Axel Brunger, Ph.D. - Related publications

Stanford University, Palo Alto, CA 
crystallography, synaptic neurotransmission
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50 most relevant papers in past 60 days:
Year Citation  Score
2021 Mori T, Jung J, Kobayashi C, Dokainish HM, Re S, Sugita Y. Elucidation of Interactions Regulating Conformational Stability and Dynamics of SARS-CoV-2 S-Protein. Biophysical Journal. PMID 33484712 DOI: 10.1016/j.bpj.2021.01.012   
2021 Smith RD, Carlson HA. Identification of Cryptic Binding Sites Using MixMD with Standard and Accelerated Molecular Dynamics. Journal of Chemical Information and Modeling. PMID 33599485 DOI: 10.1021/acs.jcim.0c01002   
2021 Ching WY, Adhikari P, Jawad B, Podgornik R. Ultra-large-scale quantum chemical computation of bio-molecular systems: the case of Spike protein of SARS-CoV-2 virus. Computational and Structural Biotechnology Journal. PMID 33623641 DOI: 10.1016/j.csbj.2021.02.004   
2021 Gupta D, Tiwari P, Haque MA, Sachdeva E, Hassan MI, Ethayathulla AS, Kaur P. Structural insights into the transient closed conformation and pH dependent ATPase activity of S.Typhi GyraseB N- terminal domain. Archives of Biochemistry and Biophysics. 108786. PMID 33548211 DOI: 10.1016/   
2021 Buchholz I, McDonnell T, Nestler P, Tharad S, Kulke M, Radziszewska A, Ripoll VM, Schmidt F, Hammer E, Toca-Herrera JL, Rahman A, Delcea M. Specific domain V reduction of beta-2-glycoprotein I induces protein flexibility and alters pathogenic antibody binding. Scientific Reports. 11: 4542. PMID 33633190 DOI: 10.1038/s41598-021-84021-2   
2021 Bhatia S, Krishnamoorthy G, Udgaonkar JB. Mapping Distinct Sequences of Structure Formation Differentiating Multiple Folding Pathways of a Small Protein. Journal of the American Chemical Society. PMID 33430589 DOI: 10.1021/jacs.0c11097   
2021 Dang TKL, Nguyen T, Habeck M, Gültas M, Waack S. A graph-based algorithm for detecting rigid domains in protein structures. Bmc Bioinformatics. 22: 66. PMID 33579190 DOI: 10.1186/s12859-021-03966-3   
2021 Salvi N, Bessa LM, Guseva S, Camacho-Zarco A, Maurin D, Perez LM, Malki A, Hengesbach M, Korn SM, Schlundt A, Schwalbe H, Blackledge M. H, C and N backbone chemical shift assignments of SARS-CoV-2 nsp3a. Biomolecular Nmr Assignments. PMID 33475934 DOI: 10.1007/s12104-020-10001-8   
2021 Walls B, Mazilkin AA, Mukhamedov BO, Ionov A, Smirnova IA, Ponomareva AV, Fleischer K, Kozlovskaya NA, Shulyatev DA, Abrikosov IA, Shvets IV, Bozhko SI. Nanodomain structure of single crystalline nickel oxide. Scientific Reports. 11: 3496. PMID 33568704 DOI: 10.1038/s41598-021-82070-1   
2021 Mohd-Kipli F, Claridge JK, Habjanič J, Jiang A, Schnell JR. Conformational triggers associated with influenza matrix protein 1 polymerization. The Journal of Biological Chemistry. 100316. PMID 33516724 DOI: 10.1016/j.jbc.2021.100316   
2021 Cole CA, Daigham NS, Liu G, Montelione GT, Valafar H. REDCRAFT: A computational platform using residual dipolar coupling NMR data for determining structures of perdeuterated proteins in solution. Plos Computational Biology. 17: e1008060. PMID 33524015 DOI: 10.1371/journal.pcbi.1008060   
2021 Pfab J, Phan NM, Si D. DeepTracer for fast de novo cryo-EM protein structure modeling and special studies on CoV-related complexes. Proceedings of the National Academy of Sciences of the United States of America. 118. PMID 33361332 DOI: 10.1073/pnas.2017525118   
2021 Kumar R, Saran S. Comparative modelling unravels the structural features of eukaryotic TCTP implicated in its multifunctional properties: an in silico approach. Journal of Molecular Modeling. 27: 20. PMID 33410974 DOI: 10.1007/s00894-020-04630-y   
2021 Roche R, Bhattacharya S, Bhattacharya D. Hybridized distance- and contact-based hierarchical structure modeling for folding soluble and membrane proteins. Plos Computational Biology. 17: e1008753. PMID 33621244 DOI: 10.1371/journal.pcbi.1008753   
2021 Sharma A, Kumari S, Goel M. Uncovering the structure-function aspects of an archaeal CsaA protein. Biochimica Et Biophysica Acta. Proteins and Proteomics. 140615. PMID 33561579 DOI: 10.1016/j.bbapap.2021.140615   
2021 Hays JM, Boland E, Kasson PM. Inference of Joint Conformational Distributions from Separately Acquired Experimental Measurements. The Journal of Physical Chemistry Letters. 12: 1606-1611. PMID 33596657 DOI: 10.1021/acs.jpclett.0c03623   
2021 Hiranuma N, Park H, Baek M, Anishchenko I, Dauparas J, Baker D. Improved protein structure refinement guided by deep learning based accuracy estimation. Nature Communications. 12: 1340. PMID 33637700 DOI: 10.1038/s41467-021-21511-x   
2021 Takeda S, Koike R, Nagae T, Fujiwara I, Narita A, Maéda Y, Ota M. Crystal structure of human V-1 in the apo form. Acta Crystallographica. Section F, Structural Biology Communications. 77: 13-21. PMID 33439151 DOI: 10.1107/S2053230X20016829   
2021 Qin W, Yu F, Zhou H, Li P, Zhou F, Li HJ, He CX, Xing L, Zhou X, Zhao D, Li PQ, Jin X, Wang QS, He JH, Cao HL. Complex crystal structure determination and anti-non-small-cell lung cancer activity of the Hsp90 inhibitor Debio0932. Acta Crystallographica. Section D, Structural Biology. 77: 86-97. PMID 33404528 DOI: 10.1107/S2059798320014990   
2021 Greber BJ, Remis J, Ali S, Nogales E. 2.5Å-resolution structure of the human CDK-activating kinase bound to the clinical inhibitor ICEC0942. Biophysical Journal. PMID 33476598 DOI: 10.1016/j.bpj.2020.12.030   
2021 Ayoub R, Lee Y. Protein structure search to support the development of protein structure prediction methods. Proteins. PMID 33458852 DOI: 10.1002/prot.26048   
2021 Hubbard PA, Xia C, Shen AL, Kim JP. Structural and kinetic investigations of the carboxy terminus of NADPH cytochrome P450 oxidoreductase. Archives of Biochemistry and Biophysics. 108792. PMID 33556357 DOI: 10.1016/   
2021 Gianni S, Freiberger MI, Jemth P, Ferreiro DU, Wolynes PG, Fuxreiter M. Fuzziness and Frustration in the Energy Landscape of Protein Folding, Function, and Assembly. Accounts of Chemical Research. PMID 33550810 DOI: 10.1021/acs.accounts.0c00813   
2021 Spencer SEF, Rodger A. Bayesian inference assessment of protein secondary structure analysis using circular dichroism data - how much structural information is contained in protein circular dichroism spectra? Analytical Methods : Advancing Methods and Applications. PMID 33393941 DOI: 10.1039/d0ay01645d   
2021 Croll TI, Williams CJ, Chen VB, Richardson DC, Richardson JS. Improving SARS-CoV-2 Structures: Peer Review by Early Coordinate Release. Biophysical Journal. PMID 33460600 DOI: 10.1016/j.bpj.2020.12.029   
2021 Hou Q, Pucci F, Ancien F, Kwasigroch JM, Bourgeas R, Rooman M. SWOTein: a structure-based approach to predict stability Strengths and Weaknesses of prOTEINs. Bioinformatics (Oxford, England). PMID 33471089 DOI: 10.1093/bioinformatics/btab034   
2021 Crilly CJ, Brom JA, Kowalewski ME, Piszkiewicz S, Pielak GJ. Dried Protein Structure Revealed at the Residue Level by Liquid-Observed Vapor Exchange NMR. Biochemistry. PMID 33400518 DOI: 10.1021/acs.biochem.0c00863   
2021 Bedford JT, Poutsma J, Diawara N, Greene LH. The nature of persistent interactions in two model β-grasp proteins reveals the advantage of symmetry in stability. Journal of Computational Chemistry. PMID 33534913 DOI: 10.1002/jcc.26477   
2021 Chen X, Sakurai H, Wang H, Gao S, Bi HD, Bai FQ. Theoretical study on the molecular stacking interactions and charge transport properties of triazasumanene crystals - from explanation to prediction. Physical Chemistry Chemical Physics : Pccp. PMID 33595565 DOI: 10.1039/d0cp06102f   
2021 Fàbrega-Ferrer M, Cuervo A, Fernández FJ, Machón C, Pérez-Luque R, Pous J, Vega MC, Carrascosa JL, Coll M. Using a partial atomic model from medium-resolution cryo-EM to solve a large crystal structure. Acta Crystallographica. Section D, Structural Biology. 77: 11-18. PMID 33404521 DOI: 10.1107/S2059798320015156   
2021 He J, Han Z, Farooq QUA, Li C. Study on functional sites in human multidrug resistance protein 1 (hMRP1). Proteins. PMID 33469960 DOI: 10.1002/prot.26049   
2021 Paiz EA, Lewis KA, Whitten ST. Structural and Energetic Characterization of the Denatured State from the Perspectives of Peptides, the Coil Library, and Intrinsically Disordered Proteins. Molecules (Basel, Switzerland). 26. PMID 33530506 DOI: 10.3390/molecules26030634   
2021 Ajadi MB, Soremekun OS, Elrashedy AA, Olotu FA, Kumalo HM, Soliman MES. Probing Protein-Protein Interactions and Druggable Site Identification: Mechanistic Binding Events between Ubiquitin and Zinc Finger with UFM1-Specific Peptidase Domain Protein (ZUFSP). Combinatorial Chemistry & High Throughput Screening. PMID 33538664 DOI: 10.2174/1386207324666210203175142   
2021 Li Y, Bedi RK, Wiedmer L, Sun X, Huang D, Caflisch A. Atomistic and Thermodynamic Analysis of N6-Methyladenosine (mA) Recognition by the Reader Domain of YTHDC1. Journal of Chemical Theory and Computation. PMID 33472367 DOI: 10.1021/acs.jctc.0c01136   
2021 Aiyer S, Swapna GVT, Ma LC, Liu G, Hao J, Chalmers G, Jacobs BC, Montelione GT, Roth MJ. A common binding motif in the ET domain of BRD3 forms polymorphic structural interfaces with host and viral proteins. Structure (London, England : 1993). PMID 33592170 DOI: 10.1016/j.str.2021.01.010   
2021 Thompson EJ, Paul A, Iavarone AT, Klinman JP. Identification of Thermal Conduits That Link the Protein-Water Interface to the Active Site Loop and Catalytic Base in Enolase. Journal of the American Chemical Society. PMID 33395523 DOI: 10.1021/jacs.0c09423   
2021 Chaoprasid P, Lukat P, Mühlen S, Heidler T, Gazdag EM, Dong S, Bi W, Rüter C, Kirchenwitz M, Steffen A, Jänsch L, Stradal TEB, Dersch P, Blankenfeldt W. Crystal structure of bacterial cytotoxic necrotizing factor CNF reveals molecular building blocks for intoxication. The Embo Journal. e105202. PMID 33410511 DOI: 10.15252/embj.2020105202   
2021 Jin Y, Johannissen LO, Hay S. Predicting New Protein Conformations from Molecular Dynamics Simulation Conformational Landscapes and Machine Learning. Proteins. PMID 33629765 DOI: 10.1002/prot.26068   
2021 Tsai WC, Aleem AM, Whittington C, Cortopassi WA, Kalyanaraman C, Baroz A, Iavarone AT, Skrzypczak-Jankun E, Jacobson MP, Offenbacher AR, Holman T. Mutagenesis, Hydrogen-Deuterium Exchange, and Molecular Docking Investigations Establish the Dimeric Interface of Human Platelet-Type 12-Lipoxygenase. Biochemistry. PMID 33635645 DOI: 10.1021/acs.biochem.1c00053   
2021 Escalante DE, Ferguson DM. Structural modeling and analysis of the SARS-CoV-2 cell entry inhibitor camostat bound to the trypsin-like protease TMPRSS2. Medicinal Chemistry Research : An International Journal For Rapid Communications On Design and Mechanisms of Action of Biologically Active Agents. 1-11. PMID 33564221 DOI: 10.1007/s00044-021-02708-7   
2021 Juraszek J, Rutten L, Blokland S, Bouchier P, Voorzaat R, Ritschel T, Bakkers MJG, Renault LLR, Langedijk JPM. Stabilizing the closed SARS-CoV-2 spike trimer. Nature Communications. 12: 244. PMID 33431842 DOI: 10.1038/s41467-020-20321-x   
2021 Huang Y, Jin F, Funato Y, Xu Z, Zhu W, Wang J, Sun M, Zhao Y, Yu Y, Miki H, Hattori M. Structural basis for the Mg recognition and regulation of the CorC Mg transporter. Science Advances. 7. PMID 33568487 DOI: 10.1126/sciadv.abe6140   
2021 Romero-Tamayo S, Laplaza R, Velazquez-Campoy A, Villanueva R, Medina M, Ferreira P. W196 and the -Hairpin Motif Modulate the Redox Switch of Conformation and the Biomolecular Interaction Network of the Apoptosis-Inducing Factor. Oxidative Medicine and Cellular Longevity. 2021: 6673661. PMID 33510840 DOI: 10.1155/2021/6673661   
2021 Quesada Moreno MM, Pinacho P, Perez C, Sekutor M, Schreiner PR, Schnell M. Do docking sites persist upon fluorination? The diadamantyl ether-aromatics challenge for rotational spectroscopy and theory. Chemistry (Weinheim An Der Bergstrasse, Germany). PMID 33512017 DOI: 10.1002/chem.202100078   
2021 Mondal B, Nagesh J, Reddy G. Double Domain Swapping in Human γC and γD Crystallin Drives Early Stages of Aggregation. The Journal of Physical Chemistry. B. PMID 33566611 DOI: 10.1021/acs.jpcb.0c07833   
2021 Sundaram R, Manohar K, Patel SK, Acharya N, Vasudevan D. Structural analyses of PCNA from the fungal pathogen Candida albicans identify three regions with species-specific conformations. Febs Letters. PMID 33544878 DOI: 10.1002/1873-3468.14055   
2021 Dietrich MH, Chan LJ, Adair A, Keremane S, Pymm P, Lo AW, Cao YC, Tham WH. Nanobody generation and structural characterization of Plasmodium falciparum 6-cysteine protein Pf12p. The Biochemical Journal. PMID 33480416 DOI: 10.1042/BCJ20200415   
2021 Nerli S, De Paula VS, McShan AC, Sgourakis NG. Backbone-independent NMR resonance assignments of methyl probes in large proteins. Nature Communications. 12: 691. PMID 33514730 DOI: 10.1038/s41467-021-20984-0   
2021 Fry MY, Saladi SM, Clemons WM. The STI1-domain is a flexible alpha-helical fold with a hydrophobic groove. Protein Science : a Publication of the Protein Society. PMID 33620121 DOI: 10.1002/pro.4049   
2021 Duran T, Minatovicz B, Bai J, Shin D, Mohammadiarani H, Chaudhuri B. Molecular Dynamics Simulation to Uncover the Mechanisms of Protein Instability During Freezing. Journal of Pharmaceutical Sciences. PMID 33421436 DOI: 10.1016/j.xphs.2021.01.002