A distance‐ and orientation‐dependent energy function of amino acid key blocks

Chen, Lin; He, Jing

doi:10.1002/bip.22440

Cited by 7 publications

(12 citation statements)

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“…We calculated block length (

) using the distal block of a side-chain for each of 18 types of residues (see Materials and Methods), since the position and orientation of the distal block are sensitive in distinguishing side-chain conformations [ 40 ]. The block lengths of lysine (LYS) range from 4 Å to 6 Å approximately.…”

Section: Resultsmentioning

confidence: 99%

“…A side-chain is divided into blocks and the position of the distal block was used to represent the conformation of a side-chain for 18 of the 20 residues [ 40 ]. GLY and ALA are not included due to the small size of their side-chains.…”

Section: Methodsmentioning

confidence: 99%

“…GLY and ALA are not included due to the small size of their side-chains. The position and orientation of the distal block have been used previously to characterize conformations of side-chains in an energy function [ 40 ]. A side-chain block length is the distance between Cα and the mass center of the distal block of a residue ( Figure 4 ).…”

Section: Methodsmentioning

confidence: 99%

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An Investigation of Atomic Structures Derived from X-ray Crystallography and Cryo-Electron Microscopy Using Distal Blocks of Side-Chains

Chen

Sazzed

et al. 2018

Molecules

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Cryo-electron microscopy (cryo-EM) is a structure determination method for large molecular complexes. As more and more atomic structures are determined using this technique, it is becoming possible to perform statistical characterization of side-chain conformations. Two data sets were involved to characterize block lengths for each of the 18 types of amino acids. One set contains 9131 structures resolved using X-ray crystallography from density maps with better than or equal to 1.5 Å resolutions, and the other contains 237 protein structures derived from cryo-EM density maps with 2–4 Å resolutions. The results show that the normalized probability density function of block lengths is similar between the X-ray data set and the cryo-EM data set for most of the residue types, but differences were observed for ARG, GLU, ILE, LYS, PHE, TRP, and TYR for which conformations with certain shorter block lengths are more likely to be observed in the cryo-EM set with 2–4 Å resolutions.

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“…We calculated block length (

Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

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An Investigation of Atomic Structures Derived from X-ray Crystallography and Cryo-Electron Microscopy Using Distal Blocks of Side-Chains

Chen

Sazzed

et al. 2018

Molecules

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“…d block is the distance between the CA atom on backbone and mass centroid of the distal block of a specific residue. The blocks in a residue are defined in Chen et al [25]. Histogram-based outlier score (HBOS) of each residue was calculated by equation (1).…”

Section: Histogram-based Outlier (Hbos)mentioning

confidence: 99%

“…We previously observed that block length is a simple but sensitive measure of sidechain conformations [25]. In a histogram-based outlier score (HBOS) method, we introduced two distance measures, block length and sidechain distance, that are not used in the current OneDep validation system [26,27].…”

Section: Introductionmentioning

confidence: 99%

Outlier Profiles of Atomic Structures Derived from X-ray Crystallography and from Cryo-Electron Microscopy

Chen

2020

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Background: As more protein atomic structures are determined from cryo-electron microscopy (cryo-EM) density maps, validation of such structures is an important task. Methods: We applied a histogram-based outlier score (HBOS) to six sets of cryo-EM atomic structures and five sets of X-ray atomic structures, including one derived from X-ray data with better than 1.5 Å resolution. Cryo-EM data sets contain structures released by December 2016 and those released between 2017 and 2019, derived from resolution ranges 0–4 Å and 4–6 Å respectively. Results: The distribution of HBOS values in five sets of X-ray structures show that HBOS is sensitive distinguishing sets of X-ray structures derived from different resolution ranges-higher than 1.5 Å, 1.5–2.0 Å, 2.0–2.5 Å, 2.5–3.0 Å, and 3.0–3.5 Å. The overall quality of cryo-EM structures is likely improved, as shown in a comparison of cryo-EM structures released before the end of 2016, those between 2017 and 2018, and those between 2018 and 2019. Our investigation shows that leucine (LEU) has a significantly higher rate of HBOS outliers than that of the reference data set (X-ray-1.5) and of other residue types in the cryo-EM data sets. HBOS was able to detect outliers for those residues that are currently marked as green in PDB validation reports. Conclusions: The HBOS profile of a dataset is a potential method to characterize the overall structural quality of the set. Residue LEU deserves special attention since it has a significantly higher HBOS outlier rate in sets of cryo-EM structures and those X-ray structures derived from X-ray data of lower than 2.5 Å resolutions. Most HBOS outlier residues from the EM-0-4-2019 set are located on loops for most types of residues.

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Improving the orientation-dependent statistical potential using a reference state

2014

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Statistical potentials are frequently engaged in the protein structural prediction and protein folding for conformational evaluation. Theoretically, to describe the many-body effect, pairwise interaction between two atom groups should be corrected by their relative geometric orientation. The potential functions developed by this means are called orientation-dependent statistical potentials and have exhibited substantially improved performance. However, none of the currently available orientation-dependent statistical potentials use any reference state, which has been proven to greatly enhance the power of distance-dependent statistical potentials in numerous previous studies. In this work, we designed a reasonable reference state for the orientation-dependent statistical potentials: using the average geometric relationship between atom pairs in known structures by neglecting their residue identities. The statistical potential developed using this reference state (called ORDER_AVE) prevails most available rival potentials in a series of tests on the decoy sets, although the information of side chain atoms (except the β-carbon) is absent in its construction.

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A distance‐ and orientation‐dependent energy function of amino acid key blocks

Cited by 7 publications

References 46 publications

An Investigation of Atomic Structures Derived from X-ray Crystallography and Cryo-Electron Microscopy Using Distal Blocks of Side-Chains

An Investigation of Atomic Structures Derived from X-ray Crystallography and Cryo-Electron Microscopy Using Distal Blocks of Side-Chains

Outlier Profiles of Atomic Structures Derived from X-ray Crystallography and from Cryo-Electron Microscopy

Improving the orientation-dependent statistical potential using a reference state

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