(Q35557713)

8 August 2017

Xlink Analyzer: software for analysis and visualization of cross-linking data in the context of three-dimensional structures (English)

1 reference

8 August 2017

1 reference

0 references

Jan Kosinski

1

0 references

Alessandro Ori

object named as

Alessandro Ori

3

0 references

Martin Beck

object named as

Martin Beck

6

0 references

Christoph W Müller

object named as

Christoph W Müller

5

0 references

author name string

Alexander von Appen

2

1 reference

PubMed ID

25661704

8 August 2017

Kai Karius

4

1 reference

8 August 2017

7 February 2015

1 reference

Journal of Structural Biology

8 August 2017

1 reference

8 August 2017

189

1 reference

8 August 2017

3

1 reference

8 August 2017

177-183

1 reference

Chemical cross-linking/mass spectrometry targeting acidic residues in proteins and protein complexes

8 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4359615

Distance restraints from crosslinking mass spectrometry: mining a molecular dynamics simulation database to evaluate lysine-lysine distances

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4359615

MS-based cross-linking analysis reveals the location of the PsbQ protein in cyanobacterial photosystem II.

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4359615

A mass spectrometry-based hybrid method for structural modeling of protein complexes

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4359615

Combinatorial approach for large-scale identification of linked peptides from tandem mass spectrometry spectra

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4359615

Lysine-specific chemical cross-linking of protein complexes and identification of cross-linking sites using LC-MS/MS and the xQuest/xProphet software pipeline

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4359615

Integrated structural analysis of the human nuclear pore complex scaffold

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4359615

Crystal structure of the 14-subunit RNA polymerase I

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4359615

RNA polymerase I structure and transcription regulation

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4359615

Cross-link guided molecular modeling with ROSETTA

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4359615

Structure and subunit topology of the INO80 chromatin remodeler and its nucleosome complex.

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4359615

Hekate: software suite for the mass spectrometric analysis and three-dimensional visualization of cross-linked protein samples

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4359615

XLink-DB: database and software tools for storing and visualizing protein interaction topology data

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4359615

Identification of cross-linked peptides from complex samples.

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4359615

Crosslinking-MS analysis reveals RNA polymerase I domain architecture and basis of rRNA cleavage

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4359615

Molecular architecture of the 26S proteasome holocomplex determined by an integrative approach

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4359615

Expanding the chemical cross-linking toolbox by the use of multiple proteases and enrichment by size exclusion chromatography

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4359615

StavroX--a software for analyzing crosslinked products in protein interaction studies

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4359615

Xwalk: computing and visualizing distances in cross-linking experiments

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4359615

CrossWork: software-assisted identification of cross-linked peptides.

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4359615

RNA polymerase I contains a TFIIF-related DNA-binding subcomplex

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4359615

Probing native protein structures by chemical cross-linking, mass spectrometry, and bioinformatics

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4359615

Biopython: freely available Python tools for computational molecular biology and bioinformatics

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4359615

Identification and characterization of disulfide bonds in proteins and peptides from tandem MS data by use of the MassMatrix MS/MS search engine

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4359615

Prediction of peptides observable by mass spectrometry applied at the experimental set level

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4359615

Visualizing density maps with UCSF Chimera

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4359615

Tools for integrated sequence-structure analysis with UCSF Chimera

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4359615

Analysis of protein-protein interaction surfaces using a combination of efficient lysine acetylation and nanoLC-MALDI-MS/MS applied to the E9:Im9 bacteriotoxin--immunity protein complex.

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4359615

UCSF Chimera--a visualization system for exploratory research and analysis

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4359615

AAindex: Amino Acid Index Database.

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4359615

The role of charged residues mediating low affinity protein-protein recognition at the cell surface by CD2

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4359615

A simple method for displaying the hydropathic character of a protein

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4359615

False discovery rate estimation for cross-linked peptides identified by mass spectrometry

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4359615

Charged residues at protein interaction interfaces: unexpected conservation and orchestrated divergence

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4359615

Analysis and prediction of DNA-binding proteins and their binding residues based on composition, sequence and structural information.

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4359615

Pro-CrossLink. Software tool for protein cross-linking and mass spectrometry

26 September 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/25661704

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Utilization of lysine ¹³C-methylation NMR for protein-protein interaction studies

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/25661704

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Matplotlib: A 2D Graphics Environment

1 reference

28 May 2022

https://opencitations.net/index/coci/api/v1/citations/10.1109/MCSE.2007.55

Identifiers

DOI

10.1016/J.JSB.2015.01.014

1 reference

8 August 2017

1 reference

8 August 2017

1 reference

PubMed ID

25661704