(Q30355358)

15 October 2017

Atomic-accuracy prediction of protein loop structures through an RNA-inspired Ansatz. (English)

1 reference

protein structure prediction

15 October 2017

0 references

1

Rhiju Das

1 reference

PMC publication ID

3804535

15 October 2017

language of work or name

English

0 references

publication date

21 October 2013

1 reference

15 October 2017

1 reference

15 October 2017

8

1 reference

15 October 2017

10

1 reference

15 October 2017

e74830

1 reference

Creative Commons Attribution 4.0 International

15 October 2017

start time

21 October 2013

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

cites work

Structure determination of noncanonical RNA motifs guided by ¹H NMR chemical shifts

1 reference

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Serverification of molecular modeling applications: the Rosetta Online Server that Includes Everyone (ROSIE)

3 June 2018

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T box RNA decodes both the information content and geometry of tRNA to affect gene expression

3 June 2018

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Advances, interactions, and future developments in the CNS, Phenix, and Rosetta structural biology software systems

3 June 2018

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Flexible backbone sampling methods to model and design protein alternative 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=3804535

Correcting pervasive errors in RNA crystallography through enumerative structure prediction

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3804535

Studying "invisible" excited protein states in slow exchange with a major state conformation

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3804535

Refinement of protein structure homology models via long, all-atom molecular dynamics simulations

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3804535

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

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3804535

RNA-Puzzles: a CASP-like evaluation of RNA three-dimensional structure prediction

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3804535

YbxF and YlxQ are bacterial homologs of L7Ae and bind K-turns but not K-loops

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3804535

An enumerative stepwise ansatz enables atomic-accuracy RNA loop modeling

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3804535

Automated protein structure modeling in CASP9 by I-TASSER pipeline combined with QUARK-based ab initio folding and FG-MD-based structure refinement

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3804535

CASP9 assessment of free modeling target predictions

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3804535

Ligand discovery from a dopamine D3 receptor homology model and crystal structure

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3804535

Four small puzzles that Rosetta doesn't solve

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3804535

The dead-end elimination theorem and its use in protein side-chain positioning

3 June 2018

2 references

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3804535

3 June 2018

https://api.crossref.org/works/10.1371/JOURNAL.PONE.0074830

Crystal structure of tarocystatin-papain complex: implications for the inhibition property of group-2 phytocystatins

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3804535

ROSETTA3: an object-oriented software suite for the simulation and design of macromolecules

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3804535

RNA Internal Loops with Tandem AG Pairs: The Structure of the 5′G AG U/3′U GA G Loop Can Be Dramatically Different from Others, Including 5′A AG U/3′U GA A

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3804535

Super-resolution biomolecular crystallography with low-resolution data

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3804535

NMR structure determination for larger proteins using backbone-only data

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3804535

Simultaneous prediction of protein folding and docking at high resolution

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3804535

Backbone flexibility 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=3804535

Structure prediction for CASP8 with all-atom refinement using Rosetta.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3804535

Sampling bottlenecks in de novo protein structure prediction

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3804535

Sub-angstrom accuracy in protein loop reconstruction by robotics-inspired conformational sampling

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3804535

Fast and accurate automatic structure prediction with HHpred.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3804535

Refinement of protein structures into low-resolution density maps using rosetta

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3804535

Outcome of a workshop on applications of protein models in biomedical research

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3804535

Crystal structural analysis of protein-protein interactions drastically destabilized by a single mutation

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3804535

Protein folding by zipping and assembly

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3804535

Routes are trees: the parsing perspective on protein folding.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3804535

Crystal and molecular structure of chymotrypsin inhibitor 2 from barley seeds in complex with subtilisin Novo

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3804535

The cis-Pro touch-turn: a rare motif preferred at functional sites.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3804535

Protein structure prediction using Rosetta

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3804535

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=3804535

Cyclic coordinate descent: A robotics algorithm for protein loop closure.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3804535

Modeling of loops in 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=3804535

Native protein sequences are close to optimal for their 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=3804535

RNA folding energy landscapes.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3804535

Effective energy function for proteins in solution

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3804535

Asparagine and glutamine: using hydrogen atom contacts in the choice of side-chain amide orientation

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3804535

3 June 2018

Long loops in proteins

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3804535

Crystal structural analysis of mutations in the hydrophobic cores of barnase

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3804535

A switch between two-, three-, and four-stranded coiled coils in GCN4 leucine zipper mutants

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3804535

Satisfying hydrogen bonding potential in 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=3804535

The structural basis of specific base-excision repair by uracil-DNA glycosylase

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3804535

Crystal and molecular structure of the serine proteinase inhibitor CI-2 from barley seeds

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3804535

Determining minimum energy conformations of polypeptides by dynamic programming

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3804535

The segmented anisotropic refinement of monoclinic papain by the application of the rigid-body TLS model and comparison to bovine ribonuclease A.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3804535

Long loop prediction using the protein local optimization program.

3 June 2018

1 reference

https://api.crossref.org/works/10.1371/JOURNAL.PONE.0074830

Toward better refinement of comparative models: predicting loops in inexact environments

21 January 2018

1 reference

https://api.crossref.org/works/10.1371/JOURNAL.PONE.0074830

Protein-protein docking with backbone flexibility.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371/JOURNAL.PONE.0074830

What is dynamic programming?

21 January 2018

1 reference

https://api.crossref.org/works/10.1371/JOURNAL.PONE.0074830

Stranded in isolation: structural role of isolated extended strands in proteins

21 January 2018

1 reference

https://api.crossref.org/works/10.1371/JOURNAL.PONE.0074830

An orientation-dependent hydrogen bonding potential improves prediction of specificity and structure for proteins and protein-protein complexes

21 January 2018

1 reference

https://api.crossref.org/works/10.1371/JOURNAL.PONE.0074830

Structure of Ecballium elaterium trypsin inhibitor II (EETI-II): a rigid molecular scaffold

21 January 2018

1 reference

https://api.crossref.org/works/10.1371/JOURNAL.PONE.0074830

Computational alanine scanning of protein-protein interfaces

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3804535

10.1371/JOURNAL.PONE.0074830

26 November 2018

Identifiers

DOI

1 reference

15 October 2017

0 references

1 reference

1 reference

PMC publication ID

3804535

15 October 2017

PubMed publication ID

24204571

1 reference

PMC publication ID

3804535