggests a model for protein-RNA interactions

cites work

1 reference

https://api.crossref.org/works/10.1111%2FJ.1742-4658.2007.06155.X

The role of RNA structure in the interaction of U1A protein with U1 hairpin II RNA

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1742-4658.2007.06155.X

RNA-protein recognition: single-residue ultrafast dynamical control of structural specificity and function

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1742-4658.2007.06155.X

Internal loop mutations in the ribosomal protein L30 binding site of the yeast L30 RNA transcript

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1742-4658.2007.06155.X

Structure-based analysis of protein-RNA interactions using the program ENTANGLE.

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1742-4658.2007.06155.X

Sequence-specific binding of single-stranded RNA: is there a code for recognition?

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1742-4658.2007.06155.X

Protein families and RNA recognition

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1742-4658.2007.06155.X

Protein-RNA interactions: a structural analysis

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1742-4658.2007.06155.X

Structural basis of single-stranded RNA recognition

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1742-4658.2007.06155.X

Statistical analysis of atomic contacts at RNA-protein interfaces

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1742-4658.2007.06155.X

Structural features of protein-nucleic acid recognition sites

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1742-4658.2007.06155.X

Recent advances in RNA-protein recognition.

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1742-4658.2007.06155.X

RNA sequence- and shape-dependent recognition by proteins in the ribonucleoprotein particle

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1742-4658.2007.06155.X

Fitting peptides into the RNA world

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1742-4658.2007.06155.X

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1742-4658.2007.06155.X

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/10.1111%2FJ.1742-4658.2007.06155.X

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/10.1111%2FJ.1742-4658.2007.06155.X

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1742-4658.2007.06155.X

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1742-4658.2007.06155.X

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/10.1111%2FJ.1742-4658.2007.06155.X

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1742-4658.2007.06155.X

In quest of an empirical potential for protein structure prediction.

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1742-4658.2007.06155.X

Self-consistent assignment of asparagine and glutamine amide rotamers in protein crystal structures.

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1742-4658.2007.06155.X

Development of unified statistical potentials describing protein-protein interactions.

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1742-4658.2007.06155.X

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1742-4658.2007.06155.X

SMall Molecule Growth 2001 (SMoG2001): an improved knowledge-based scoring function for protein-ligand interactions.

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1742-4658.2007.06155.X

DrugScore(CSD)-knowledge-based scoring function derived from small molecule crystal data with superior recognition rate of near-native ligand poses and better affinity prediction

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1742-4658.2007.06155.X

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1742-4658.2007.06155.X

An all-atom, distance-dependent scoring function for the prediction of protein-DNA interactions from structure

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1742-4658.2007.06155.X

Energetics of protein-DNA interactions

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1742-4658.2007.06155.X

Structural basis for recognition of AU-rich element RNA by the HuD protein

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1742-4658.2007.06155.X

The RNA recognition motif, a plastic RNA-binding platform to regulate post-transcriptional gene expression

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1742-4658.2007.06155.X

Structure of a Mycobacterium tuberculosis NusA-RNA complex

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1742-4658.2007.06155.X

Sequence-specific RNA binding by a Nova KH domain: implications for paraneoplastic disease and the fragile X syndrome

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1742-4658.2007.06155.X

The pre-mRNA binding K protein contains a novel evolutionarily conserved motif

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1742-4658.2007.06155.X

KH domain: one motif, two folds

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1742-4658.2007.06155.X

U1-snRNP-A protein selects a ten nucleotide consensus sequence from a degenerate RNA pool presented in various structural contexts

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1742-4658.2007.06155.X

RNA-binding proteins: modular design for efficient function

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1742-4658.2007.06155.X

The three-dimensional structures of two complexes between recombinant MS2 capsids and RNA operator fragments reveal sequence-specific protein-RNA interactions

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1742-4658.2007.06155.X

A thermodynamic analysis of the sequence-specific binding of RNA by bacteriophage MS2 coat protein.

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1742-4658.2007.06155.X

Molecular basis of RNA recognition by the human alternative splicing factor Fox-1

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1742-4658.2007.06155.X

Crystal structure at 1.92 A resolution of the RNA-binding domain of the U1A spliceosomal protein complexed with an RNA hairpin

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1742-4658.2007.06155.X

Specificity of ribonucleoprotein interaction determined by RNA folding during complex formulation

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1742-4658.2007.06155.X

Structural and energetic analysis of RNA recognition by a universally conserved protein from the signal recognition particle

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1742-4658.2007.06155.X

RNA-binding proteins as regulators of gene expression.

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1742-4658.2007.06155.X

Poly(A)-binding protein-interacting protein 2, a strong regulator of vascular endothelial growth factor mRNA.

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1742-4658.2007.06155.X

HRP-2, a heterogeneous nuclear ribonucleoprotein, is essential for embryogenesis and oogenesis in Caenorhabditis elegans

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1742-4658.2007.06155.X

A simple physical model for the prediction and design of protein-DNA interactions

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1742-4658.2007.06155.X

Structure-based design of a leucine zipper protein with new DNA contacting region

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1742-4658.2007.06155.X

Computational redesign of endonuclease DNA binding and cleavage specificity

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1742-4658.2007.06155.X

High-resolution protein-protein docking

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1742-4658.2007.06155.X

Improved protein structure selection using decoy-dependent discriminatory functions

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1742-4658.2007.06155.X

Recognition of errors in three-dimensional structures of proteins

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1742-4658.2007.06155.X

Announcing the worldwide Protein Data Bank

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1742-4658.2007.06155.X

Protein-protein docking predictions for the CAPRI experiment

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1742-4658.2007.06155.X

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1742-4658.2007.06155.X

10.1111/J.1742-4658.2007.06155.X

21 January 2018

Identifiers

DOI

1 reference

17 April 2018

1 reference

17 April 2018