| scholarly article | Q13442814 |
| P2093 | author name string | Sangdun Choi | |
| Muhammad Ayaz Anwar | |||
| Han-Kyul Kim | |||
| Dhanusha Yesudhas | |||
| Suresh Panneerselvam | |||
| P2860 | cites work | Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project | Q21061203 |
| Nonequilibrium Equality for Free Energy Differences | Q21698763 | ||
| Canonical dynamics: Equilibrium phase-space distributions | Q21709091 | ||
| Base-stacking and base-pairing contributions into thermal stability of the DNA double helix | Q22065979 | ||
| An RNA gene expressed during cortical development evolved rapidly in humans | Q22122233 | ||
| Core transcriptional regulatory circuitry in human embryonic stem cells | Q24322016 | ||
| Computational prediction of transcription-factor binding site locations | Q24568149 | ||
| Improved side-chain torsion potentials for the Amber ff99SB protein force field | Q24616749 | ||
| Molecular basis for the genome engagement by Sox proteins | Q26741572 | ||
| Solution structure of the HMG protein NHP6A and its interaction with DNA reveals the structural determinants for non-sequence-specific binding | Q27618091 | ||
| Solvent mediated interactions in the structure of the nucleosome core particle at 1.9 a resolution | Q27639217 | ||
| EMBOSS: the European Molecular Biology Open Software Suite | Q27860491 | ||
| Pairing SOX off: with partners in the regulation of embryonic development | Q28139502 | ||
| Stacked-unstacked equilibrium at the nick site of DNA | Q28280129 | ||
| Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project | Q28301622 | ||
| Structural Mechanism behind Distinct Efficiency of Oct4/Sox2 Proteins in Differentially Spaced DNA Complexes | Q28552687 | ||
| The transcription factor encyclopedia | Q28727892 | ||
| DNA-binding specificities of human transcription factors | Q28854562 | ||
| Mapping and analysis of chromatin state dynamics in nine human cell types | Q29547552 | ||
| GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit | Q29615867 | ||
| Diversity and complexity in DNA recognition by transcription factors | Q29619632 | ||
| JASPAR 2014: an extensively expanded and updated open-access database of transcription factor binding profiles | Q30486475 | ||
| DNA Basepair Step Deformability Inferred from Molecular Dynamics Simulations | Q34183456 | ||
| Hydrogen bonding, base stacking, and steric effects in dna replication | Q34243200 | ||
| Zinc finger phage: affinity selection of fingers with new DNA-binding specificities | Q34349299 | ||
| Discovery of novel transcription factor binding sites by statistical overrepresentation | Q34446050 | ||
| MINT: software to identify motifs and short-range interactions in trajectories of nucleic acids | Q34478538 | ||
| SOX2 co-occupies distal enhancer elements with distinct POU factors in ESCs and NPCs to specify cell state | Q34597982 | ||
| Combinatorial regulation of endothelial gene expression by ets and forkhead transcription factors | Q34900031 | ||
| Additivity in protein-DNA interactions: how good an approximation is it? | Q34971620 | ||
| Convergence and error estimation in free energy calculations using the weighted histogram analysis method | Q35734759 | ||
| The role of water in protein-DNA recognition | Q35771586 | ||
| Origins of specificity in protein-DNA recognition. | Q35774615 | ||
| Calculating potentials of mean force from steered molecular dynamics simulations | Q35842453 | ||
| Protein-DNA recognition patterns and predictions. | Q36115484 | ||
| Oct4 switches partnering from Sox2 to Sox17 to reinterpret the enhancer code and specify endoderm | Q36739541 | ||
| From "simple" DNA-protein interactions to the macromolecular machines of gene expression | Q36810334 | ||
| DNA base repair--recognition and initiation of catalysis | Q37573870 | ||
| Sox proteins: regulators of cell fate specification and differentiation | Q38148534 | ||
| Transcriptional enhancers: from properties to genome-wide predictions | Q38194866 | ||
| Recent applications of boxed molecular dynamics: a simple multiscale technique for atomistic simulations. | Q38225090 | ||
| Predicting the effects of basepair mutations in DNA-protein complexes by thermodynamic integration. | Q38272815 | ||
| Molecular Modeling of Cetylpyridinium Bromide, a Cationic Surfactant, in Solutions and Micelle. | Q40315610 | ||
| Specificity, free energy and information content in protein-DNA interactions | Q40859873 | ||
| Assessing the stability of Alzheimer's amyloid protofibrils using molecular dynamics | Q43200637 | ||
| Structural basis for the SOX-dependent genomic redistribution of OCT4 in stem cell differentiation. | Q44419770 | ||
| Molecular dynamics - potential of mean force calculations as a tool for understanding ion permeation and selectivity in narrow channels | Q46357860 | ||
| Free energy profile and mechanism of self-assembly of peptide amphiphiles based on a collective assembly coordinate | Q46380134 | ||
| Good practices in free-energy calculations | Q46484190 | ||
| Protein-DNA interactions: amino acid conservation and the effects of mutations on binding specificity | Q47615859 | ||
| A structure-based approach for prediction of protein binding sites in gene upstream regions | Q47619130 | ||
| Defining the thermodynamics of protein/DNA complexes and their components using micro-calorimetry | Q47981501 | ||
| THE weighted histogram analysis method for free-energy calculations on biomolecules. I. The method | Q56157177 | ||
| Structure-based design of transcription factors | Q72380123 | ||
| EMBOSS opens up sequence analysis. European Molecular Biology Open Software Suite | Q74059193 | ||
| Short EMBOSS User Guide. European Molecular Biology Open Software Suite | Q74059197 | ||
| A free energy pathway for the interaction of the SRY protein with its binding site on DNA from atomistic simulations | Q84180944 | ||
| P433 | issue | 11 | |
| P304 | page(s) | 1750-1767 | |
| P577 | publication date | 2017-10-09 | |
| P1433 | published in | FEBS Open Bio | Q27724062 |
| P1476 | title | Evaluation of Sox2 binding affinities for distinct DNA patterns using steered molecular dynamics simulation | |
| P478 | volume | 7 |
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