Assessing PDB macromolecular crystal structure confidence at the individual amino acid residue level.
Assessing PDB macromolecular crystal structure confidence at the individual amino acid residue level.
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DOI：
10.1016/j.str.2022.08.004
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发表时间：
2022-10-06
期刊：
影响因子：
5.7
通讯作者：
Burley, Stephen K.
中科院分区：
文献类型：
--
作者：
Shao, Chenghua;Bittrich, Sebastian;Wang, Sijian;Burley, Stephen K.
在蛋白质数据库（PDB）中，19万多个原子级别的三维生物结构里，约87%是通过大分子晶体学（MX）测定的。我们详细分析了约15万个PDB MX结构中超过1亿个单个氨基酸残基的三维原子坐标与实验数据之间的一致性。利用每个残基的三维原子坐标和源自实验数据的电子密度计算得出的实空间相关系数（RSCC），能够检测出不可靠的原子坐标异常值（这对于分辨率较差的侧链原子尤为重要），方便PDB用户对局部结构质量进行评估。对于PDB中的人类蛋白质MX结构，将每个残基的RSCC指标与AlphaFold2计算得出的结构模型置信度（pLDDT——预测局部距离差异测试）进行比较，结果表明：（i）RSCC值与pLDDT分数相关（中位相关系数约为0.41）；（ii）实验测定的MX结构（分辨率为3.5埃或更高）比AlphaFold2计算得出的结构模型更可靠，应尽可能优先使用。
邵等人利用实空间相关系数（RSCC）分析了晶体结构中每个残基的质量，并严格识别出异常值。每个残基的RSCC值与AlphaFold2计算得出的结构模型中每个残基的预测置信度相关。PDB晶体结构通常比AlphaFold2模型更可靠，并且每个残基的质量采用类似于AlphaFoldDB的配色方案来展示。
Approximately 87% of the more than 190,000 atomic-level, (three-dimensional) 3D biostructures in the Protein Data Bank (PDB) were determined using macromolecular crystallography (MX). Agreement between 3D atomic coordinates and experimental data for >100 million individual amino acid residues occurring within ~150,000 PDB MX structures was analyzed in detail. The Real-Space-Correlation-Coefficient (RSCC) calculated using the 3D atomic coordinates for each residue and experimental-data-derived electron density enables outlier detection of unreliable atomic coordinates (particularly important for poorly-resolved sidechain atoms) and ready evaluation of local structure quality by PDB users. For human protein MX structures in PDB, comparisons of the per-residue RSCC metric with AlphaFold2 computed structure model confidence (pLDDT-predicted local distance difference test) document (i) that RSCC values and pLDDT scores are correlated (median correlation coefficient~0.41), and (ii) that experimentally-determined MX structures (3.5 Å resolution or better) are more reliable than AlphaFold2 computed structure models and should be used preferentially whenever possible. Shao et al. analyzed crystal structure per-residue quality using Real-Space-Correlation-Coefficient (RSCC) and identified outliers rigorously. Per-residue RSCC values are correlated with the AlphaFold2 computed structure model per-residue prediction confidence. PDB crystal structures are generally more reliable than AlphaFold2 models, and per-residue quality is displayed using a color scheme like AlphaFoldDB.
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DOI：
10.1016/j.str.2017.10.009
发表时间：
2017-12-05
期刊：
Structure (London, England : 1993)
影响因子：
--
作者：
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通讯作者：
Kleywegt GJ
影响因子：
64.8
作者：
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通讯作者：
Hassabis D
DOI：
10.1016/j.str.2021.10.008
发表时间：
2022-01-06
期刊：
Structure (London, England : 1993)
影响因子：
--
作者：
Goodsell DS;Burley SK
通讯作者：
Burley SK
影响因子：
14.9
作者：
wwPDB consortium
通讯作者：
wwPDB consortium
影响因子：
14.9
作者：
Mir S;Alhroub Y;Anyango S;Armstrong DR;Berrisford JM;Clark AR;Conroy MJ;Dana JM;Deshpande M;Gupta D;Gutmanas A;Haslam P;Mak L;Mukhopadhyay A;Nadzirin N;Paysan-Lafosse T;Sehnal D;Sen S;Smart OS;Varadi M;Kleywegt GJ;Velankar S
通讯作者：
Velankar S