Restriction of access to the central cavity is a major contributor to substrate selectivity in plant ABCG transporters
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The input and main output files used for the paper "Restriction of access to the central cavity is a major contributor to substrate selectivity in plant ABCG transporters" are separated in the different tar files depending the MD stage they belong to. Content 00_AlphaFold2: The models predicted from AlphaFold2 01_build_system: The parameters for ATP and the initial pdb file used to build each system 02_minimization: Minimization input files for each variant 03_equilibration: Equilibration input files for each variant 04_long_equilibration: ATP restrained equilibration input files for each variant 05_free_equilibration: Free equilibration input files for each variant 06_production: Free production input files for each variant 07_caver: Caver calculations for each variant and replica 08_transport_tools: Analysis of tunnel networks using TransportTools software 09_tunnel_selection: Selection of the tunnels with widest bottleneck radius to perform CaverDock experiments 10_caverdock: CaverDock calculations for each variant and for each ligand tested 11_membrane_patch: MD simulations for liquiritigenin and POPC membrane only 12_MD_analysis: Calculations of RMSD, RMSF of each system. Calculation of helical parameters for trans-membrane helices 2, 5, 8 and 11 (not for APO). Calculation of X1 and X2 angles for residue N1331 in each variant (not for APO) 13_US_closed_to_open: Umbrella Sampling simulations to obtain the inward facing (IF) open state of each variant. Not used for PMF analysis. 14_US_opening_energy: Umbrella Sampling simulations to obtain the Potential of Mean Force for the transition from IF-closed to IF-open conformations. 15_US_equilibration: Equilibration input files for WT and F562L variants in IF-open states. 16_US_production: Production input files for WT and F562L variants in IF-open states. 17_US_caver: Caver calculations for WT and F562L variants in IF-open states. 18_US_transport_tools: Analysis of tunnel networks using TransportTools software of WT and F562L variants in IF-open states. 19_US_tunnel_selection: Selection of the tunnels with widest bottleneck radius to perform CaverDock experiments for WT and F562L variants in IF-open states. 20_US_caverdock: CaverDock calculations for WT and F562L variants in IF-open states. 21_US_MD_analysis: Calculations of RMSD, RMSF of each system. Calculation of helical parameters for trans-membrane helices 2, 5, 8 and 11. ABC_Sequences.fasta: Sequences from 1KP analysis
本论文《中央腔体通路受限是植物ABCG转运蛋白底物选择性的核心驱动因素》所使用的输入文件与主输出文件，将根据其所属的分子动力学（Molecular Dynamics, MD）阶段，被归类至不同的tar压缩包文件中。 00_AlphaFold2：由AlphaFold2预测得到的模型文件 01_build_system：用于构建各实验体系的三磷酸腺苷（ATP）参数与初始pdb文件 02_minimization：各突变体的能量最小化输入文件 03_equilibration：各突变体的平衡模拟输入文件 04_long_equilibration：各突变体的ATP约束平衡模拟输入文件 05_free_equilibration：各突变体的无约束平衡模拟输入文件 06_production：各突变体的生产模拟输入文件 07_caver：各突变体与复本的Caver计算结果文件 08_transport_tools：采用TransportTools软件对各体系的隧道网络开展的分析结果 09_tunnel_selection：筛选瓶颈半径最大的隧道，以开展CaverDock实验的相关文件 10_caverdock：各突变体与所有测试配体的CaverDock计算结果文件 11_membrane_patch：仅针对甘草素与POPC膜的MD模拟文件 12_MD_analysis：各体系的均方根偏差（RMSD）、均方根波动（RMSF）计算；跨膜螺旋2、5、8及11的螺旋参数计算（不包含apo状态的相关数据）；各突变体中残基N1331的X1与X2二面角计算（不包含apo状态的相关数据） 13_US_closed_to_open：用于获取各突变体内向开放（IF-open）构象的伞形采样（Umbrella Sampling, US）模拟文件，该数据集未用于势能均值函数（Potential of Mean Force, PMF）分析 14_US_opening_energy：用于获取内向闭合（IF-closed）向内开放（IF-open）构象转变的势能均值函数的伞形采样模拟文件 15_US_equilibration：针对内向开放构象下的野生型（WT）与F562L突变体的平衡模拟输入文件 16_US_production：针对内向开放构象下的野生型与F562L突变体的生产模拟输入文件 17_US_caver：针对内向开放构象下的野生型与F562L突变体的Caver计算结果文件 18_US_transport_tools：采用TransportTools软件，对内向开放构象下的野生型与F562L突变体的隧道网络开展的分析结果 19_US_tunnel_selection：筛选瓶颈半径最大的隧道，以针对内向开放构象下的野生型与F562L突变体开展CaverDock实验的相关文件 20_US_caverdock：针对内向开放构象下的野生型与F562L突变体的CaverDock计算结果文件 21_US_MD_analysis：各体系的均方根偏差、均方根波动计算；跨膜螺旋2、5、8及11的螺旋参数计算 ABC_Sequences.fasta：1KP分析得到的序列数据
