Brian Kelley - Related publications

2014- Cheminformatics Novartis Institute for BioMedical Research 
NOTE: We are testing a new system for identifying relevant work based on semantic analysis that identifies similarities between recently published papers and the current author's publications. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches.
50 most relevant papers in past 60 days:
Year Citation  Score
2021 Sladek V, Yamamoto Y, Harada R, Shoji M, Shigeta Y, Sladek V. pyProGA-A PyMOL plugin for protein residue network analysis. Plos One. 16: e0255167. PMID 34329304 DOI: 10.1371/journal.pone.0255167   
2021 Zhang Z, Jiang M, Wu D, Zhang W, Yan W, Qu X. A Novel Method for Identifying Essential Proteins Based on Non-negative Matrix Tri-Factorization. Frontiers in Genetics. 12: 709660. PMID 34422014 DOI: 10.3389/fgene.2021.709660   
2021 Li Y, Wang Z, Li LP, You ZH, Huang WZ, Zhan XK, Wang YB. Robust and accurate prediction of protein-protein interactions by exploiting evolutionary information. Scientific Reports. 11: 16910. PMID 34413375 DOI: 10.1038/s41598-021-96265-z   
2021 Hong Z, Liu J, Chen Y. An interpretable machine learning method for homo-trimeric protein interface residue-residue interaction prediction. Biophysical Chemistry. 278: 106666. PMID 34418678 DOI: 10.1016/j.bpc.2021.106666   
2021 Liu Y, Chen W, He Z. Essential Protein Recognition via Community Significance. Ieee/Acm Transactions On Computational Biology and Bioinformatics. PMID 34347602 DOI: 10.1109/TCBB.2021.3102018   
2021 Hu L, Wang X, Huang YA, Hu P, You ZH. A Novel Network-Based Algorithm for Predicting Protein-Protein Interactions Using Gene Ontology. Frontiers in Microbiology. 12: 735329. PMID 34512614 DOI: 10.3389/fmicb.2021.735329   
2021 Li S, Zhang Z, Li X, Tan Y, Wang L, Chen Z. An iteration model for identifying essential proteins by combining comprehensive PPI network with biological information. Bmc Bioinformatics. 22: 430. PMID 34496745 DOI: 10.1186/s12859-021-04300-7   
2021 Liu G, Liu B, Li A, Wang X, Yu J, Zhou X. Identifying Protein Complexes With Clear Module Structure Using Pairwise Constraints in Protein Interaction Networks. Frontiers in Genetics. 12: 664786. PMID 34512712 DOI: 10.3389/fgene.2021.664786   
2021 Mesbahuddin MS, Ganesan A, Kalyaanamoorthy S. Engineering stable carbonic anhydrases for CO2 capture: a critical review. Protein Engineering, Design & Selection : Peds. 34. PMID 34427656 DOI: 10.1093/protein/gzab021   
2021 Fukuzawa K, Kato K, Watanabe C, Kawashima Y, Handa Y, Yamamoto A, Watanabe K, Ohyama T, Kamisaka K, Takaya D, Honma T. Special Features of COVID-19 in the FMODB: Fragment Molecular Orbital Calculations and Interaction Energy Analysis of SARS-CoV-2-Related Proteins. Journal of Chemical Information and Modeling. PMID 34506132 DOI: 10.1021/acs.jcim.1c00694   
2021 Velasquez EF, Garcia YA, Ramirez I, Gholkar AA, Torres JZ. CANVS: an easy-to-use application for the analysis and visualization of mass spectrometry-based protein-protein interaction/association data. Molecular Biology of the Cell. mbcE21050257. PMID 34432510 DOI: 10.1091/mbc.E21-05-0257   
2021 Vu TTD, Jung J. Protein function prediction with gene ontology: from traditional to deep learning models. Peerj. 9: e12019. PMID 34513334 DOI: 10.7717/peerj.12019   
2021 Nasiri E, Berahmand K, Rostami M, Dabiri M. A novel link prediction algorithm for protein-protein interaction networks by attributed graph embedding. Computers in Biology and Medicine. 137: 104772. PMID 34450380 DOI: 10.1016/j.compbiomed.2021.104772   
2021 Kong L, Ju F, Zhang H, Sun S, Bu D. FALCON2: a web server for high-quality prediction of protein tertiary structures. Bmc Bioinformatics. 22: 439. PMID 34525939 DOI: 10.1186/s12859-021-04353-8   
2021 Bennett JL, Nguyen GTH, Donald WA. Protein-Small Molecule Interactions in Native Mass Spectrometry. Chemical Reviews. PMID 34449207 DOI: 10.1021/acs.chemrev.1c00293   
2021 Bouatta N, Sorger P, AlQuraishi M. Protein structure prediction by AlphaFold2: are attention and symmetries all you need? Acta Crystallographica. Section D, Structural Biology. 77: 982-991. PMID 34342271 DOI: 10.1107/S2059798321007531   
2021 Ferruz N, Michel F, Lobos F, Schmidt S, Höcker B. Fuzzle 2.0: Ligand Binding in Natural Protein Building Blocks. Frontiers in Molecular Biosciences. 8: 715972. PMID 34485385 DOI: 10.3389/fmolb.2021.715972   
2021 Antony JV, Madhu P, Balakrishnan JP, Yadav H. Assigning secondary structure in proteins using AI. Journal of Molecular Modeling. 27: 252. PMID 34402969 DOI: 10.1007/s00894-021-04825-x   
2021 Perszyk RE, Kristensen AS, Lyuboslavsky P, Traynelis SF. Three-dimensional missense tolerance ratio analysis. Genome Research. PMID 34301626 DOI: 10.1101/gr.275528.121   
2021 Zaitzeff A, Leiby N, Motta FC, Haase SB, Singer JM. Improved data sets and evaluation methods for the automatic prediction of DNA-binding proteins. Bioinformatics (Oxford, England). PMID 34415301 DOI: 10.1093/bioinformatics/btab603   
2021 Christoffer C, Bharadwaj V, Luu R, Kihara D. LZerD Protein-Protein Docking Webserver Enhanced With Structure Prediction. Frontiers in Molecular Biosciences. 8: 724947. PMID 34466411 DOI: 10.3389/fmolb.2021.724947   
2021 Pereira J, Alva V. How do I get the most out of my protein sequence using bioinformatics tools? Acta Crystallographica. Section D, Structural Biology. 77: 1116-1126. PMID 34473083 DOI: 10.1107/S2059798321007907   
2021 Wang S, Jiang M, Zhang S, Wang X, Yuan Q, Wei Z, Li Z. MCN-CPI: Multiscale Convolutional Network for Compound-Protein Interaction Prediction. Biomolecules. 11. PMID 34439785 DOI: 10.3390/biom11081119   
2021 Murali R, Zhang H, Cai Z, Lam L, Greene M. Rational Design of Constrained Peptides as Protein Interface Inhibitors. Antibodies (Basel, Switzerland). 10. PMID 34449551 DOI: 10.3390/antib10030032   
2021 Xu J, Mcpartlon M, Li J. Improved protein structure prediction by deep learning irrespective of co-evolution information. Nature Machine Intelligence. 3: 601-609. PMID 34368623 DOI: 10.1038/s42256-021-00348-5   
2021 Duek P, Mary C, Zahn-Zabal M, Bairoch A, Lane L. Functionathon: a manual data mining workflow to generate functional hypotheses for uncharacterized human proteins and its application by undergraduate students. Database : the Journal of Biological Databases and Curation. 2021. PMID 34318869 DOI: 10.1093/database/baab046   
2021 McCullough J, Fey P, Rahman RJ, Wallace M, Morey S, Sahlberg K, McGonagle E, Hess D, Hatfield C, Sarmiento MR, Velasquez J, Gomer RH. Annotating Putative Proteins Using I-TASSER. Micropublication Biology. 2021. PMID 34278246 DOI: 10.17912/micropub.biology.000420   
2021 Hou Z, Yang Y, Li H, Wong KC, Li X. iDeepSubMito: identification of protein submitochondrial localization with deep learning. Briefings in Bioinformatics. PMID 34337657 DOI: 10.1093/bib/bbab288   
2021 Johnson RL, Blaber HG, Evans T, Worthy HL, Pope JR, Jones DD. Designed Artificial Protein Heterodimers With Coupled Functions Constructed Using Bio-Orthogonal Chemistry. Frontiers in Chemistry. 9: 733550. PMID 34422774 DOI: 10.3389/fchem.2021.733550   
2021 Liu G, Singha M, Pu L, Neupane P, Feinstein J, Wu HC, Ramanujam J, Brylinski M. GraphDTI: A robust deep learning predictor of drug-target interactions from multiple heterogeneous data. Journal of Cheminformatics. 13: 58. PMID 34380569 DOI: 10.1186/s13321-021-00540-0   
2021 Habibi M, Taheri G. Topological network based drug repurposing for coronavirus 2019. Plos One. 16: e0255270. PMID 34324563 DOI: 10.1371/journal.pone.0255270   
2021 Yuan Q, Chen J, Zhao H, Zhou Y, Yang Y. Structure-aware protein-protein interaction site prediction using deep graph convolutional network. Bioinformatics (Oxford, England). PMID 34498061 DOI: 10.1093/bioinformatics/btab643   
2021 Liu X, Zhang Y, Ward LD, Yan Q, Bohnuud T, Hernandez R, Lao S, Yuan J, Fan F. A proteomic platform to identify off-target proteins associated with therapeutic modalities that induce protein degradation or gene silencing. Scientific Reports. 11: 15856. PMID 34349202 DOI: 10.1038/s41598-021-95354-3   
2021 Robin X, Haas J, Gumienny R, Smolinski A, Tauriello G, Schwede T. Continuous Automated Model EvaluatiOn (CAMEO)-Perspectives on the future of fully automated evaluation of structure prediction methods. Proteins. PMID 34387007 DOI: 10.1002/prot.26213   
2021 Ozturk K, Carter H. Predicting functional consequences of mutations using molecular interaction network features. Human Genetics. PMID 34432150 DOI: 10.1007/s00439-021-02329-5   
2021 Sanchez TW, Owens A, Martinez NJ, Wallgren E, Simeonov A, Henderson MJ. High-Throughput Detection of Ligand-Protein Binding Using a SplitLuc Cellular Thermal Shift Assay. Methods in Molecular Biology (Clifton, N.J.). 2365: 21-41. PMID 34432237 DOI: 10.1007/978-1-0716-1665-9_2   
2021 Zeng X, Xiang Y, Liu Q, Wang L, Ma Q, Ma W, Zeng D, Yin Y, Wang D. Nanopore Technology for the Application of Protein Detection. Nanomaterials (Basel, Switzerland). 11. PMID 34443773 DOI: 10.3390/nano11081942   
2021 Popescu VB, Sanchez-Martinez JA, Schacherer D, Safadoust S, Majidi N, Andronescu A, Nedea A, Ion D, Mititelu E, Czeizler E, Petre I. NetControl4BioMed: A web-based platform for controllability analysis of protein-protein interaction networks. Bioinformatics (Oxford, England). PMID 34352070 DOI: 10.1093/bioinformatics/btab570   
2021 Morgunov AS, Liis Saar K, Vendruscolo M, Knowles TPJ. New frontiers for machine learning in protein science. Journal of Molecular Biology. 167232. PMID 34499920 DOI: 10.1016/j.jmb.2021.167232   
2021 Yang YH, Wang JS, Yuan SS, Liu ML, Su W, Lin H, Zhang ZY. A Survey for Predicting ATP Binding Residues of Proteins Using Machine Learning Methods. Current Medicinal Chemistry. PMID 34514982 DOI: 10.2174/0929867328666210910125802   
2021 Aguilar-Pineda GE, Olivares-Quiroz L. Catalytic and binding sites prediction in globular proteins through discrete Markov chains and network centrality measures. Physical Biology. PMID 34433159 DOI: 10.1088/1478-3975/ac211b   
2021 Li XY, Xiang J, Wu FX, Li M. NetAUC: A network-based multi-biomarker identification method by AUC optimization. Methods (San Diego, Calif.). PMID 34364986 DOI: 10.1016/j.ymeth.2021.08.001   
2021 Jia LL, Sun TT, Wang Y, Shen Y. A Machine Learning Study on the Thermostability Prediction of (R)--Selective Amine Transaminase from Aspergillus terreus. Biomed Research International. 2021: 2593748. PMID 34447850 DOI: 10.1155/2021/2593748   
2021 Orsburn BC. Evaluation of the Sensitivity of Proteomics Methods Using the Absolute Copy Number of Proteins in a Single Cell as a Metric. Proteomes. 9. PMID 34287363 DOI: 10.3390/proteomes9030034   
2021 Orsburn BC. Evaluation of the Sensitivity of Proteomics Methods Using the Absolute Copy Number of Proteins in a Single Cell as a Metric. Proteomes. 9. PMID 34287363 DOI: 10.3390/proteomes9030034   
2021 Hong Z, Zhang T, Zhang Y, Xie Z, Lu Y, Yao Y, Yang Y, Wu H, Liu B. Reveals of candidate active ingredients in Justicia and its anti-thrombotic action of mechanism based on network pharmacology approach and experimental validation. Scientific Reports. 11: 17187. PMID 34433871 DOI: 10.1038/s41598-021-96683-z   
2021 Peng J, Kuang L, Zhang Z, Tan Y, Chen Z, Wang L. A Novel Model for Identifying Essential Proteins Based on Key Target Convergence Sets. Frontiers in Genetics. 12: 721486. PMID 34394201 DOI: 10.3389/fgene.2021.721486   
2021 Wang L, Liu J, Xia Y, Xu J, Zhou X, Zhang G. Distance-guided protein folding based on generalized descent direction. Briefings in Bioinformatics. PMID 34355233 DOI: 10.1093/bib/bbab296   
2021 Pedreira T, Elfmann C, Singh N, Stülke J. SynWiki: Functional annotation of the first artificial organism Mycoplasma mycoides JCVI-syn3A. Protein Science : a Publication of the Protein Society. PMID 34515387 DOI: 10.1002/pro.4179   
2021 Lu W, Kostic M, Zhang T, Che J, Patricelli MP, Jones LH, Chouchani ET, Gray NS. Fragment-based covalent ligand discovery. Rsc Chemical Biology. 2: 354-367. PMID 34458789 DOI: 10.1039/d0cb00222d