Molecular mechanisms of the protein-protein interaction–regulated binding specificity of basic-region leucine zipper transcription factors

Relative Ligand-Binding Free Energies Calculated from Multiple Short QM/MM MD Simulations

(2018) Casper Steinmann et al.   Journal of Chemical Theory and Computation

How a single 5-methylation of cytosine regulates the recognition of C/EBPβ transcription factor: a molecular dynamic simulation study

(2018) Lihua Bie et al.   JOURNAL OF MOLECULAR MODELING

The MM/PBSA and MM/GBSA methods to estimate ligand-binding affinities

(2015) Samuel Genheden et al.   Expert Opinion on Drug Discovery

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

(2015) Arttu Jolma et al.   NATURE

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

(2015) Felipe Merino et al.   PLoS Computational Biology

Data-Driven Prediction and Design of bZIP Coiled-Coil Interactions

(2015) Vladimir Potapov et al.   PLoS Computational Biology

A survey on prediction of specificity-determining sites in proteins

(2014) A. Chakraborty et al.   BRIEFINGS IN BIOINFORMATICS

Single-Molecule Dynamics of Enhanceosome Assembly in Embryonic Stem Cells

(2014) Jiji Chen et al.   CELL

Looping Back to Leap Forward: Transcription Enters a New Era

(2014) Michael Levine et al.   CELL

Assessing the performance of MM/PBSA and MM/GBSA methods. 5. Improved docking performance using high solute dielectric constant MM/GBSA and MM/PBSA rescoring

(2014) Huiyong Sun et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Design of a bZip Transcription Factor with Homo/Heterodimer-Induced DNA-Binding Preference

(2014) Vivian Pogenberg et al.   STRUCTURE

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

(2014) Matthew Slattery et al.   TRENDS IN BIOCHEMICAL SCIENCES

MEGA6: Molecular Evolutionary Genetics Analysis Version 6.0

(2013) Koichiro Tamura et al.   MOLECULAR BIOLOGY AND EVOLUTION

Networks of bZIP Protein-Protein Interactions Diversified Over a Billion Years of Evolution

(2013) A. W. Reinke et al.   SCIENCE

MMPBSA.py: An Efficient Program for End-State Free Energy Calculations

(2012) Bill R. Miller et al.   Journal of Chemical Theory and Computation

The Role of Methylation in the Intrinsic Dynamics of B- and Z-DNA

(2012) Nuri A. Temiz et al.   PLoS One

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

(2011) Matthew Slattery et al.   CELL

Assessing the Performance of the MM/PBSA and MM/GBSA Methods. 1. The Accuracy of Binding Free Energy Calculations Based on Molecular Dynamics Simulations

(2010) Tingjun Hou et al.   Journal of Chemical Information and Modeling

Combining specificity determining and conserved residues improves functional site prediction

(2009) Olga V Kalinina et al.   BMC BIOINFORMATICS

Structural Basis of Alternative DNA Recognition by Maf Transcription Factors

(2009) H. Kurokawa et al.   MOLECULAR AND CELLULAR BIOLOGY

ProteDNA: a sequence-based predictor of sequence-specific DNA-binding residues in transcription factors

(2009) Wen-Yi Chu et al.   NUCLEIC ACIDS RESEARCH