Trinucleotide Base Pair Stacking Free Energy for Understanding TF-DNA Recognition and the Functions of SNPs (Q61813242)

2

0 references

Xiaocong Wang

3

0 references

Rong Liu

4

0 references

Lihua Bie

5

0 references

Jun Gao

6

0 references

Hong-Yu Zhang

Creative Commons Attribution 4.0 International

7

0 references

language of work or name

English

0 references

publication date

2018

0 references

published in

Frontiers in Chemistry

0 references

volume

6

0 references

page(s)

666

0 references

copyright license

start time

18 January 2019

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

cites work

Theoretical studies of enzymic reactions: dielectric, electrostatic and steric stabilization of the carbonium ion in the reaction of lysozyme

1 reference

12 December 2020

Sequence-specific recognition of double helical nucleic acids by proteins

1 reference

12 December 2020

Conformational and helicoidal analysis of the molecular dynamics of proteins: "curves," dials and windows for a 50 psec dynamic trajectory of BPTI

1 reference

12 December 2020

DNA conformation and protein binding

1 reference

12 December 2020

Proton magnetic resonance studies of ribose dinucleoside monophosphates in aqueous solution. I. Nature of the base-stacking interaction in adenylyl(3'->5')adenosine

1 reference

12 December 2020

Optical properties of sixteen dinucleoside phosphates

1 reference

12 December 2020

Determinants of repressor/operator recognition from the structure of the trp operator binding site.

1 reference

12 December 2020

A free energy analysis of nucleic acid base stacking in aqueous solution

1 reference

12 December 2020

HOXA9 forms triple complexes with PBX2 and MEIS1 in myeloid cells

1 reference

12 December 2020

Amino acid-base interactions: a three-dimensional analysis of protein-DNA interactions at an atomic level

1 reference

12 December 2020

Electrostatic control of half-site spacing preferences by the cyclic AMP response element-binding protein CREB.

1 reference

12 December 2020

A standard reference frame for the description of nucleic acid base-pair geometry.

1 reference

12 December 2020

Recognition of specific DNA sequences.

1 reference

12 December 2020

Single-Strand Stacking Free Energy from DNA Beacon Kinetics

1 reference

12 December 2020

The thermodynamics of DNA structural motifs

1 reference

12 December 2020

How do site-specific DNA-binding proteins find their targets?

1 reference

12 December 2020

Stacked-unstacked equilibrium at the nick site of DNA

1 reference

12 December 2020

Base-stacking and base-pairing contributions into thermal stability of the DNA double helix

1 reference

12 December 2020

Application of a Theory of Enzyme Specificity to Protein Synthesis

1 reference

12 December 2020

A gene-centered C. elegans protein-DNA interaction network

1 reference

12 December 2020

Statistical mechanical modeling of genome-wide transcription factor occupancy data by MatrixREDUCE.

1 reference

12 December 2020

Indirect readout of DNA sequence by proteins: the roles of DNA sequence-dependent intrinsic and extrinsic forces

1 reference

12 December 2020

Comparison of multiple Amber force fields and development of improved protein backbone parameters

1 reference

12 December 2020

Compact, universal DNA microarrays to comprehensively determine transcription-factor binding site specificities

1 reference

12 December 2020

A multicomponent self-diffusion NMR study of aggregation of nucleotides, nucleosides, nucleic acid bases and some derivatives in aqueous solution with divalent metal ions added

1 reference

12 December 2020

A "silent" polymorphism in the MDR1 gene changes substrate specificity

1 reference

12 December 2020

Role of aromatic amino acids in protein-nucleic acid recognition.

1 reference

12 December 2020

Ligand configurational entropy and protein binding

1 reference

12 December 2020

Distinguishing protein-coding and noncoding genes in the human genome

1 reference

12 December 2020

Stacking interactions and the twist of DNA.

1 reference

12 December 2020

The role of DNA shape in protein-DNA recognition

1 reference

12 December 2020

Origins of specificity in protein-DNA recognition.

1 reference

12 December 2020

Sequence dependence of DNA bending rigidity

1 reference

12 December 2020

Single-molecule derivation of salt dependent base-pair free energies in DNA

1 reference

12 December 2020

Determining the specificity of protein–DNA interactions

1 reference

12 December 2020

Experimental Measurement of Aromatic Stacking Affinities in the Context of Duplex DNA

1 reference

12 December 2020

Application of SNPs for population genetics of nonmodel organisms: new opportunities and challenges

1 reference

12 December 2020

CURVES web server for analyzing and visualizing the helical, backbone and groove parameters of nucleic acid structures

1 reference

12 December 2020

Quantitative analysis demonstrates most transcription factors require only simple models of specificity

1 reference

12 December 2020

GWASdb: a database for human genetic variants identified by genome-wide association studies

1 reference

12 December 2020

Cofactor Binding Evokes Latent Differences in DNA Binding Specificity between Hox Proteins

1 reference

12 December 2020

Improved models for transcription factor binding site identification using nonindependent interactions

1 reference

12 December 2020

Annotation of functional variation in personal genomes using RegulomeDB

1 reference

12 December 2020

Quantum-mechanical analysis of the energetic contributions to π stacking in nucleic acids versus rise, twist, and slide

1 reference

12 December 2020

Evaluation of methods for modeling transcription factor sequence specificity

1 reference

12 December 2020

Genomic regions flanking E-box binding sites influence DNA binding specificity of bHLH transcription factors through DNA shape

1 reference

12 December 2020

DNAshape: a method for the high-throughput prediction of DNA structural features on a genomic scale.

1 reference

12 December 2020

Nature and magnitude of aromatic base stacking in DNA and RNA: Quantum chemistry, molecular mechanics and experiment

1 reference

12 December 2020

Stability selection for regression-based models of transcription factor-DNA binding specificity.

1 reference

12 December 2020

TFBSshape: a motif database for DNA shape features of transcription factor binding sites

1 reference

12 December 2020

A comparative analysis of transcription factor binding models learned from PBM, HT-SELEX and ChIP data

1 reference

12 December 2020

AutoDock4(Zn): an improved AutoDock force field for small-molecule docking to zinc metalloproteins

1 reference

12 December 2020

Absence of a simple code: how transcription factors read the genome

1 reference

12 December 2020

Evolving insights on how cytosine methylation affects protein-DNA binding.

1 reference

12 December 2020

Understanding the structural and dynamic consequences of DNA epigenetic modifications: computational insights into cytosine methylation and hydroxymethylation

1 reference

12 December 2020

Quantitative modeling of transcription factor binding specificities using DNA shape

1 reference

12 December 2020

Human gene-centered transcription factor networks for enhancers and disease variants

1 reference

12 December 2020

DNA Structural Correlation in Short and Long Ranges

1 reference

12 December 2020

IFNL3 mRNA structure is remodeled by a functional non-coding polymorphism associated with hepatitis C virus clearance

1 reference

12 December 2020

DNA-dependent formation of transcription factor pairs alters their binding specificity

1 reference

12 December 2020

Parmbsc1: a refined force field for DNA simulations

1 reference

12 December 2020

Sequence-Dependent Effects in the Cyclization of Short DNA.

1 reference

12 December 2020

1 reference

12 December 2020

Effects of cytosine modifications on DNA flexibility and nucleosome mechanical stability

1 reference

12 December 2020

Free energy analysis and mechanism of base pair stacking in nicked DNA.

1 reference

12 December 2020

Single-molecule dissection of stacking forces in DNA.

1 reference

12 December 2020

Protein-DNA interfaces: a molecular dynamics analysis of time-dependent recognition processes for three transcription factors

1 reference

12 December 2020

A real-time study of the interaction of TBP with a TATA box-containing duplex identical to an ancestral or minor allele of human gene LEP or TPI.

1 reference

12 December 2020

2D-IR Spectroscopy Shows that Optimized DNA Minor Groove Binding of Hoechst33258 Follows an Induced Fit Model.

1 reference

12 December 2020

miRNAs, single nucleotide polymorphisms (SNPs) and age-related macular degeneration (AMD).

1 reference

12 December 2020

DNA partitions into triplets under tension in the presence of organic cations, with sequence evolutionary age predicting the stability of the triplet phase

1 reference

12 December 2020

Comprehensive review and annotation of susceptibility SNPs associated with obesity-related traits

1 reference

12 December 2020