Insights into protein-protein binding by binding free energy calculation and free energy decomposition for the Ras-Raf and Ras-RalGDS complexes. (Q30333153)

From Wikidata

Jump to navigation Jump to search

scientific article

Language	Label	Description	Also known as
English	Insights into protein-protein binding by binding free energy calculation and free energy decomposition for the Ras-Raf and Ras-RalGDS complexes.	scientific article

Statements

scholarly article

1 reference

Europe PubMed Central

PubMed publication ID

18 June 2017

Insights into protein-protein binding by binding free energy calculation and free energy decomposition for the Ras-Raf and Ras-RalGDS complexes. (English)

1 reference

Europe PubMed Central

PubMed publication ID

18 June 2017

author name string

Holger Gohlke

1

1 reference

Europe PubMed Central

PubMed publication ID

18 June 2017

Christina Kiel

2

1 reference

Europe PubMed Central

PubMed publication ID

18 June 2017

David A Case

3

1 reference

Europe PubMed Central

PubMed publication ID

18 June 2017

language of work or name

0 references

publication date

1 July 2003

1 reference

Europe PubMed Central

PubMed publication ID

18 June 2017

Journal of Molecular Biology

1 reference

Europe PubMed Central

PubMed publication ID

18 June 2017

330

1 reference

Europe PubMed Central

PubMed publication ID

18 June 2017

4

1 reference

Europe PubMed Central

PubMed publication ID

18 June 2017

891-913

1 reference

Europe PubMed Central

PubMed publication ID

18 June 2017

Protein−Protein Interactions: Interface Structure, Binding Thermodynamics, and Mutational Analysis

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900610-7

7 January 2021

Analysis of the intermolecular contacts within sickle hemoglobin fibers: effect of site-specific substitutions, fiber pitch, and double-strand disorder

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900610-7

7 January 2021

Inhibiting the assembly of protein-protein interfaces.

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900610-7

7 January 2021

A computer screening approach to immunoglobulin superfamily structures and interactions: discovery of small non-peptidic CD4 inhibitors as novel immunotherapeutics

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900610-7

7 January 2021

Designing small-molecule switches for protein-protein interactions

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900610-7

7 January 2021

Design of inhibitors of Ras--Raf interaction using a computational combinatorial algorithm

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900610-7

7 January 2021

Selective inhibition of Ras interaction with its particular effector by synthetic peptides corresponding to the Ras effector region

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900610-7

7 January 2021

Anatomy of hot spots in protein interfaces

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900610-7

7 January 2021

Mini-review: computational structure-based design of inhibitors that target protein surfaces

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900610-7

7 January 2021

Principles of protein-protein interactions

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900610-7

7 January 2021

Interactions of protein antigens with antibodies

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900610-7

7 January 2021

Stability of macromolecular complexes

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900610-7

7 January 2021

Studies of protein-protein interfaces: a statistical analysis of the hydrophobic effect

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900610-7

7 January 2021

Dominant forces in protein folding

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900610-7

7 January 2021

Energetics of protein-protein interactions: analysis of the barnase-barstar interface by single mutations and double mutant cycles

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900610-7

7 January 2021

Dissecting the energetics of an antibody-antigen interface by alanine shaving and molecular grafting

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900610-7

7 January 2021

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

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900610-7

7 January 2021

Structural and functional analysis of the 1:1 growth hormone:receptor complex reveals the molecular basis for receptor affinity

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900610-7

7 January 2021

Conservation of polar residues as hot spots at protein interfaces

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900610-7

7 January 2021

Comparison of a structural and a functional epitope

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900610-7

7 January 2021

Rational design of faster associating and tighter binding protein complexes

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900610-7

7 January 2021

Unraveling hot spots in binding interfaces: progress and challenges

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900610-7

7 January 2021

Biomolecular simulations: recent developments in force fields, simulations of enzyme catalysis, protein-ligand, protein-protein, and protein-nucleic acid noncovalent interactions

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900610-7

7 January 2021

The GTPase superfamily: conserved structure and molecular mechanism

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900610-7

7 January 2021

How Ras-related proteins talk to their effectors

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900610-7

7 January 2021

Regulation of Ras-mediated signalling: more than one way to skin a cat.

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900610-7

7 January 2021

Mammalian Ras interacts directly with the serine/threonine kinase Raf

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900610-7

7 January 2021

Increasing complexity of Ras signaling.

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900610-7

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900610-7

7 January 2021

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

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900610-7

7 January 2021

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

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900610-7

7 January 2021

Refined crystal structure of the triphosphate conformation of H-ras p21 at 1.35 A resolution: implications for the mechanism of GTP hydrolysis

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900610-7

7 January 2021

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

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900610-7

7 January 2021

Structural and biochemical analysis of Ras-effector signaling via RalGDS

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900610-7

7 January 2021

Structural basis for the interaction of Ras with RalGDS

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900610-7

7 January 2021

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

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900610-7

7 January 2021

Ras/Rap effector specificity determined by charge reversal

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900610-7

7 January 2021

Transient Kinetic Studies on the Interaction of Ras and the Ras-Binding Domain of c-Raf-1 Reveal Rapid Equilibration of the Complex†

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900610-7

7 January 2021

Conformational transitions in p21ras and in its complexes with the effector protein Raf-RBD and the GTPase activating protein GAP.

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900610-7

7 January 2021

Interactions between Ras proteins and their effectors

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900610-7

7 January 2021

Purification of a Ras-dependent mitogen-activated protein kinase kinase kinase from bovine brain cytosol and its identification as a complex of B-Raf and 14-3-3 proteins

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900610-7

7 January 2021

Regulation of the Raf kinase by phosphorylation

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900610-7

7 January 2021

Thermodynamics of Ras/effector and Cdc42/effector interactions probed by isothermal titration calorimetry

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900610-7

7 January 2021

Molecular Dynamics on Complexes of ras-p21 and Its Inhibitor Protein, rap-1A, Bound to the ras-Binding Domain of the raf-p74 Protein: Identification of Effector Domains in the raf Protein

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900610-7

7 January 2021

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

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900610-7

7 January 2021

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

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900610-7

7 January 2021

Electrostatic contributions to protein–protein binding affinities: Application to Rap/Raf interaction

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900610-7

7 January 2021

Calculating structures and free energies of complex molecules: combining molecular mechanics and continuum models

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900610-7

7 January 2021

2.1 and 1.8 A average C(alpha) RMSD structure predictions on two small proteins, HP-36 and s15.

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900610-7

7 January 2021

Use of MM-PBSA in reproducing the binding free energies to HIV-1 RT of TIBO derivatives and predicting the binding mode to HIV-1 RT of efavirenz by docking and MM-PBSA.

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900610-7

7 January 2021

Free energy calculations on dimer stability of the HIV protease using molecular dynamics and a continuum solvent model

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900610-7

7 January 2021

Computational alanine scanning of the 1:1 human growth hormone-receptor complex

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900610-7

7 January 2021

Polarization of the nucleic acid bases in aqueous solution

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900610-7

7 January 2021

Nuclear magnetic resonance and molecular dynamics studies on the interactions of the Ras-binding domain of Raf-1 with wild-type and mutant Ras proteins

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900610-7

7 January 2021

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

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900610-7

7 January 2021

Metal Activation of Enzymes in Nucleic Acid Biochemistry

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900610-7

7 January 2021

A fast flexible docking method using an incremental construction algorithm.

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900610-7

7 January 2021

Optimization of binding electrostatics: charge complementarity in the barnase-barstar protein complex.

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900610-7

7 January 2021

On the role of electrostatic interactions in the design of protein-protein interfaces

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900610-7

7 January 2021

Free energy decomposition of protein-protein interactions.

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900610-7

7 January 2021

Empirical scale of side-chain conformational entropy in protein folding

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900610-7

7 January 2021

Entropy calculations on the molten globule state of a protein: Side-chain entropies of α-lactalbumin

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900610-7

7 January 2021

On the magnitude of the electrostatic contribution to ligand-DNA interactions

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900610-7

7 January 2021

Salt effects on ligand-DNA binding. Minor groove binding antibiotics.

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900610-7

7 January 2021

Structural response to mutation at a protein-protein interface

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900610-7

7 January 2021

Dynamic properties of the Ras switch I region and its importance for binding to effectors

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900610-7

7 January 2021

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

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900610-7

7 January 2021

Decomposition of interaction free energies in proteins and other complex systems.

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900610-7

7 January 2021

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

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900610-7

7 January 2021

Binding free energies and free energy components from molecular dynamics and Poisson-Boltzmann calculations. Application to amino acid recognition by aspartyl-tRNA synthetase

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900610-7

7 January 2021

Hidden thermodynamics of mutant proteins: a molecular dynamics analysis

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900610-7

7 January 2021

Electrostatic interactions in the GCN4 leucine zipper: substantial contributions arise from intramolecular interactions enhanced on binding

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900610-7

7 January 2021

Discrimination of Amino Acids Mediating Ras Binding from Noninteracting Residues Affecting Raf Activation by Double Mutant Analysis

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900610-7

7 January 2021

Analysis of protein–protein interactions by mutagenesis: direct versus indirect effects

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900610-7

7 January 2021

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

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900610-7

7 January 2021

Long-range interactions in the dimer interface of ornithine decarboxylase are important for enzyme function

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900610-7

7 January 2021

The propagation of binding interactions to remote sites in proteins: analysis of the binding of the monoclonal antibody D1.3 to lysozyme

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900610-7

7 January 2021

Folding and binding cascades: shifts in energy landscapes

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900610-7

7 January 2021

Wet and dry interfaces: the role of solvent in protein-protein and protein-DNA recognition

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900610-7

7 January 2021

Quantitative analysis of the complex between p21ras and the Ras-binding domain of the human Raf-1 protein kinase

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900610-7

7 January 2021

Pfam 3.1: 1313 multiple alignments and profile HMMs match the majority of proteins

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900610-7

7 January 2021

Protein folding intermediates: native-state hydrogen exchange

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900610-7

7 January 2021

Structure-based calculation of the equilibrium folding pathway of proteins. Correlation with hydrogen exchange protection factors.

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900610-7

7 January 2021

Observation of signal transduction in three-dimensional domain swapping

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900610-7

7 January 2021

Can allosteric regulation be predicted from structure?

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900610-7

7 January 2021

Binding sites in Escherichia coli dihydrofolate reductase communicate by modulating the conformational ensemble

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900610-7

7 January 2021

Enthalpy-entropy compensation and heat capacity changes for protein-ligand interactions: general thermodynamic models and data for the binding of nucleotides to ribonuclease A.

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900610-7

7 January 2021

Global changes in amide hydrogen exchange rates for a protein antigen in complex with three different antibodies.

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900610-7

7 January 2021

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

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900610-7

7 January 2021

Evolutionarily conserved pathways of energetic connectivity in protein families

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900610-7

7 January 2021

A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900610-7

7 January 2021

The Protein Data Bank: a computer-based archival file for macromolecular structures

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900610-7

7 January 2021

Comparison of simple potential functions for simulating liquid water

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900610-7

7 January 2021

Particle mesh Ewald: An N⋅log(N) method for Ewald sums in large systems

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900610-7

7 January 2021

Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900610-7

7 January 2021

Parametrized Models of Aqueous Free Energies of Solvation Based on Pairwise Descreening of Solute Atomic Charges from a Dielectric Medium

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900610-7

7 January 2021

Molecular dynamics study of the energetic, mechanistic, and structural implications of a closed phosphate tube in ncd

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900610-7

7 January 2021

Semianalytical treatment of solvation for molecular mechanics and dynamics

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900610-7

7 January 2021

Self consistent field theory of solvent effects representation by continuum models: Introduction of desolvation contribution

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900610-7

7 January 2021

Approximate atomic surfaces from linear combinations of pairwise overlaps (LCPO)

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900610-7

7 January 2021

For Guldberg and Waage, with love and cratic entropy

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900610-7

7 January 2021

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

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900610-7

7 January 2021

On the calculation of absolute macromolecular binding free energies

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900610-7

7 January 2021

Double-mutant cycles: a powerful tool for analyzing protein structure and function

1 reference

https://api.crossref.org/works/10.1016%2FS0022-2836%2803%2900610-7

7 January 2021

Identifiers

10.1016/S0022-2836(03)00610-7

1 reference

Europe PubMed Central

PubMed publication ID

18 June 2017

PubMed publication ID

1 reference

Europe PubMed Central

PubMed publication ID

18 June 2017

ResearchGate publication ID

0 references

Sitelinks

Wikipedia(0 entries)

Wikibooks(0 entries)

Wikinews(0 entries)

Wikiquote(0 entries)

Wikisource(0 entries)

Wikiversity(0 entries)

Wikivoyage(0 entries)

Wiktionary(0 entries)

Multilingual sites(0 entries)

Retrieved from "https://www.wikidata.org/w/index.php?title=Q30333153&oldid=1990588440"