Scientific benchmarks for guiding macromolecular energy function improvement (Q28914728)

13

Jane S Richardson

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Jeffrey J. Gray

Jeffrey J Gray

11

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Jack Snoeyink

Jack Snoeyink

15

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David Baker

David Baker

16

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Brian Kuhlman

17

Brian Kuhlman

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Andrew Leaver-Fay

1

Andrew Leaver-Fay

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Sergey Lyskov

10

Sergey Lyskov

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author name string

Matthew J O'Meara

2

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Mike Tyka

3

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Ron Jacak

4

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Yifan Song

5

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Elizabeth H Kellogg

6

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James Thompson

7

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Ian W Davis

8

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Roland A Pache

9

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James J Havranek

describes a project that uses

14

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language of work or name

English

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publication date

2013

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language of work

Methods in Enzymology

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volume

523

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page(s)

109-43

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1 reference

10 June 2022

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pmc&rettype=xml&id=3724755

SQL

1 reference

Europe PubMed Central

26 June 2022

https://europepmc.org/article/PMC/PMC3724755

inferred from PubMed Central ID database lookup

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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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Protein design is NP-hard

20 June 2018

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20 June 2018

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20 June 2018

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An analysis of incorrectly folded protein models. Implications for structure predictions.

20 June 2018

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Hydrogen bonding and biological specificity analysed by protein engineering

20 June 2018

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

20 June 2018

1 reference

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Structure-guided forcefield optimization

20 June 2018

1 reference

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Optimizing energy functions for protein-protein interface design.

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3724755

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

26 November 2018

1 reference

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

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3724755

Protein-protein docking with backbone flexibility.

26 November 2018

1 reference

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SODOCK: swarm optimization for highly flexible protein-ligand docking.

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3724755

C-H...O hydrogen bonds in beta-sheets

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3724755

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

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3724755

Predicting protein stability changes upon mutation using database-derived potentials: solvent accessibility determines the importance of local versus non-local interactions along the sequence

26 November 2018

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12 December 2020

Protein sidechain conformer prediction: a test of the energy function

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12 December 2020

Improved recognition of native-like protein structures using a combination of sequence-dependent and sequence-independent features of proteins

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12 December 2020

Conformational diversity and protein evolution--a 60-year-old hypothesis revisited

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12 December 2020

Crystallographic evidence for the existence of CH...O, CH...N and CH...Cl hydrogen bonds

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COCI

https://opencitations.net/index/coci/api/v1/citations/10.1021/JA00383A012

10.1016/B978-0-12-394292-0.00006-0

5 March 2023

Identifiers

DOI

1 reference

1 reference

1 reference

PubMed publication ID

23422428

1 reference