Protein inter‐residue contact and distance prediction by coupling complementary coevolution features with deep residual networks in CASP14

2021 ◽  
Author(s):  
Yang Li ◽  
Chengxin Zhang ◽  
Wei Zheng ◽  
Xiaogen Zhou ◽  
Eric W. Bell ◽  
...  
Keyword(s):  
Residue Contact ◽  
Distance Prediction

A Review of Protein Inter-residue Distance Prediction

2021 ◽  
Vol 15 (8) ◽  
pp. 821-830
Author(s):  
He Huang ◽  
Xinqi Gong
Keyword(s):  
Structure Prediction ◽  
Tertiary Structure ◽  
Contact Map ◽  
Distance Information ◽  
Distance Map ◽  
Large Molecules ◽  
Residue Contact ◽  
Linear Sequence ◽  
Residue Contacts ◽  
Distance Prediction

Proteins are large molecules consisting of a linear sequence of amino acids. Protein performs biological functions with specific 3D structures. The main factors that drive proteins to form these structures are constraint between residues. These constraints usually lead to important inter-residue relationships, including short-range inter-residue contacts and long-range interresidue distances. Thus, a highly accurate prediction of inter-residue contact and distance information is of great significance for protein tertiary structure computations. Some methods have been proposed for inter-residue contact prediction, most of which focus on contact map prediction and some reviews have summarized the progresses. However, inter-residue distance prediction is found to provide better guidance for protein structure prediction than contact map prediction in recent years. The methods for inter-residue distance prediction can be roughly divided into two types according to the consideration of distance value: one is based on multi-classification with discrete value and the other is based on regression with continuous value. Here, we summarize these algorithms and show that they have obtained good results. Compared to contact map prediction, distance map prediction is in its infancy. There is a lot to do in the future including improving distance map prediction precision and incorporating them into residue-residue distanceguided ab initio protein folding.

TNDP: Tensor-based Network Distance Prediction with Confidence Intervals

2021 ◽  
pp. 1-1
Author(s):  
Haojun Huang ◽  
Li Li ◽  
Geyong Min ◽  
Wang Miao ◽  
Yingying Zhu ◽  
...  
Keyword(s):  
Confidence Intervals ◽  
Network Distance ◽  
Distance Prediction

A qualitative characteristic scheme and a fast distance prediction method of multi-probe azimuthal gamma-ray logging in geosteering

2021 ◽  
Vol 199 ◽  
pp. 108244
Author(s):  
Zhen Qin ◽  
Bin Tang ◽  
Dong Wu ◽  
Shaocheng Luo ◽  
Xiugang Ma ◽  
...  
Keyword(s):  
Gamma Ray ◽  
Prediction Method ◽  
Qualitative Characteristic ◽  
Characteristic Scheme ◽  
Distance Prediction

scholarly journals Identification of residue pairing in interacting β-strands from a predicted residue contact map

2018 ◽  
Vol 19 (1) ◽  
Author(s):  
Wenzhi Mao ◽  
Tong Wang ◽  
Wenxuan Zhang ◽  
Haipeng Gong
Keyword(s):  
Contact Map ◽  
Residue Contact

scholarly journals Evolutionarily Conserved and Divergent Residue-Residue Contact Dynamics Provide Insights into the Allosteric Regulation of Cyclophilins

2018 ◽  
Vol 114 (3) ◽  
pp. 337a
Author(s):  
Phuoc J. Vu ◽  
Xin-Qiu Yao ◽  
Mohamed Momin ◽  
Donald Hamelberg
Keyword(s):  
Allosteric Regulation ◽  
Contact Dynamics ◽  
Residue Contact ◽  
Evolutionarily Conserved
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