MDs dataset

The data described here are derived from insights into binding selectivity of inhibitors toward BRD4 and CBP by using MD simulations. The analyses were performed on six systems, including the F3J-BRD4/CBP, EX1-BRD4/CBP, and E2T-BRD4/CBP complexes. There are four folder: Eigenvalue, Porcupine, MSA, and Loop. The Eigenvalue folder includes the data of the eigenvalues against eigenvector indexes obtained from the diagonalization of the covariance matrix constructed by utilizing atomic coordinates saved at MD trajectories of six complexes. The Porcupine folder shows the first six eigenvectors (fort.71-fort.76), the initialized structure of six complexes, and k.txt file. Take fort.71 as an example, the first triple of numbers determine coordinates of the Cα atoms of the residues 53-166 in BRD4 and that of the residues 1083–1196 in CBP. They defined the starting point, and the unit is Å. The second triple of numbers show the motion directions of BRD4 and CBP, and they represent the movement vectors. The MSA folder includes the data of Molecular surface area (MSA) of six systems were calculated by the CPPTRAJ module in AMBER18, each *.dat file gives the MSA of 100,000 conformations, and the number in the second column represents MSA of each conformation, and the unit is the square of Å. The Loop folder indicates the data of the distance between the Cα atoms of Leu92/Leu1120 in the ZA-loop of BRD4/CBP and that of Pro142/Lys1170 in the BC-loop of BRD4/CBP, representing the distance of the ZA-loop away from the BC-loop, each *.dat file gives the distance of 100,000 conformations, and the number in the second column represents distance of the ZA-loop away from the BC-loop in each conformation, and the unit is Å. The two frequency.xlsx files give the data of the frequency distributions of MSA and that of distance, respectively . These data are useful for understanding internal dynamics and conformations of BRD4 and CBP due to inhibitor bindings.

本数据集所描述的内容源自通过分子动力学模拟对BRD4和CBP抑制剂的结合选择性进行深入洞察所得。分析涉及六个系统，包括F3J-BRD4/CBP、EX1-BRD4/CBP和E2T-BRD4/CBP复合物。数据集分为四个文件夹：特征值（Eigenvalue）、刺猬（Porcupine）、分子表面积（MSA）和环（Loop）。特征值文件夹包含了由六个复合物的分子动力学轨迹中保存的原子坐标构建的协方差矩阵的对角化所得的特征值及其对应特征向量索引的数据。刺猬文件夹展示了前六个特征向量（fort.71-fort.76）、六个复合物的初始化结构以及k.txt文件。以fort.71为例，前三个数字确定了BRD4中53-166位残基以及CBP中1083-1196位残基的Cα原子坐标，并以此为起点，单位为埃（Å）。第二组三个数字显示了BRD4和CBP的运动方向，代表运动矢量。分子表面积（MSA）文件夹包含了六个系统的分子表面积数据，由AMBER18中的CPPTRAJ模块计算得出，每个*.dat文件提供了10万个构象的MSA数据，第二列的数字表示每个构象的MSA，单位为埃的平方。环文件夹提供了BRD4/CBP的ZA-loop中Leu92/Leu1120的Cα原子与BC-loop中Pro142/Lys1170的Cα原子之间的距离数据，代表了ZA-loop相对于BC-loop的距离，每个*.dat文件提供了10万个构象的距离数据，第二列的数字表示每个构象中ZA-loop相对于BC-loop的距离，单位为埃。两个frequency.xlsx文件分别给出了MSA和距离的频率分布数据。这些数据有助于理解由于抑制剂结合而导致的BRD4和CBP的内部动力学和构象变化。