Persistent spectral hypergraph based machine learning (PSH-ML) for protein-ligand binding affinity prediction by Liu, Xiang, Feng, Huitao, Wu, Jie, Xia, Kelin

“…We test our PSH-GBT model on three most commonly used datasets, including PDBbind-2007, PDBbind-2013 and PDBbind-2016. Our results, for all these databases, are better than all existing machine learning models with traditional molecular descriptors, as far as we know.…”
Get full text

Structural analysis of protein tyrosine phosphatase 1B reveals potentially druggable allosteric binding sites by Kumar, Ammu Prasanna, Nguyen, Minh Nhan, Verma, Chandra, Lukman, Suryani

Get full text

Analysis of the role played by ligand-induced folding of the cocaine-binding aptamer in the photochrome aptamer switch assay by Shoara, Aron A., Churcher, Zachary R., Steele, Terry W. J., Johnson, Philip E.

Get full text

Alternative splicing in the DBD linker region of p63 modulates binding to DNA and iASPP in vitro by Lotz, R, Osterburg, C, Chaikuad, A, Weber, S, Akutsu, M, Machel, AC, Beyer, U, Gebel, J, Löhr, F, Knapp, S, Dobbelstein, M, Lu, X, Dötsch, V

“…Here we characterize the interaction of iASPP with p63 and show that it binds to the linker region between the DNA binding domain and the oligomerization domain. …”

Characterizing the conformational landscape of MDM2-binding p53 peptides using molecular dynamics simulations by Yadahalli, Shilpa, Li, Jianguo, Lane, David P., Gosavi, Shachi, Verma, Chandra Shekhar

“…The conformational landscapes of p53 peptide variants and phage derived peptide (12/1) variants, all known to bind to MDM2, are studied using hamiltonian replica exchange molecular dynamics simulations. …”
Get full text
Get full text

Multiscale topological indices for the quantitative prediction of SARS CoV-2 binding affinity change upon mutations by Bi, Jialin, Wee, JunJie, Liu, Xiang, Qu, Cunquan, Wang, Guanghui, Xia, Kelin

Get full text

Molecular insights into evolution, mutations and receptor-binding specificity of influenza A and B viruses from outpatients and hospitalized patients in Singapore by Ivan, Fransiskus Xaverius, Zhou, Xinrui, Lau, Suk Hiang, Rashid, Shamima, Teo, Jasmine S. M., Lee, Hong Kai, Koay, Evelyn S., Chan, Kwai Peng, Leo, Yee Sin, Chen, Mark I. Cheng, Kwoh, Chee Keong, Chow, Vincent T.

“…Background: This study compared the genomes of influenza viruses that caused mild infections among outpatients and severe infections among hospitalized patients in Singapore, and characterized their molecular evolution and receptor-binding specificity. …”
Get full text

Impact of molecular linker size on physicochemical properties of assembled gold nanoparticle mono-/multi-layers and their applicability for functional binding of biomolecules by Krikstolaityte, Vida, Hamit-Eminovski, Jildiz, Abariute, Laura, Niaura, Gediminas, Meskys, Rolandas, Arnebrant, Thomas, Lisak, Grzegorz, Ruzgas, Tautgirdas

Get full text

Linking dual mode of action of host defense antimicrobial peptide thanatin: structures, lipopolysaccharide and LptAm binding of designed analogs by Sinha, Sheetal, Dhanabal, Vidhya Bharathi, Sperandeo, Paola, Polissi, Alessandra, Bhattacharjya, Surajit

Get full text

Curvature sensing amphipathic helix in the C-terminus of RTNLB13 is conserved in all endoplasmic reticulum shaping reticulons in Arabidopsis thaliana by Brooks, Rhiannon L., Mistry, Chandni S., Dixon, Ann M.

“…The reticulon family of integral membrane proteins are conserved across all eukaryotes and typically localize to the endoplasmic reticulum (ER), where they are involved in generating highly-curved tubules. …”
Get full text

A conserved arginine in NS5 binds genomic 3' stem-loop RNA for primer-independent initiation of flavivirus RNA replication by Wang, Sai, Chan, Kitti Wing Ki, Tan, Min Jie Alvin, Flory, Charlotte, Luo, Dahai, Lescar, Julian, Forwood, Jade K., Vasudevan, Subhash G.

“…We show that DENV2 NS5 arginine 888, located within the carboxy-terminal 18 residues, is completely conserved in all flaviviruses and interacts specifically with the top-loop of 3'SL in the 3'UTR which contains the pentanucleotide 5'-CACAG-3' previously shown to be critical for flavivirus RNA replication. …”
Get full text

21W.730-2 Expository Writing - Food for Thought: Writing and Reading about Food and Culture, Fall 2005 by Boiko, Karen

Get full text

The binding interface of kindlin-2 and ILK involves Asp344/Asp352/Thr356 in kindlin-2 and Arg243/Arg334 in ILK by Tan, Hui-Foon, Guan, Si-Yu, Chng, Choon-Peng, Ong, Li-Teng, Tan, Suet-Mien, Law, Alex Sai Kit

Get full text
Get full text

Sequence- and structure-specific probing of RNAs by short nucleobase-modified dsRNA-binding PNAs incorporating a fluorescent light-up uracil analog by Krishna, Manchugondanahalli Shivakumar, Toh, Desiree-Faye Kaixin, Meng, Zhenyu, Ong, Alan Ann Lerk, Wang, Zhenzhang, Lu, Yunpeng, Xia, Kelin, Prabakaran, Mookkan, Chen, Gang

Get full text

Anisotropic protein diffusion on nanosurface by Liu, Yang, Song, Xiaohan, Yang, Yanmei, Li, Yong-Qiang, Zhao, Mingwen, Mu, Yuguang, Li, Weifeng

“…On the MBP surface, HP35 migrates mainly along the zigzag direction but can also easily stride over the ridges and grooves along the armchair direction. Moreover, the mild binding strength between α-PC and HP35 does not cause distortion in the protein structure. …”
Get full text

Elucidating the mechanism of mRNA transport using novel imaging technologies by Stoychev, D

“…The MS2-MCP system is used to insert into mRNAs of interest special structures to which RNA-binding proteins, fused to a fluorescent protein such as GFP, can then bind. …”

Enzymatic preparation of diacylglycerols: lipase screening, immobilization, characterization and glycerolysis performance by Xie, Rui, Peng, Xianwu, Lee, Yee-Ying, Xie, Pengkai, Tan, Chin-Ping, Wang, Yong, Zhang, Zhen

“…Backgrounds: Glycerolysis, with its advantages of readily available raw materials, simple operation, and mild reaction conditions, is a primary method for producing diacylglycerol (DAG). …”

Membrane reconstitution of monoamine oxidase enzymes on supported lipid bilayers by Wang, Liulin, Kabir H. Biswas, Yoon, Bo Kyeong, Kawakami, Lisa M., Park, Soohyun, Groves, Jay T., Li, Lin, Huang, Wei, Cho, Nam-Joon

Get full text

Bifunctional diazirine reagent for covalent dyeing of Kevlar and inert polymer materials by Liu, Richard Y., Luo, Shao-Xiong Lennon, Hirst, Elizabeth S., Doona, Christopher J., Swager, Timothy M.

“…The reagent's structure features a trifluoromethyl diazirine group as a precursor to a carbene that binds the textile surface. On the reagent's other terminus, a benzyl bromide group acts as a site accessible for substitution reactions. …”
Get full text

Unconventional split aptamers cleaved at functionally essential sites preserve biorecognition capability by Wang, Ruoyu, Zhang, Qiansen, Zhang, Yi, Shi, Hanchang, Nguyen, Kim Truc, Zhou, Xiaohong

“…An allosteric binding mechanism of BPSPAs, in which a new binding pocket is formed upon the target binding, is revealed by all-atom microsecond-scale molecular dynamics simulations. …”
Get full text