(Q36281165)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:10210183%20AND%20SRC:MED&resulttype=core&format=json

4 December 2019

title

Protein-protein recognition: an experimental and computational study of the R89K mutation in Raf and its effect on Ras binding (English)

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:10210183%20AND%20SRC:MED&resulttype=core&format=json

4 December 2019

main subject

computational biology

1 reference

5

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:10210183%20AND%20SRC:MED&resulttype=core&format=json

4 December 2019

author name string

Zeng J

1

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:10210183%20AND%20SRC:MED&resulttype=core&format=json

4 December 2019

Fridman M

2

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:10210183%20AND%20SRC:MED&resulttype=core&format=json

4 December 2019

Maruta H

3

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:10210183%20AND%20SRC:MED&resulttype=core&format=json

4 December 2019

Treutlein HR

4

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:10210183%20AND%20SRC:MED&resulttype=core&format=json

4 December 2019

publication date

1 January 1999

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:10210183%20AND%20SRC:MED&resulttype=core&format=json

4 December 2019

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:10210183%20AND%20SRC:MED&resulttype=core&format=json

4 December 2019

volume

8

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:10210183%20AND%20SRC:MED&resulttype=core&format=json

4 December 2019

page(s)

50-64

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:10210183%20AND%20SRC:MED&resulttype=core&format=json

4 December 2019

issue

1

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:10210183%20AND%20SRC:MED&resulttype=core&format=json

Structure of the Ras-binding domain of RalGEF and implications for Ras binding and signalling

4 December 2019

cites work

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2144096

Three-dimensional structure of the Ras-interacting domain of RalGDS

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2144096

The statistical-thermodynamic basis for computation of binding affinities: a critical review

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2144096

Interactions between Ras proteins and their effectors

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2144096

Ras/Rap effector specificity determined by charge reversal

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2144096

Complexes of Ras.GTP with Raf-1 and mitogen-activated protein kinase kinase

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2144096

Mammalian Ras interacts directly with the serine/threonine kinase Raf

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2144096

Normal and oncogenic p21ras proteins bind to the amino-terminal regulatory domain of c-Raf-1

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2144096

Solution structure and dynamics of ras p21.GDP determined by heteronuclear three- and four-dimensional NMR spectroscopy

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2144096

A single amino acid change in Raf-1 inhibits Ras binding and alters Raf-1 function

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2144096

The 2.2 A crystal structure of the Ras-binding domain of the serine/threonine kinase c-Raf1 in complex with Rap1A and a GTP analogue

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2144096

Solution structure of the Ras-binding domain of c-Raf-1 and identification of its Ras interaction surface

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2144096

Protein-protein interactions: a review of protein dimer structures

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2144096

Proline cis-trans isomerization in staphylococcal nuclease: multi-substrate free energy perturbation calculations

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2144096

Intrinsic GTPase activity distinguishes normal and oncogenic ras p21 molecules

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2144096

A general method of in vitro preparation and specific mutagenesis of DNA fragments: study of protein and DNA interactions

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2144096

Site-directed mutagenesis by overlap extension using the polymerase chain reaction

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2144096

Structure of the guanine-nucleotide-binding domain of the Ha-ras oncogene product p21 in the triphosphate conformation

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2144096

Molecular switch for signal transduction: structural differences between active and inactive forms of protooncogenic ras proteins

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2144096

The Role of Raf-1 Phosphorylation in Signal Transduction

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2144096

Dynamic information from protein crystallography. An analysis of temperature factors from refinement of the hen egg-white lysozyme structure

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2144096

Protein-protein recognition

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2144096

Free energy calculations of the mutation of Ile96-->Ala in barnase: contributions to the difference in stability.

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2144096

Active site dynamics in protein molecules: a stochastic boundary molecular-dynamics approach.

29 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2144096

The residues of Ras and Rap proteins that determine their GAP specificities.

29 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2144096

Binding of an antiviral agent to a sensitive and a resistant human rhinovirus. Computer simulation studies with sampling of amino acid side-chain conformations. II. Calculation of free-energy differences by thermodynamic integration.

29 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2144096

Conformation of the Ras-binding domain of Raf studied by molecular dynamics and free energy simulations.

29 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2144096

Absolute and relative binding free energy calculations of the interaction of biotin and its analogs with streptavidin using molecular dynamics/free energy perturbation approaches

22 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2144096

Molecular recognition in proteins. Simulation analysis of substrate binding by a tyrosyl-tRNA synthetase mutant.

22 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2144096

The minimal fragments of c-Raf-1 and NF1 that can suppress v-Ha-Ras-induced malignant phenotype.

22 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2144096

Free energy simulations: the meaning of the individual contributions from a component analysis.

22 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2144096

The meaning of component analysis: decomposition of the free energy in terms of specific interactions.

22 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2144096

On the use of normal modes in thermal parameter refinement: theory and application to the bovine pancreatic trypsin inhibitor

22 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2144096

Specific amino acid recognition by aspartyl-tRNA synthetase studied by free energy simulations 1 1A. R. Fersht

22 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2144096

Decomposition of the Free Energy of a System in Terms of Specific Interactions

21 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2144096

Surface, subunit interfaces and interior of oligomeric proteins

21 October 2018

1 reference

12 December 2020

Hidden thermodynamics of mutant proteins: a molecular dynamics analysis

1 reference

12 December 2020

Thermodynamics of protein-peptide interactions in the ribonuclease-S system studied by molecular dynamics and free energy calculations

1 reference

12 December 2020

Free energy simulations of the HyHEL-10/HEL antibody-antigen complex

1 reference

12 December 2020

Quantitative structure-activity analysis correlating Ras/Raf interaction in vitro to Raf activation in vivo

1 reference

12 December 2020

On the decomposition of free energies

1 reference

12 December 2020

Mutations that abolish the ability of Ha-Ras to associate with Raf-1

1 reference

12 December 2020

Identifiers

DOI

10.1110/PS.8.1.50

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:10210183%20AND%20SRC:MED&resulttype=core&format=json

4 December 2019

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:10210183%20AND%20SRC:MED&resulttype=core&format=json

4 December 2019

1 reference