MolProbity: all-atom contacts and structure validation for proteins and nucleic acids (Q24684673)

10

0 references

David C. Richardson

11

0 references

Jack Snoeyink

9

0 references

Andrew Leaver-Fay

2

Andrew Leaver-Fay

0 references

Vincent B Chen

3

Vincent B Chen

0 references

Gary J Kapral

5

Gary J Kapral

0 references

Jeremy Block

4

Jeremy N Block

0 references

W Bryan Arendall

8

W Bryan Arendall

0 references

author name string

Ian W Davis

1

0 references

Xueyi Wang

6

0 references

Laura W Murray

Lipid A modification systems in gram-negative bacteria

7

0 references

language of work or name

English

0 references

publication date

July 2007

0 references

published in

Nucleic Acids Research

0 references

volume

35

0 references

issue

Web Server issue

0 references

page(s)

W375-83

0 references

cites work

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1933162

7 April 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=1933162

Molecular recognition in the bovine immunodeficiency virus Tat peptide-TAR RNA complex

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1933162

A left-handed parallel beta helix in the structure of UDP-N-acetylglucosamine acyltransferase

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1933162

Free R value: a novel statistical quantity for assessing the accuracy of crystal structures

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1933162

Coot: model-building tools for molecular graphics

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1933162

MOLPROBITY: structure validation and all-atom contact analysis for nucleic acids and their complexes

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1933162

Structure validation by Calpha geometry: phi,psi and Cbeta deviation

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1933162

SFCHECK: a unified set of procedures for evaluating the quality of macromolecular structure-factor data and their agreement with the atomic model

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1933162

AQUA and PROCHECK-NMR: programs for checking the quality of protein structures solved by NMR

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1933162

WHAT IF: a molecular modeling and drug design program

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1933162

Improved methods for building protein models in electron density maps and the location of errors in these models

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1933162

The penultimate rotamer library

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1933162

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

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1933162

The nucleic acid database. A comprehensive relational database of three-dimensional structures of nucleic acids

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1933162

Structural basis for understanding oncogenic p53 mutations and designing rescue drugs

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1933162

The backrub motion: how protein backbone shrugs when a sidechain dances

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1933162

A test of enhancing model accuracy in high-throughput crystallography

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1933162

An adaptive dynamic programming algorithm for the side chain placement problem.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1933162

Asparagine and glutamine side-chain conformation in solution and crystal: a comparison for hen egg-white lysozyme using residual dipolar couplings

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1933162

Protein NMR recall, precision, and F-measure scores (RPF scores): structure quality assessment measures based on information retrieval statistics

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1933162

The Uppsala Electron-Density Server

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1933162

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

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1933162

New tools and data for improving structures, using all-atom contacts

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1933162

RNA backbone is rotameric

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1933162

Protein design is NP-hard

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1933162

Visualizing and quantifying molecular goodness-of-fit: small-probe contact dots with explicit hydrogen atoms

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1933162

Biosynthesis and function of phospholipids in Escherichia coli

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1933162

The RNA Ontology Consortium: an open invitation to the RNA community

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1933162

Difference density quality (DDQ): a method to assess the global and local correctness of macromolecular crystal structures

28 November 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/17452350

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Is one solution good enough?

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/17452350

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

The active site of Escherichia coli UDP-N-acetylglucosamine acyltransferase. Chemical modification and site-directed mutagenesis

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/17452350

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1093/NAR/GKM216

1 reference

journals/nar/DavisLCBKWMASRR07

DBLP publication ID

1 reference

DBLP Dataset 2021-01-02

28 January 2021

1 reference

1 reference

PubMed publication ID

17452350

1 reference