Yao Chi Chen
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Explore the profile of Yao Chi Chen including associated specialties, affiliations and a list of published articles.
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11
Citations
126
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Recent Articles
1.
Chen Y, Sargsyan K, Wright J, Chen Y, Huang Y, Lim C
Elife
. 2024 Sep;
13.
PMID: 39283314
Experimental detection of residues critical for protein-protein interactions (PPI) is a time-consuming, costly, and labor-intensive process. Hence, high-throughput PPI-hot spot prediction methods have been developed, but they have been validated...
2.
Chen Y, Chen Y, Wright J, Lim C
J Chem Inf Model
. 2022 Feb;
62(4):1052-1060.
PMID: 35147037
Single-point mutations of certain residues (so-called hot spots) impair/disrupt protein-protein interactions (PPIs), leading to pathogenesis and drug resistance. Conventionally, a PPI-hot spot is identified when its replacement decreased the binding...
3.
Chen Y, Sargsyan K, Wright J, Huang Y, Lim C
Nucleic Acids Res
. 2013 Dec;
42(3):e15.
PMID: 24343026
Increasing numbers of protein structures are solved each year, but many of these structures belong to proteins whose sequences are homologous to sequences in the Protein Data Bank. Nevertheless, the...
4.
Weinkam P, Chen Y, Pons J, Sali A
J Mol Biol
. 2012 Dec;
425(3):647-61.
PMID: 23228330
Allostery in a protein involves effector binding at an allosteric site that changes the structure and/or dynamics at a distant, functional site. In addition to the chemical equilibrium of ligand...
5.
Chen Y, Wright J, Lim C
Nucleic Acids Res
. 2012 Jun;
40(Web Server issue):W249-56.
PMID: 22661576
DR_bind is a web server that automatically predicts DNA-binding residues, given the respective protein structure based on (i) electrostatics, (ii) evolution and (iii) geometry. In contrast to machine-learning methods, DR_bind...
6.
Wu C, Hwa Y, Chen Y, Lim C
J Phys Chem B
. 2012 Apr;
116(19):5644-52.
PMID: 22530587
A one-dimensional (1D) motif usually comprises conserved essential residues involved in catalysis, ligand binding, or maintaining a specific structure. However, it cannot be easily detected in proteins with low sequence...
7.
Wu C, Chen Y, Lim C
Nucleic Acids Res
. 2010 Jun;
38(14):e150.
PMID: 20525797
Proteins with insignificant sequence and overall structure similarity may still share locally conserved contiguous structural segments; i.e. structural/3D motifs. Most methods for finding 3D motifs require a known motif to...
8.
Lee Y, Babu C, Chen Y, Milcic M, Qu Y, Lim C
J Med Chem
. 2010 Apr;
53(10):4038-49.
PMID: 20420408
The ADP-ribosylating toxins (ADPRTs) and poly(ADP-ribose) polymerases (PARPs) are two important drug-target protein families. Although the Y-X(10)-Y motif for the diphtheria toxin group and the STS motif for the other...
9.
Chen Y, Lim C
Nucleic Acids Res
. 2008 Nov;
36(22):7078-87.
PMID: 18988628
Protein-DNA/RNA/protein interactions play critical roles in many biological functions. Previous studies have focused on the different features characterizing the different macromolecule-binding sites and approaches to detect these sites. However, no...
10.
Chen Y, Lim C
Nucleic Acids Res
. 2008 Feb;
36(5):e29.
PMID: 18276647
An RNA-binding protein places a surface helix, beta-ribbon, or loop in an RNA helix groove and/or uses a cavity to accommodate unstacked bases. Hence, our strategy for predicting RNA-binding residues...