Docking glycosaminoglycans to proteins: analysis of solvent inclusion (Q38335016)

2 September 2017

Docking glycosaminoglycans to proteins: analysis of solvent inclusion (English)

1 reference

2 September 2017

Sergey A Samsonov

1

1 reference

2 September 2017

Joan Teyra

series ordinal

2

1 reference

2 September 2017

M Teresa Pisabarro

series ordinal

3

1 reference

2 September 2017

20 May 2011

1 reference

Journal of Computer - Aided Molecular Design

2 September 2017

1 reference

2 September 2017

25

1 reference

2 September 2017

5

1 reference

2 September 2017

477-489

1 reference

Computational glycoscience: characterizing the spatial and temporal properties of glycans and glycan-protein complexes

2 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3107433

Water in cavity-ligand recognition

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3107433

Regenerative medicine in dermatology: biomaterials, tissue engineering, stem cells, gene transfer and beyond

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3107433

MM-PBSA Captures Key Role of Intercalating Water Molecules at a Protein-Protein Interface

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3107433

Analysis of the impact of solvent on contacts prediction in proteins

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3107433

Antithrombin-binding octasaccharides and role of extensions of the active pentasaccharide sequence in the specificity and strength of interaction. Evidence for very high affinity induced by an unusual glucuronic acid residue

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3107433

Platelet endothelial cell adhesion molecule 1 (PECAM-1) and its interactions with glycosaminoglycans: 1. Molecular modeling studies

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3107433

GLYCAM06: a generalizable biomolecular force field. Carbohydrates

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3107433

Solvated docking: introducing water into the modelling of biomolecular complexes.

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3107433

eHiTS: a new fast, exhaustive flexible ligand docking system

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3107433

Computational approaches to the identification of heparin-binding sites on the surfaces of proteins

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3107433

SCOWLP: a web-based database for detailed characterization and visualization of protein interfaces

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3107433

The specificity of interactions between proteins and sulfated polysaccharides

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3107433

The ternary complex of antithrombin-anhydrothrombin-heparin reveals the basis of inhibitor specificity

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3107433

A structural and dynamic model for the interaction of interleukin-8 and glycosaminoglycans: support from isothermal fluorescence titrations

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3107433

A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3107433

Deducing polymeric structure from aqueous molecular dynamics simulations of oligosaccharides: predictions from simulations of hyaluronan tetrasaccharides compared with hydrodynamic and X-ray fibre diffraction data

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3107433

Identification of a glycosaminoglycan binding surface on human interleukin-8.

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3107433

Binding of human phospholipase A2 type II to proteoglycans. Differential effect of glycosaminoglycans on enzyme activity

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3107433

Heparin structure and interactions with basic fibroblast growth factor

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3107433

A computational procedure for determining energetically favorable binding sites on biologically important macromolecules

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3107433

Glycosaminoglycans: molecular properties, protein interactions, and role in physiological processes

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3107433

Glycosaminoglycans as potential regulators of osteoprotegerin therapeutic activity in osteosarcoma

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3107433

Conformational changes mediate interleukin-10 receptor 2 (IL-10R2) binding to IL-10 and assembly of the signaling complex

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3107433

Less is more when simulating unsulfated glycosaminoglycan 3D-structure: comparison of GLYCAM06/TIP3P, PM3-CARB1/TIP3P, and SCC-DFTB-D/TIP3P predictions with experiment

23 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3107433

Water and trehalose: how much do they interact with each other?

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3107433

Ligand-protein cross-docking with water molecules

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3107433

Modifications of hyaluronan influence the interaction with human bone morphogenetic protein-4 (hBMP-4).

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3107433

BALLDock/SLICK: a new method for protein-carbohydrate docking.

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3107433

A molecular dynamics approach to study the importance of solvent in protein interactions

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3107433

Protein-protein recognition and interaction hot spots in an antigen-antibody complex: free energy decomposition identifies "efficient amino acids".

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3107433

Predicting the molecular shape of polysaccharides from dynamic interactions with water

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3107433

Analysis and prediction of carbohydrate binding sites

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3107433

Molecular dynamics simulations of the two disaccharides of hyaluronan in aqueous solution.

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3107433

A fast flexible docking method using an incremental construction algorithm.

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3107433

SLICK − Scoring and Energy Functions for Protein−Carbohydrate Interactions

31 August 2018

1 reference

Crossref

https://api.crossref.org/works/10.1007%2FS10822-011-9433-1

Docking of Glycosaminoglycans to Heparin-Binding Proteins: Validation for aFGF, bFGF, and Antithrombin and Application to IL-8

21 January 2018

1 reference

Crossref

https://api.crossref.org/works/10.1007%2FS10822-011-9433-1

Heparin and heparan sulfate bind interleukin-10 and modulate its activity

21 January 2018

1 reference

12 December 2020

Ligand-protein docking with water molecules

1 reference

12 December 2020

Molecular Docking of Carbohydrate Ligands to Antibodies: Structural Validation against Crystal Structures

1 reference

12 December 2020

Characterization of interfacial solvent in protein complexes and contribution of wet spots to the interface description

1 reference

12 December 2020

The activation of fibroblast growth factors (FGFs) by glycosaminoglycans: influence of the sulfation pattern on the biological activity of FGF-1

1 reference

12 December 2020

Glycosaminoglycan conformation: do aqueous molecular dynamics simulations agree with x-ray fiber diffraction?

1 reference

12 December 2020

10.1007/S10822-011-9433-1

Identifiers

DOI

1 reference

journals/jcamd/SamsonovTP11

2 September 2017

1 reference

DBLP Dataset 2021-01-02

28 January 2021

1 reference

2 September 2017

PubMed publication ID

21597992

1 reference