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binding affinity

A linear model for transcription factor binding affinity prediction in protein binding microarrays.

A linear model for transcription factor binding affinity prediction in protein binding microarrays.

... from binding-enriched unaligned sequenc- ...quantitative binding affinity measurements: The MDScan algorithm takes a list of DNA sequences ranked according to their expected motif enrichment, and ...

13

Inference of binding affinity from neuronal receptors in humans

Inference of binding affinity from neuronal receptors in humans

... For this work, a database was created using different types of data sources with binding affinity values. Three machine learning methods, Random Forests, support vector machines and LASSO were used to build ...

62

Structural Determinants for the Binding of Morphinan Agonists to the μ-Opioid Receptor.

Structural Determinants for the Binding of Morphinan Agonists to the μ-Opioid Receptor.

... complexes. In particular, the H-bond pattern emerged from both forward and reverse alchemi- cal transformations is consistent with that in the standard MD simulations, i.e. water-mediated H-bonds between HMP and H297, ...

15

PARP-1 and YY1 are important novel regulators of CXCL12 gene transcription in rat pancreatic beta cells.

PARP-1 and YY1 are important novel regulators of CXCL12 gene transcription in rat pancreatic beta cells.

... YY1 binding affinity toward the Cxcl12 ...PARP-1 binding exclusively to DNA-internal ...YY1 binding was verified for each Cxcl12 promoter fragment; fragment 1 is 246 bp; fragment 2 is 265 bp; ...

15

Structure-based stabilization of HIV-1 gp120 enhances humoral immune responses to the induced co-receptor binding site.

Structure-based stabilization of HIV-1 gp120 enhances humoral immune responses to the induced co-receptor binding site.

... high affinity even in the absence of CD4, and that CD4 binding affinity of this protein was markedly ...(CD4 binding site, see Figure ...17b binding, this suggests that CD4 can ...

15

Search for β2 adrenergic receptor ligands by virtual screening via grid computing and investigation of binding modes by docking and molecular dynamics simulations.

Search for β2 adrenergic receptor ligands by virtual screening via grid computing and investigation of binding modes by docking and molecular dynamics simulations.

... The MolGridCal program was designed by using grid computing based on the framework of JPPF. MolGridCal could package small molecule database, IP address of FTP server, docking program and corresponding folder ...

10

Med5(Nut1) and Med17(Srb4) are direct targets of mediator histone H4 tail interactions.

Med5(Nut1) and Med17(Srb4) are direct targets of mediator histone H4 tail interactions.

... tail binding affinity of this mutant ...of affinity-purified rgr1(Med14)-D2 and WT Mediator complexes after 10% ...tail binding experiment comparing the H4 tail binding affinity ...

11

The ticket to transport.

The ticket to transport.

... relative binding affinity of the three regions varies from one PY-NLS to another: mutations in some regions in some PY-NLSs substantially affected binding, while others had little if any effect on ...

1

ZNF675 evolutionary history and its novel role in neuronal regulatory networks

ZNF675 evolutionary history and its novel role in neuronal regulatory networks

... by binding to the internal part of the ...have affinity for these elements when they were active, a new ZNF675 arose in order to silence ...the binding affinity may have not been strong ...

74

Viral reverse transcriptases show selective high affinity binding to DNA-DNA primer-templates that resemble the polypurine tract.

Viral reverse transcriptases show selective high affinity binding to DNA-DNA primer-templates that resemble the polypurine tract.

... duplexes binding with high affinity to HIV reverse transcriptase (RT) showed that primers mimicking the 39 end, and in particular the six nt terminal G tract, of the RNA polypurine tract (PPT; HIV PPT: ...

10

Cooperative DNA Recognition Modulated by an Interplay between Protein-Protein Interactions and DNA-Mediated Allostery.

Cooperative DNA Recognition Modulated by an Interplay between Protein-Protein Interactions and DNA-Mediated Allostery.

... fluence their relative contribution to the binding affinity [17,18]. In addition, ChIP experi- ments suggest that OCT4 binds to DNA alone during the initial stages of reprogramming to pluripotency [19]. ...

23

FINDING NEW INHIBITORS FOR EML4-ALK FUSION PROTEIN:  A COMPUTATIONAL APPROACH

FINDING NEW INHIBITORS FOR EML4-ALK FUSION PROTEIN: A COMPUTATIONAL APPROACH

... shows binding affinity of active inhibitors for the EML4-ALK, downloaded from ligand database to characterize interaction features using GLIDE (Schrodinger) and to interpret inhibition mechanism of small ...

6

RESUMO.- [Características de ligação da insulina no tecido muscular canino: efeitos da fase do ciclo es- tral.] As flutuações hormonais durante as diferentes fases

RESUMO.- [Características de ligação da insulina no tecido muscular canino: efeitos da fase do ciclo es- tral.] As flutuações hormonais durante as diferentes fases

... insulin binding sites - high-affinity and low-affinity ones - were detected by Scatchard analysis, and signifi- cant statistical differences were observed in the dissociation constant (Kd1) and ...

6

Maximum-Entropy Models of Sequenced Immune Repertoires Predict Antigen-Antibody Affinity.

Maximum-Entropy Models of Sequenced Immune Repertoires Predict Antigen-Antibody Affinity.

... the affinity maturation process by applying a MaxEnt inference techniques originally developed for the analysis of homologous protein fam- ...of binding affinity for the target antibody related to ...

20

Functional analysis of genetic variants associated  with risk for breast cancer: 12q24, a candidate risk locus

Functional analysis of genetic variants associated with risk for breast cancer: 12q24, a candidate risk locus

... the binding affinity of transcription ...post-transcriptional binding to their target site (frequently in the 3’UTR of mRNA sequence), affecting the translation and the mRNA stability (Liu et ...

96

J. Braz. Chem. Soc.  vol.27 número9

J. Braz. Chem. Soc. vol.27 número9

... higher binding affinity to PPARα than tesaglitazar (PDB1I7I), a known agonist of this subtype, but candidate 7 showed lower affinity (Figure 6 and Supplementary Information section, see Table ...

12

J. Braz. Chem. Soc.  vol.13 número6

J. Braz. Chem. Soc. vol.13 número6

... the binding site it does not matter whether a certain acceptor atom of the ligand is either nitrogen or ...reduces binding affinity but a significant enhancement of affinity is observed for ...

10

CENTRO DE CIÊNCIAS EXATAS E DE TECNOLOGIA DEPARTAMENTO DE QUÍMICA PROGRAMA DE PÓS-GRADUAÇÃO EM QUÍMICA

CENTRO DE CIÊNCIAS EXATAS E DE TECNOLOGIA DEPARTAMENTO DE QUÍMICA PROGRAMA DE PÓS-GRADUAÇÃO EM QUÍMICA

... resolved experiments (spectroscopy) of ligand-protein systems. The absorbance of the UV light in protein depends upon some factors like, presence of chromophores, by the process of oxidation, by ligations and different ...

249

Global analysis of small molecule binding to related protein targets.

Global analysis of small molecule binding to related protein targets.

... the binding site, as molecules of greater size rely on a larger number of interactions with the target protein ...ligand binding between paralogs in terms of molecular size (approximat- ed here by molecular ...

9

Characterization of the p53 cistrome--DNA binding cooperativity dissects p53's tumor suppressor functions.

Characterization of the p53 cistrome--DNA binding cooperativity dissects p53's tumor suppressor functions.

... DNA binding cooperativity that slightly exceeds that of the wild-type (wt) ...p53 binding peaks were called applying a stringent false discovery rate (FDR) of 10 25 ...EE binding sites and additional ...

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