Evaluation of Sox2 binding affinities for distinct DNA patterns using steered molecular dynamics simulation

Molecular basis for the genome engagement by Sox proteins

(2017) Linlin Hou et al.   SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY

Structural and conformational insights into SOX2/OCT4-bound enhancer DNA: a computational perspective

(2016) Muhammad Ayaz Anwar et al.   RSC Advances

Structural Mechanism behind Distinct Efficiency of Oct4/Sox2 Proteins in Differentially Spaced DNA Complexes

(2016) Dhanusha Yesudhas et al.   PLoS One

Molecular Modeling of Cetylpyridinium Bromide, a Cationic Surfactant, in Solutions and Micelle

(2015) Rajni Verma et al.   Journal of Chemical Theory and Computation

MINT: software to identify motifs and short-range interactions in trajectories of nucleic acids

(2015) Anna Górska et al.   NUCLEIC ACIDS RESEARCH

Transcriptional enhancers: from properties to genome-wide predictions

(2014) Daria Shlyueva et al.   NATURE REVIEWS GENETICS

Recent applications of boxed molecular dynamics: a simple multiscale technique for atomistic simulations

(2014) J. Booth et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY A-MATHEMATICAL PHYSICAL AND ENGINEERING SCIENCES

Structural Basis for the SOX-Dependent Genomic Redistribution of OCT4 in Stem Cell Differentiation

(2014) Felipe Merino et al.   STRUCTURE

GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit

(2013) Sander Pronk et al.   BIOINFORMATICS

DNA-Binding Specificities of Human Transcription Factors

(2013) Arttu Jolma et al.   CELL

Sox proteins: regulators of cell fate specification and differentiation

(2013) Y. Kamachi et al.   DEVELOPMENT

Oct4 switches partnering from Sox2 to Sox17 to reinterpret the enhancer code and specify endoderm

(2013) Irene Aksoy et al.   EMBO JOURNAL

Free Energy Profile and Mechanism of Self-Assembly of Peptide Amphiphiles Based on a Collective Assembly Coordinate

(2013) Tao Yu et al.   JOURNAL OF PHYSICAL CHEMISTRY B

JASPAR 2014: an extensively expanded and updated open-access database of transcription factor binding profiles

(2013) Anthony Mathelier et al.   NUCLEIC ACIDS RESEARCH

SOX2 Co-Occupies Distal Enhancer Elements with Distinct POU Factors in ESCs and NPCs to Specify Cell State

(2013) Michael A. Lodato et al.   PLoS Genetics

The Transcription Factor Encyclopedia

(2012) Dimas Yusuf et al.   GENOME BIOLOGY

Predicting the Effects of Basepair Mutations in DNA-Protein Complexes by Thermodynamic Integration

(2011) Frank R. Beierlein et al.   BIOPHYSICAL JOURNAL

Convergence and error estimation in free energy calculations using the weighted histogram analysis method

(2011) Fangqiang Zhu et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Mapping and analysis of chromatin state dynamics in nine human cell types

(2011) Jason Ernst et al.   NATURE

Origins of Specificity in Protein-DNA Recognition

(2010) Remo Rohs et al.   Annual Review of Biochemistry

Good Practices in Free-Energy Calculations

(2010) Andrew Pohorille et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Assessing the Stability of Alzheimer’s Amyloid Protofibrils Using Molecular Dynamics

(2010) Justin A. Lemkul et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Integrative Analysis of the Caenorhabditis elegans Genome by the modENCODE Project

(2010) M. B. Gerstein et al.   SCIENCE

A Free Energy Pathway for the Interaction of the SRY Protein with Its Binding Site on DNA from Atomistic Simulations

(2009) Benjamin Bouvier et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Diversity and Complexity in DNA Recognition by Transcription Factors

(2009) G. Badis et al.   SCIENCE

Combinatorial Regulation of Endothelial Gene Expression by Ets and Forkhead Transcription Factors

(2008) Sarah De Val et al.   CELL