David Baker - Related publications

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50 most relevant papers in past 60 days:
Year Citation  Score
2021 Xu YC, ShangGuan TJ, Ding XM, Cheung NJ. Accurate prediction of protein torsion angles using evolutionary signatures and recurrent neural network. Scientific Reports. 11: 21033. PMID 34702851 DOI: 10.1038/s41598-021-00477-2   
2021 Catalano C, Al Mughram MH, Guo Y, Kellogg GE. 3D interaction homology: Hydropathic interaction environments of serine and cysteine are strikingly different and their roles adapt in membrane proteins. Current Research in Structural Biology. 3: 239-256. PMID 34693344 DOI: 10.1016/j.crstbi.2021.09.002   
2021 Wong SWK, Liu Z. Conformational variability of loops in the SARS-CoV-2 spike protein. Proteins. PMID 34661307 DOI: 10.1002/prot.26266   
2021 Collu G, Bierig T, Krebs AS, Engilberge S, Varma N, Guixà-González R, Sharpe T, Deupi X, Olieric V, Poghosyan E, Benoit RM. Chimeric single α-helical domains as rigid fusion protein connections for protein nanotechnology and structural biology. Structure (London, England : 1993). PMID 34587504 DOI: 10.1016/j.str.2021.09.002   
2021 Nijhawan AK, Chan AM, Hsu DJ, Chen LX, Kohlstedt KL. Resolving Dynamics in the Ensemble: Finding Paths through Intermediate States and Disordered Protein Structures. The Journal of Physical Chemistry. B. PMID 34748336 DOI: 10.1021/acs.jpcb.1c05820   
2021 Kumar A, Kumar P, Saumya KU, Giri R. Investigating the conformational dynamics of SARS-CoV-2 NSP6 protein with emphasis on non-transmembrane 91-112 & 231-290 regions. Microbial Pathogenesis. 161: 105236. PMID 34648928 DOI: 10.1016/j.micpath.2021.105236   
2021 Wang Z, Zheng L, Liu Y, Qu Y, Li YQ, Zhao M, Mu Y, Li W. OnionNet-2: A Convolutional Neural Network Model for Predicting Protein-Ligand Binding Affinity Based on Residue-Atom Contacting Shells. Frontiers in Chemistry. 9: 753002. PMID 34778208 DOI: 10.3389/fchem.2021.753002   
2021 Vankayala SL, Warrensford LC, Pittman AR, Pollard BC, Kearns FL, Larkin JD, Woodcock HL. CIFDock: A novel CHARMM-based flexible receptor-flexible ligand docking protocol. Journal of Computational Chemistry. PMID 34741467 DOI: 10.1002/jcc.26759   
2021 Hussain M, Cummins MC, Endo-Streeter S, Sondek J, Kuhlman B. Designer proteins that competitively inhibit Gα by targeting its effector site. The Journal of Biological Chemistry. 101348. PMID 34715131 DOI: 10.1016/j.jbc.2021.101348   
2021 Zhao Q, Yuan JJ, Hu F, Qian C, Tian CF, Wang JT, Gao D, Yi W, Wang HB. Isolation, physicochemical, and structure-function relationship of the hydrophobic variant of Fc-fusion proteins that bind to TNF-α receptor, HS002 and HS002A. Journal of Chromatography. B, Analytical Technologies in the Biomedical and Life Sciences. 1186: 123026. PMID 34781108 DOI: 10.1016/j.jchromb.2021.123026   
2021 Tanramluk D*, Pakotiprapha D, Phoochaijaroen S, Chantravisut P, Thampradid S, Vanichtanankul J, Narupiyakul L, Akavipat R, Yuvaniyama J. MANORAA: A machine learning platform to guide protein-ligand design by anchors and influential distances. Structure. PMID 34614393 DOI: 10.1016/j.str.2021.09.004   
2021 Sun Z, Zheng S, Zhao H, Niu Z, Lu Y, Pan Y, Yang Y. To improve the predictions of binding residues with DNA, RNA, carbohydrate, and peptide via multi-task deep neural networks. Ieee/Acm Transactions On Computational Biology and Bioinformatics. PMID 34637380 DOI: 10.1109/TCBB.2021.3118916   
2021 Du Z, Su H, Wang W, Ye L, Wei H, Peng Z, Anishchenko I, Baker D, Yang J. The trRosetta server for fast and accurate protein structure prediction. Nature Protocols. PMID 34759384 DOI: 10.1038/s41596-021-00628-9   
2021 Zagotta WN, Sim BS, Nhim AK, Raza MM, Evans EG, Venkatesh Y, Jones CM, Mehl RA, Petersson EJ, Gordon SE. An improved fluorescent noncanonical amino acid for measuring conformational distributions using time-resolved transition metal ion FRET. Elife. 10. PMID 34623258 DOI: 10.7554/eLife.70236   
2021 Robertson AJ, Courtney JM, Shen Y, Ying J, Bax A. Concordance of X-ray and AlphaFold2 Models of SARS-CoV-2 Main Protease with Residual Dipolar Couplings Measured in Solution. Journal of the American Chemical Society. PMID 34757725 DOI: 10.1021/jacs.1c10588   
2021 Sanejouand YH. Normal-mode driven exploration of protein domain motions. Journal of Computational Chemistry. 42: 2250-2257. PMID 34599620 DOI: 10.1002/jcc.26755   
2021 Keshtvarz M, Mahboobi M, Kieliszek M, Miecznikowski A, Sedighian H, Rezaei M, Haghighi MA, Zareh Z, Rezaei E. Engineering of Cytolethal Distending Toxin B by Its Reducing Immunogenicity and Maintaining Stability as a New Drug Candidate for Tumor Therapy; an In Silico Study. Toxins. 13. PMID 34822569 DOI: 10.3390/toxins13110785   
2021 Berta D, Badaoui M, Martino SA, Buigues PJ, Pisliakov AV, Elghobashi-Meinhardt N, Wells G, Harris SA, Frezza E, Rosta E. Modelling the active SARS-CoV-2 helicase complex as a basis for structure-based inhibitor design. Chemical Science. 12: 13492-13505. PMID 34777769 DOI: 10.1039/d1sc02775a   
2021 Cuy-Chaparro L, Bohórquez MD, Arévalo-Pinzón G, Castañeda-Ramírez JJ, Suárez CF, Pabón L, Ordóñez D, Gallego-López GM, Suárez CE, Moreno-Pérez DA, Patarroyo MA. Ligand-Receptor Interaction: AMA-1 Contains Small Regions Governing Bovine Erythrocyte Binding. International Journal of Molecular Sciences. 22. PMID 33450807 DOI: 10.3390/ijms22020714   
2021 Jia Z, Liu C, Chen Y, Jiang H, Wang Z, Yao J, Yang J, Zhu J, Zhang B, Yuchi Z. Crystal structures of the SARS-CoV-2 nucleocapsid protein C-terminal domain and development of nucleocapsid-targeting nanobodies. The Febs Journal. PMID 34665939 DOI: 10.1111/febs.16239   
2021 Raj N, Click T, Yang H, Chu JW. Mechanical couplings of protein backbone and side chains exhibit scale-free network properties and specific hotspots for function. Computational and Structural Biotechnology Journal. 19: 5309-5320. PMID 34765086 DOI: 10.1016/j.csbj.2021.09.004   
2021 Milorey B, Schwalbe H, O'Neill N, Schweitzer-Stenner R. Repeating Aspartic Acid Residues Prefer Turn-like Conformations in the Unfolded State: Implications for Early Protein Folding. The Journal of Physical Chemistry. B. PMID 34619031 DOI: 10.1021/acs.jpcb.1c06472   
2021 Juanes-Gusano D, Santos M, Reboto V, Alonso M, Rodríguez-Cabello JC. Self-assembling systems comprising intrinsically disordered protein polymers like elastin-like recombinamers. Journal of Peptide Science : An Official Publication of the European Peptide Society. e3362. PMID 34545666 DOI: 10.1002/psc.3362   
2021 Modi V, Dunbrack RL. Kincore: a web resource for structural classification of protein kinases and their inhibitors. Nucleic Acids Research. PMID 34643709 DOI: 10.1093/nar/gkab920   
2021 Bradford SYC, El Khoury L, Ge Y, Osato M, Mobley DL, Fischer M. Temperature artifacts in protein structures bias ligand-binding predictions. Chemical Science. 12: 11275-11293. PMID 34667539 DOI: 10.1039/d1sc02751d   
2021 Perišić O, Wriggers W. Mechanism for the Unfolding of the TOP7 Protein in Steered Molecular Dynamics Simulations as Revealed by Mutual Information Analysis. Frontiers in Molecular Biosciences. 8: 696609. PMID 34660691 DOI: 10.3389/fmolb.2021.696609   
2021 Agarwal N, Jaiswal N, Gulati K, Gangele K, Nagar N, Kumar D, Poluri KM. Molecular Insights into Conformational Heterogeneity and Enhanced Structural Integrity of DNA Binding Protein Hup at Low pH. Biochemistry. PMID 34665609 DOI: 10.1021/acs.biochem.1c00395   
2021 Ashraf S, Ranaghan KE, Woods CJ, Mulholland AJ, Ul-Haq Z. Exploration of the structural requirements of Aurora Kinase B inhibitors by a combined QSAR, modelling and molecular simulation approach. Scientific Reports. 11: 18707. PMID 34548506 DOI: 10.1038/s41598-021-97368-3   
2021 Hallinan JP, Doyle LA, Shen BW, Gewe MM, Takushi B, Kennedy MA, Friend D, Roberts JM, Bradley P, Stoddard BL. Design of functionalised circular tandem repeat proteins with longer repeat topologies and enhanced subunit contact surfaces. Communications Biology. 4: 1240. PMID 34716407 DOI: 10.1038/s42003-021-02766-y   
2021 Goodsell DS, Burley SK. RCSB Protein Data Bank resources for structure-facilitated design of mRNA vaccines for existing and emerging viral pathogens. Structure (London, England : 1993). PMID 34739839 DOI: 10.1016/j.str.2021.10.008   
2021 Soltanikazemi E, Quadir F, Roy RS, Guo Z, Cheng J. Distance-based Reconstruction of Protein Quaternary Structures from Inter-Chain Contacts. Proteins. PMID 34716620 DOI: 10.1002/prot.26269   
2021 Beuvin F, de Givry S, Schiex T, Verel S, Simoncini D. Iterated local search with partition crossover for computational protein design. Proteins. 89: 1522-1529. PMID 34228826 DOI: 10.1002/prot.26174   
2021 Zheng S, Lei Z, Ai H, Chen H, Deng D, Yang Y. Deep scaffold hopping with multimodal transformer neural networks. Journal of Cheminformatics. 13: 87. PMID 34774103 DOI: 10.1186/s13321-021-00565-5   
2021 Dubois C, Planelles-Herrero VJ, Tillatte-Tripodi C, Delbecq S, Mammri L, Sirkia EM, Ropars V, Roumestand C, Barthe P. Pressure and Chemical Unfolding of an α-Helical Bundle Protein: The GH2 Domain of the Protein Adaptor GIPC1. International Journal of Molecular Sciences. 22. PMID 33808390 DOI: 10.3390/ijms22073597   
2021 Vongsouthi V, Whitfield JH, Unichenko P, Mitchell JA, Breithausen B, Khersonsky O, Kremers L, Janovjak H, Monai H, Hirase H, Fleishman SJ, Henneberger C, Jackson CJ. A Rationally and Computationally Designed Fluorescent Biosensor for d-Serine. Acs Sensors. 6: 4193-4205. PMID 34783546 DOI: 10.1021/acssensors.1c01803   
2021 Sheikh AY, Mattei A, Miglani Bhardwaj R, Hong RS, Abraham NS, Schneider-Rauber G, Engstrom KM, Diwan M, Henry RF, Gao Y, Juarez V, Jordan E, DeGoey DA, Hutchins CW. Implications of the Conformationally Flexible, Macrocyclic Structure of the First-Generation, Direct-Acting Anti-Viral Paritaprevir on Its Solid Form Complexity and Chameleonic Behavior. Journal of the American Chemical Society. PMID 34637297 DOI: 10.1021/jacs.1c06837   
2021 Yang J, Zhang P, Cheng WX, Lu Y, Gang W, Ren G. Exposing structural variations in SARS-CoV-2 evolution. Scientific Reports. 11: 22042. PMID 34764391 DOI: 10.1038/s41598-021-01650-3   
2021 Tam C, Kumar A, Zhang KYJ. NbX: Machine Learning-Guided Re-Ranking of Nanobody-Antigen Binding Poses. Pharmaceuticals (Basel, Switzerland). 14. PMID 34681192 DOI: 10.3390/ph14100968   
2021 Hendrikse SIS, Contreras-Montoya R, Ellis AV, Thordarson P, Steed JW. Biofunctionality with a twist: the importance of molecular organisation, handedness and configuration in synthetic biomaterial design. Chemical Society Reviews. PMID 34846055 DOI: 10.1039/d1cs00896j   
2021 Seok J, Hong J, Park J, Kim KJ. Structural analysis of the peptidoglycan editing factor PdeF from Bacillus cereus ATCC 14579. Biochemical and Biophysical Research Communications. 583: 43-48. PMID 34735878 DOI: 10.1016/j.bbrc.2021.10.051   
2021 Fuzo CA, de Araujo LFL, Pontes RS, Évora PM, Stabeli RG. Adjacent dimer epitope of envelope protein as an important region for Zika virus serum neutralization: a computational investigation. Journal of Biomolecular Structure & Dynamics. 39: 1082-1092. PMID 32090677 DOI: 10.1080/07391102.2020.1728385   
2021 Suleman M, Yousafi Q, Ali J, Ali SS, Hussain Z, Ali S, Waseem M, Iqbal A, Ahmad S, Khan A, Wang Y, Wei DQ. Bioinformatics analysis of the differences in the binding profile of the wild-type and mutants of the SARS-CoV-2 spike protein variants with the ACE2 receptor. Computers in Biology and Medicine. 138: 104936. PMID 34655895 DOI: 10.1016/j.compbiomed.2021.104936   
2021 Chandonia JM, Guan L, Lin S, Yu C, Fox NK, Brenner SE. SCOPe: improvements to the structural classification of proteins - extended database to facilitate variant interpretation and machine learning. Nucleic Acids Research. PMID 34850923 DOI: 10.1093/nar/gkab1054   
2021 Morand J, Nunes A, Faísca PFN. The folding space of protein2-microglobulin is modulated by a single disulfide bridge. Physical Biology. 18. PMID 34098544 DOI: 10.1088/1478-3975/ac08ec   
2021 Corbeil CR, Manenda MS, Sulea T, Baardsnes J, Picard MÈ, Hogues H, Gaudreault F, Deprez C, Shi R, Purisima EO. Redesigning an antibody H3 loop by virtual screening of a small library of human germline-derived sequences. Scientific Reports. 11: 21362. PMID 34725391 DOI: 10.1038/s41598-021-00669-w   
2021 Saporiti S, Parravicini C, Pergola C, Guerrini U, Rossi M, Centola F, Eberini I. IgG1 conformational behavior: elucidation of the N-glycosylation role via molecular dynamics. Biophysical Journal. PMID 34710380 DOI: 10.1016/j.bpj.2021.10.026   
2021 Kolos JM, Pomplun S, Jung S, Rieß B, Purder PL, Voll AM, Merz S, Gnatzy M, Geiger TM, Quist-Løkken I, Jatzlau J, Knaus P, Holien T, Bracher A, Meyners C, et al. Picomolar FKBP inhibitors enabled by a single water-displacing methyl group in bicyclic [4.3.1] aza-amides. Chemical Science. 12: 14758-14765. PMID 34820091 DOI: 10.1039/d1sc04638a   
2021 Do HN, Haldane A, Levy RM, Miao Y. Unique features of different classes of G-protein-coupled receptors revealed from sequence coevolutionary and structural analysis. Proteins. PMID 34599827 DOI: 10.1002/prot.26256   
2021 Pacheco-Garcia JL, Anoz-Carbonell E, Vankova P, Kannan A, Palomino-Morales R, Mesa-Torres N, Salido E, Man P, Medina M, Naganathan AN, Pey AL. Structural basis of the pleiotropic and specific phenotypic consequences of missense mutations in the multifunctional NAD(P)H:quinone oxidoreductase 1 and their pharmacological rescue. Redox Biology. 46: 102112. PMID 34537677 DOI: 10.1016/j.redox.2021.102112   
2021 Chan HTH, Moesser MA, Walters RK, Malla TR, Twidale RM, John T, Deeks HM, Johnston-Wood T, Mikhailov V, Sessions RB, Dawson W, Salah E, Lukacik P, Strain-Damerell C, Owen CD, et al. Discovery of SARS-CoV-2 M peptide inhibitors from modelling substrate and ligand binding. Chemical Science. 12: 13686-13703. PMID 34760153 DOI: 10.1039/d1sc03628a