A Web Resource for Standardized Benchmark Datasets, Metrics, and Rosetta Protocols for Macromolecular Modeling and Design (Q28914715)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26335248%20AND%20SRC:MED&resulttype=core&format=json

23 February 2020

title

A Web Resource for Standardized Benchmark Datasets, Metrics, and Rosetta Protocols for Macromolecular Modeling and Design (English)

1 reference

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23 February 2020

1 reference

8

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23 February 2020

Kyle A Barlow

2

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23 February 2020

Roland A Pache

3

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23 February 2020

Colin A Smith

7

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23 February 2020

4

Noah Ollikainen

1 reference

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23 February 2020

1

Shane Ó Conchúir

1 reference

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23 February 2020

author name string

Kale Kundert

5

1 reference

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23 February 2020

Matthew J O'Meara

6

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23 February 2020

language of work or name

English

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publication date

3 September 2015

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23 February 2020

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23 February 2020

volume

10

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23 February 2020

page(s)

e0130433

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23 February 2020

issue

9

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Creative Commons Attribution 4.0 International

23 February 2020

copyright license

start time

3 September 2015

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

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cites work

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1 reference

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16 March 2017

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The ChEMBL bioactivity database: an update

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16 March 2017

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Scientific benchmarks for guiding macromolecular energy function improvement

16 March 2017

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Flexible backbone sampling methods to model and design protein alternative conformations

16 March 2017

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Predicting the tolerated sequences for proteins and protein interfaces using RosettaBackrub flexible backbone design

16 March 2017

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A smoothed backbone-dependent rotamer library for proteins derived from adaptive kernel density estimates and regressions

16 March 2017

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

16 March 2017

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

16 March 2017

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CHARMM: the biomolecular simulation program

16 March 2017

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Backrub-like backbone simulation recapitulates natural protein conformational variability and improves mutant side-chain prediction

16 March 2017

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ProTherm and ProNIT: thermodynamic databases for proteins and protein-nucleic acid interactions

16 March 2017

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16 March 2017

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Protein-Protein Docking Benchmark 2.0: an update

16 March 2017

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WebLogo: A Sequence Logo Generator

16 March 2017

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A simple physical model for binding energy hot spots in protein-protein complexes

16 March 2017

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Native protein sequences are close to optimal for their structures

16 March 2017

1 reference

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16 March 2017

The Protein Data Bank

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Critical assessment of methods of protein structure prediction (CASP)--round x

16 March 2017

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A hot spot of binding energy in a hormone-receptor interface

6 April 2017

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A hierarchical approach to all-atom protein loop prediction

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7 April 2017

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7 April 2017

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Anatomy of hot spots in protein interfaces

7 April 2017

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Comparative Protein Structure Modeling Using MODELLER

7 April 2017

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20 June 2018

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20 June 2018

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Role of conformational sampling in computing mutation-induced changes in protein structure and stability

20 June 2018

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20 June 2018

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20 June 2018

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20 June 2018

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20 June 2018

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20 June 2018

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20 June 2018

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The third CAPRI assessment meeting Toronto, Canada, April 20-21, 2007.

20 June 2018

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Protein-protein docking benchmark version 4.0.

21 January 2018

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Assessing computational methods for predicting protein stability upon mutation: good on average but not in the details.

21 January 2018

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KFC2: a knowledge-based hot spot prediction method based on interface solvation, atomic density, and plasticity features.

21 January 2018

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Computational alanine scanning of protein-protein interfaces

21 January 2018

1 reference

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Within the twilight zone: a sensitive profile-profile comparison tool based on information theory.

21 January 2018

1 reference

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Mutual information without the influence of phylogeny or entropy dramatically improves residue contact prediction.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0130433

Structure-based prediction of the peptide sequence space recognized by natural and synthetic PDZ domains

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0130433

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

21 January 2018

1 reference

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Protein-protein docking with backbone flexibility.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0130433

Long loop prediction using the protein local optimization program.

21 January 2018

1 reference

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A kinematic view of loop closure.

21 January 2018

1 reference

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Understanding hierarchical protein evolution from first principles 1 1Edited by J. Thornton

21 January 2018

1 reference

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Predicting free energy changes using structural ensembles

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/26335248

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1371/JOURNAL.PONE.0130433

2 references

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26335248%20AND%20SRC:MED&resulttype=core&format=json

23 February 2020

ADS bibcode

2015PLoSO..1030433O

0 references

1 reference

2 references

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26335248%20AND%20SRC:MED&resulttype=core&format=json

23 February 2020

2 references

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26335248%20AND%20SRC:MED&resulttype=core&format=json