(Q33246009)

English

Finding a needle in a haystack: development of a combinatorial virtual screening approach for identifying high specificity heparin/heparan sulfate sequence(s).

scientific article

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scholarly article

1 reference

Europe PubMed Central

PubMed publication ID

24 July 2017

Finding a needle in a haystack: development of a combinatorial virtual screening approach for identifying high specificity heparin/heparan sulfate sequence(s). (English)

1 reference

Europe PubMed Central

PubMed publication ID

24 July 2017

virtual screening

1 reference

based on heuristic

inferred from title

author name string

Arjun Raghuraman

1

1 reference

Europe PubMed Central

PubMed publication ID

24 July 2017

Philip D Mosier

2

1 reference

Europe PubMed Central

PubMed publication ID

24 July 2017

Umesh R Desai

3

1 reference

Europe PubMed Central

PubMed publication ID

24 July 2017

language of work or name

0 references

publication date

1 June 2006

1 reference

Europe PubMed Central

PubMed publication ID

24 July 2017

Journal of Medicinal Chemistry

1 reference

Europe PubMed Central

PubMed publication ID

24 July 2017

49

1 reference

Europe PubMed Central

PubMed publication ID

24 July 2017

12

1 reference

Europe PubMed Central

PubMed publication ID

24 July 2017

3553-3562

1 reference

Europe PubMed Central

PubMed publication ID

24 July 2017

Control of the coagulation system by serpins. Getting by with a little help from glycosaminoglycans

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2516555

21 June 2018

Importance of tryptophan 49 of antithrombin in heparin binding and conformational activation.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2516555

21 June 2018

Heparan sulfate: a complex polymer charged with biological activity

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2516555

21 June 2018

Fibroblast growth factor/fibroblast growth factor receptor system in angiogenesis

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2516555

21 June 2018

The pathophysiology of heparin-induced thrombocytopenia: biological basis for treatment

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2516555

21 June 2018

Docking and scoring in virtual screening for drug discovery: methods and applications

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2516555

21 June 2018

Structure of the antithrombin-thrombin-heparin ternary complex reveals the antithrombotic mechanism of heparin.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2516555

21 June 2018

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2516555

21 June 2018

Structural analysis of the sulfotransferase (3-o-sulfotransferase isoform 3) involved in the biosynthesis of an entry receptor for herpes simplex virus 1

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2516555

21 June 2018

Heparan sulfate proteoglycans in glomerular inflammation.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2516555

21 June 2018

New antithrombin-based anticoagulants

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2516555

21 June 2018

Improved protein-ligand docking using GOLD

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2516555

21 June 2018

Crystal structure of antithrombin in a heparin-bound intermediate state

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2516555

21 June 2018

Heparin-protein interactions

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2516555

21 June 2018

Serpin structure, mechanism, and function

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2516555

21 June 2018

Heparan sulfate fine structure and specificity of proteoglycan functions

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2516555

21 June 2018

Specificity of the basic side chains of Lys114, Lys125, and Arg129 of antithrombin in heparin binding.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2516555

21 June 2018

Interaction of designed sulfated flavanoids with antithrombin: lessons on the design of organic activators.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2516555

21 June 2018

Heparin and heparan sulfate: structure and function

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2516555

21 June 2018

Roles of heparan-sulphate glycosaminoglycans in cancer

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2516555

21 June 2018

Characterization of a heparan sulfate octasaccharide that binds to herpes simplex virus type 1 glycoprotein D.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2516555

21 June 2018

Order out of chaos: assembly of ligand binding sites in heparan sulfate

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2516555

21 June 2018

Designing small, nonsugar activators of antithrombin using hydropathic interaction analyses.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2516555

21 June 2018

Cell surface heparan sulfate and its roles in assisting viral infections

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2516555

21 June 2018

Conformation of heparin pentasaccharide bound to antithrombin III

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2516555

21 June 2018

Lysine 114 of antithrombin is of crucial importance for the affinity and kinetics of heparin pentasaccharide binding

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2516555

21 June 2018

Annexin V--heparin oligosaccharide complex suggests heparan sulfate--mediated assembly on cell surfaces

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2516555

21 June 2018

Conformation and dynamics of heparin and heparan sulfate

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2516555

21 June 2018

Crystal structure of fibroblast growth factor receptor ectodomain bound to ligand and heparin

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2516555

21 June 2018

Crystal structure of a ternary FGF-FGFR-heparin complex reveals a dual role for heparin in FGFR binding and dimerization

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2516555

21 June 2018

The effect of a reducing-end extension on pentasaccharide binding by antithrombin

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2516555

21 June 2018

A novel role for 3-O-sulfated heparan sulfate in herpes simplex virus 1 entry

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2516555

21 June 2018

Mechanism of heparin activation of antithrombin: evidence for an induced-fit model of allosteric activation involving two interaction subsites

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2516555

21 June 2018

Mechanism of heparin activation of antithrombin. Role of individual residues of the pentasaccharide activating sequence in the recognition of native and activated states of antithrombin.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2516555

21 June 2018

The anticoagulant activation of antithrombin by heparin

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2516555

21 June 2018

NMR solution conformation of heparin-derived hexasaccharide

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2516555

21 June 2018

Development and validation of a genetic algorithm for flexible docking

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2516555

21 June 2018

Heparin structure and interactions with basic fibroblast growth factor

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2516555

21 June 2018

Comparative analysis of structurally defined heparin binding sequences reveals a distinct spatial distribution of basic residues.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2516555

21 June 2018

Mode of interaction between platelet factor 4 and heparin

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2516555

21 June 2018

N.m.r. and molecular-modelling studies of the solution conformation of heparin

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2516555

21 June 2018

Sequence variation in heparin octasaccharides with high affinity for antithrombin III.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2516555

21 June 2018

Extension and structural variability of the antithrombin-binding sequence in heparin.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2516555

21 June 2018

Molecular modeling of protein-glycosaminoglycan interactions.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2516555

21 June 2018

Conformation of the pentasaccharide corresponding to the binding site of heparin for antithrombin III.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2516555

21 June 2018

Conformer populations of L-iduronic acid residues in glycosaminoglycan sequences

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2516555

21 June 2018

Quantitative characterization of the thrombin-heparin interaction. Discrimination between specific and nonspecific binding models

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2516555

21 June 2018

Crystal structure of thrombin bound to heparin

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2516555

31 October 2018

The X-ray structure of RANTES: heparin-derived disaccharides allows the rational design of chemokine inhibitors.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2516555

31 October 2018

Hydropathic interaction analyses of small organic activators binding to antithrombin

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2516555

31 October 2018

Lessons in molecular recognition: the effects of ligand and protein flexibility on molecular docking accuracy.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2516555

31 October 2018

Importance of lysine 125 for heparin binding and activation of antithrombin.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2516555

31 October 2018

Glycosaminoglycan-protein interactions: definition of consensus sites in glycosaminoglycan binding proteins

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2516555

31 October 2018

Energetic characterization of the basic fibroblast growth factor-heparin interaction: identification of the heparin binding domain

1 reference

https://pubmed.ncbi.nlm.nih.gov/16759098

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

The effect of variation of substitution on the solution conformation of heparin: a spectroscopic and molecular modelling study

1 reference

https://pubmed.ncbi.nlm.nih.gov/16759098

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Role of arginine 129 in heparin binding and activation of antithrombin

1 reference

https://pubmed.ncbi.nlm.nih.gov/16759098

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Direct isolation and sequencing of specific protein-binding glycosaminoglycans

1 reference

https://pubmed.ncbi.nlm.nih.gov/16759098

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Accelerating ability of synthetic oligosaccharides on antithrombin inhibition of proteinases of the clotting and fibrinolytic systems. Comparison with heparin and low-molecular-weight heparin

1 reference

https://pubmed.ncbi.nlm.nih.gov/16759098

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Assessment of Docking Poses: Interactions-Based Accuracy Classification (IBAC) versus Crystal Structure Deviations

1 reference

https://pubmed.ncbi.nlm.nih.gov/16759098

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Crystalline Structure of Heparin

1 reference

https://pubmed.ncbi.nlm.nih.gov/16759098

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Identifiers

10.1021/JM060092O

1 reference

Europe PubMed Central

PubMed publication ID

24 July 2017

PMC publication ID

1 reference

Europe PubMed Central

PubMed publication ID

24 July 2017

PubMed publication ID

1 reference

Europe PubMed Central

PubMed publication ID

24 July 2017

ResearchGate publication ID

0 references

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