Song Yang, Ph.D. - Related publications

Affiliations: 
2007 University of California, San Diego, La Jolla, CA 
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50 most relevant papers in past 60 days:
Year Citation  Score
2020 Ferdous N, Reza MN, Emon MTH, Islam MS, Mohiuddin AKM, Hossain MU. Molecular characterization and functional annotation of a hypothetical protein (SCO0618) of Streptomyces coelicolor A3(2). Genomics & Informatics. 18: e28. PMID 33017872 DOI: 10.5808/GI.2020.18.3.e28   
2020 Ferdous N, Reza MN, Emon MTH, Islam MS, Mohiuddin AKM, Hossain MU. Molecular characterization and functional annotation of a hypothetical protein (SCO0618) of Streptomyces coelicolor A3(2). Genomics & Informatics. 18: e28. PMID 33017872 DOI: 10.5808/GI.2020.18.3.e28   
2020 Das S, Scholes HM, Sen N, Orengo C. CATH functional families predict functional sites in proteins. Bioinformatics (Oxford, England). PMID 33135053 DOI: 10.1093/bioinformatics/btaa937   
2020 Vitorino R, Guedes S, Trindade F, Correia I, Moura G, Carvalho P, Santos M, Amado F. sequencing of proteins by mass spectrometry. Expert Review of Proteomics. PMID 33016158 DOI: 10.1080/14789450.2020.1831387   
2020 Kraus A, Weskamp M, Zierles J, Balzer M, Busch R, Eisfeld J, Lambertz J, Nowaczyk MM, Narberhaus F. Arginine-Rich Small Proteins with a Domain of Unknown Function, DUF1127, Play a Role in Phosphate and Carbon Metabolism of Agrobacterium tumefaciens. Journal of Bacteriology. 202. PMID 33093235 DOI: 10.1128/JB.00309-20   
2020 Gao M, Skolnick J. A novel sequence alignment algorithm based on deep learning of the protein folding code. Bioinformatics (Oxford, England). PMID 32960943 DOI: 10.1093/bioinformatics/btaa810   
2020 Joshi AG, Harini K, Meenakshi I, Shafi KM, Pasha SN, Mahita J, Sajeevan RS, Karpe SD, Ghosh P, Nitish S, Gandhimathi A, Mathew OK, Prasanna SH, Malini M, Mutt E, et al. A knowledge-driven protocol for prediction of proteins of interest with an emphasis on biosynthetic pathways. Methodsx. 7: 101053. PMID 33024710 DOI: 10.1016/j.mex.2020.101053   
2020 Kocyła A, Tran JB, Krężel A. Galvanization of Protein-Protein Interactions in a Dynamic Zinc Interactome. Trends in Biochemical Sciences. PMID 32958327 DOI: 10.1016/j.tibs.2020.08.011   
2020 Nash MA. Single-molecule and Single-cell Approaches in Molecular Bioengineering. Chimia. 74: 704-709. PMID 32958108 DOI: 10.2533/chimia.2020.704   
2020 Lipsh-Sokolik R, Listov D, Fleishman SJ. The AbDesign computational pipeline for modular backbone assembly and design of binders and enzymes. Protein Science : a Publication of the Protein Society. PMID 33040418 DOI: 10.1002/pro.3970   
2020 Ahmed J, Mercx S, Boutry M, Chaumont F. Evolutionary and Predictive Functional Insights into the Aquaporin Gene Family in the Allotetraploid Plant . International Journal of Molecular Sciences. 21. PMID 32635213 DOI: 10.3390/ijms21134743   
2020 Zhang J, Lv L, Lu D, Kong D, Al-Alashaari MAA, Zhao X. Variable selection from a feature representing protein sequences: a case of classification on bacterial type IV secreted effectors. Bmc Bioinformatics. 21: 480. PMID 33109082 DOI: 10.1186/s12859-020-03826-6   
2020 Sharma AK, Srivastava R. Variable Length Character N-Gram Embedding of Protein Sequences for Secondary Structure Prediction. Protein and Peptide Letters. PMID 33143605 DOI: 10.2174/0929866527666201103145635   
2020 Jha K, Saha S. Amalgamation of 3D structure and sequence information for protein-protein interaction prediction. Scientific Reports. 10: 19171. PMID 33154416 DOI: 10.1038/s41598-020-75467-x   
2020 Mirela-Bota P, Aguirre-Plans J, Meseguer A, Galletti C, Segura J, Planas-Iglesias J, Garcia-Garcia J, Guney E, Oliva B, Fernandez-Fuentes N. Galaxy InteractoMIX: An Integrated Computational Platform for the Study of Protein-Protein Interaction Data. Journal of Molecular Biology. PMID 32976910 DOI: 10.1016/j.jmb.2020.09.015   
2020 Trueba-Santiso A, Wasmund K, Soder-Walz JM, Marco-Urrea E, Adrian L. Genome Sequence, Proteome Profile, and Identification of a Multiprotein Reductive Dehalogenase Complex in Strain BRE15M. Journal of Proteome Research. PMID 32975419 DOI: 10.1021/acs.jproteome.0c00569   
2020 Badal VD, Kundrotas PJ, Vakser IA. Text mining for modeling of protein complexes enhanced by machine learning. Bioinformatics (Oxford, England). PMID 32960948 DOI: 10.1093/bioinformatics/btaa823   
2020 Shang J, Han N, Chen Z, Peng Y, Li L, Zhou H, Ji C, Meng J, Jiang T, Wu A. Compositional diversity and evolutionary pattern of coronavirus accessory proteins. Briefings in Bioinformatics. PMID 33126244 DOI: 10.1093/bib/bbaa262   
2020 Baruah C, Devi P, Sharma DK. Sequence Analysis and Structure Prediction of SARS-CoV-2 Accessory Proteins 9b and ORF14: Evolutionary Analysis Indicates Close Relatedness to Bat Coronavirus. Biomed Research International. 2020: 7234961. PMID 33102591 DOI: 10.1155/2020/7234961   
2020 Du Z, He Y, Li J, Uversky VN. DeepAdd: Protein function prediction from k-mer embedding and additional features. Computational Biology and Chemistry. 89: 107379. PMID 33011616 DOI: 10.1016/j.compbiolchem.2020.107379   
2020 Fiorentini F, Esposito D, Rittinger K. Does it take two to tango? RING domain self-association and activity in TRIM E3 ubiquitin ligases. Biochemical Society Transactions. PMID 33170204 DOI: 10.1042/BST20200383   
2020 Preto AJ, Moreira IS. SPOTONE: Hot Spots on Protein Complexes with Extremely Randomized Trees via Sequence-Only Features. International Journal of Molecular Sciences. 21. PMID 33019775 DOI: 10.3390/ijms21197281   
2020 Tan F, Sun N, Zhang L, Wu J, Xiao S, Tan Q, Uversky VN, Liu Y. Functional characterization of an unknown soybean intrinsically disordered protein in vitro and in Escherichia coli. International Journal of Biological Macromolecules. PMID 33137381 DOI: 10.1016/j.ijbiomac.2020.10.211   
2020 Sinha S, Lynn AM, Desai DK. Implementation of homology based and non-homology based computational methods for the identification and annotation of orphan enzymes: using Mycobacterium tuberculosis H37Rv as a case study. Bmc Bioinformatics. 21: 466. PMID 33076816 DOI: 10.1186/s12859-020-03794-x   
2020 Zhao B, Katuwawala A, Oldfield CJ, Dunker AK, Faraggi E, Gsponer J, Kloczkowski A, Malhis N, Mirdita M, Obradovic Z, Söding J, Steinegger M, Zhou Y, Kurgan L. DescribePROT: database of amino acid-level protein structure and function predictions. Nucleic Acids Research. PMID 33119734 DOI: 10.1093/nar/gkaa931   
2020 Stollar EJ, Smith DP. Uncovering protein structure. Essays in Biochemistry. PMID 32975287 DOI: 10.1042/EBC20190042   
2020 Blum M, Chang HY, Chuguransky S, Grego T, Kandasaamy S, Mitchell A, Nuka G, Paysan-Lafosse T, Qureshi M, Raj S, Richardson L, Salazar GA, Williams L, Bork P, Bridge A, et al. The InterPro protein families and domains database: 20 years on. Nucleic Acids Research. PMID 33156333 DOI: 10.1093/nar/gkaa977   
2020 Agostino M. Comprehensive analysis of carbohydrate-protein recognition in the Protein Data Bank. Carbohydrate Research. 498: 108180. PMID 33096507 DOI: 10.1016/j.carres.2020.108180   
2020 Rawlings ND, Bateman A. How to use the MEROPS database and website to help understand peptidase specificity. Protein Science : a Publication of the Protein Society. PMID 32920969 DOI: 10.1002/pro.3948   
2020 Haq SR, Survery S, Hurtig F, Lindås AC, Chi CN. NMR resonance assignment and dynamics of profilin from Heimdallarchaeota. Scientific Reports. 10: 15867. PMID 32985518 DOI: 10.1038/s41598-020-72550-1   
2020 Haq SR, Survery S, Hurtig F, Lindås AC, Chi CN. NMR resonance assignment and dynamics of profilin from Heimdallarchaeota. Scientific Reports. 10: 15867. PMID 32985518 DOI: 10.1038/s41598-020-72550-1   
2020 Tian H, Trozzi F, Zoltowski BD, Tao P. Deciphering the Allosteric Process of Aureochrome 1a LOV Domain. The Journal of Physical Chemistry. B. PMID 32970438 DOI: 10.1021/acs.jpcb.0c05842   
2020 Guo Y, Yan K, Wu H, Liu B. ReFold-MAP: protein remote homology detection and fold recognition based on features extracted from profiles. Analytical Biochemistry. 114013. PMID 33160906 DOI: 10.1016/j.ab.2020.114013   
2020 Veith PD, Gorasia DG, Reynolds EC. Towards defining the outer membrane proteome of Porphyromonas gingivalis. Molecular Oral Microbiology. PMID 33124778 DOI: 10.1111/omi.12320   
2020 Arooj M, Shehadi I, Nassab CN, Mohamed AA. Physicochemical stability study of protein-benzoic acid complexes using molecular dynamics simulations. Amino Acids. 52: 1353-1362. PMID 33006112 DOI: 10.1007/s00726-020-02897-2   
2020 Trihemasava K, Chakraborty S, Blackburn K, Xu G. Expression, purification, and phylogenetic analysis of MDIS1-INTERACTING RECEPTOR-LIKE KINASE1 (MIK1). The Protein Journal. PMID 33104960 DOI: 10.1007/s10930-020-09926-9   
2020 Shin G, Lim SI. Site-specific proximity ligation provides molecular insights into biologically relevant interfaces of protein-protein interaction. Biochemical and Biophysical Research Communications. PMID 33008597 DOI: 10.1016/j.bbrc.2020.09.097   
2020 Shin G, Lim SI. Site-specific proximity ligation provides molecular insights into biologically relevant interfaces of protein-protein interaction. Biochemical and Biophysical Research Communications. PMID 33008597 DOI: 10.1016/j.bbrc.2020.09.097   
2020 Diaz N, Lico C, Capodicasa C, Baschieri S, Dessì D, Benvenuto E, Fiori PL, Rappelli P. Production and Functional Characterization of a Recombinant Predicted Pore-Forming Protein (TVSAPLIP12) of in Plants. Frontiers in Cellular and Infection Microbiology. 10: 581066. PMID 33117734 DOI: 10.3389/fcimb.2020.581066   
2020 Urban G, Torrisi M, Magnan CN, Pollastri G, Baldi P. Protein profiles: Biases and protocols. Computational and Structural Biotechnology Journal. 18: 2281-2289. PMID 32994887 DOI: 10.1016/j.csbj.2020.08.015   
2020 Steglich M, Lombide R, López I, Portela M, Fló M, Marín M, Alvarez B, Turell L. Expression, purification and initial characterization of human serum albumin domain I and its cysteine 34. Plos One. 15: e0240580. PMID 33045024 DOI: 10.1371/journal.pone.0240580   
2020 Bandekar D, Mohapatra S, Hazra M, Hazra S, Biswas S. N-terminal truncation of VC0395_0300 protein from Vibrio cholerae does not lead to loss of diguanylate cyclase activity. Biophysical Chemistry. 268: 106493. PMID 33152620 DOI: 10.1016/j.bpc.2020.106493   
2020 Ou J, Liu H, Nirala NK, Stukalov A, Acharya U, Green MR, Zhu LJ. dagLogo: An R/Bioconductor package for identifying and visualizing differential amino acid group usage in proteomics data. Plos One. 15: e0242030. PMID 33156866 DOI: 10.1371/journal.pone.0242030   
2020 Hong K, Song D, Jung Y. Behavior control of membrane-less protein liquid condensates with metal ion-induced phase separation. Nature Communications. 11: 5554. PMID 33144560 DOI: 10.1038/s41467-020-19391-8   
2020 Xue W, Zhang SX, He WT, Hong JY, Jiang LL, Hu HY. Domain interactions reveal auto-inhibition of the deubiquitinating enzyme USP19 and its activation by HSP90 in modulation of huntingtin aggregation. The Biochemical Journal. PMID 33094816 DOI: 10.1042/BCJ20200536   
2020 Hu X, Wang JH, Chen XW. Exploiting arginine distributions for the selective and efficient depletion of arginine-rich plasma proteins. Chemical Communications (Cambridge, England). 56: 12375-12378. PMID 32930244 DOI: 10.1039/d0cc04744a   
2020 Mallik S, Tawfik DS. Determining the interaction status and evolutionary fate of duplicated homomeric proteins. Plos Computational Biology. 16: e1008145. PMID 32853212 DOI: 10.1371/journal.pcbi.1008145   
2020 Gaynor AS, Chen W. Conditional Protein Rescue by Binding-Induced Protective Shielding. Acs Synthetic Biology. PMID 33025786 DOI: 10.1021/acssynbio.0c00367   
2020 Wegner LH, Hao Z. A quantitative approach relating emergent features of complex traits to protein expression. Progress in Biophysics and Molecular Biology. PMID 33035591 DOI: 10.1016/j.pbiomolbio.2020.10.002   
2020 Pritišanac I, Zarin T, Forman-Kay JD, Moses AM. Whence Blobs? Phylogenetics of functional protein condensates. Biochemical Society Transactions. PMID 32985656 DOI: 10.1042/BST20200355