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Helen M. Berman - Related publications

Chemistry and Chemical Biology Rutgers University, New Brunswick, New Brunswick, NJ, United States 
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50 most relevant papers in past 60 days:
Year Citation  Score
2021 Jaskolski M, Dauter Z, Shabalin IG, Gilski M, Brzezinski D, Kowiel M, Rupp B, Wlodawer A. Crystallographic models of SARS-CoV-2 3CL: in-depth assessment of structure quality and validation. Iucrj. 8: 238-256. PMID 33708401 DOI: 10.1107/S2052252521001159   
2021 Caldararu O, Blundell TL, Kepp KP. A base measure of precision for protein stability predictors: structural sensitivity. Bmc Bioinformatics. 22: 88. PMID 33632133 DOI: 10.1186/s12859-021-04030-w   
2021 Matsumoto S, Sugimoto N. New Insights into the Functions of Nucleic Acids Controlled by Cellular Microenvironments. Topics in Current Chemistry (Cham). 379: 17. PMID 33782792 DOI: 10.1007/s41061-021-00329-7   
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 Gong W, Guerler A, Zhang C, Warner E, Li C, Zhang Y. Integrating multimeric threading with high-throughput experiments for structural interactome of Escherichia coli. Journal of Molecular Biology. 166944. PMID 33741411 DOI: 10.1016/j.jmb.2021.166944   
2021 Estrada Pabón JD, Haddox HK, Van Aken G, Pendleton IM, Eramian H, Singer JM, Schrier J. The Role of Configurational Entropy in Miniprotein Stability. The Journal of Physical Chemistry. B. PMID 33739115 DOI: 10.1021/acs.jpcb.0c09888   
2021 Rahman T, Du Y, Zhao L, Shehu A. Generative Adversarial Learning of Protein Tertiary Structures. Molecules (Basel, Switzerland). 26. PMID 33668217 DOI: 10.3390/molecules26051209   
2021 Sikkema HR, Poolman B. In silico method for selecting residue pairs for single-molecule microscopy and spectroscopy. Scientific Reports. 11: 5756. PMID 33707507 DOI: 10.1038/s41598-021-85003-0   
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 Assaiya A, Burada AP, Dhingra S, Kumar J. An overview of the recent advances in cryo-electron microscopy for life sciences. Emerging Topics in Life Sciences. PMID 33760078 DOI: 10.1042/ETLS20200295   
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 Hu H, Laufkötter O, Miljković F, Bajorath J. Data set of competitive and allosteric protein kinase inhibitors confirmed by X-ray crystallography. Data in Brief. 35: 106816. PMID 33604432 DOI: 10.1016/j.dib.2021.106816   
2021 Blaber M. Cooperative hydrophobic core interactions in the β-trefoil architecture. Protein Science : a Publication of the Protein Society. PMID 33686691 DOI: 10.1002/pro.4059   
2021 Mohanty AK, Choudhary S, Kaushik JK, Fisher AJ. Crystal structure of BRP39, a signaling glycoprotein expressed during mammary gland apoptosis at 2.6 Å resolution. Journal of Structural Biology. 107737. PMID 33838225 DOI: 10.1016/j.jsb.2021.107737   
2021 Prestegard JH. A perspective on the PDB's impact on the field of glycobiology. The Journal of Biological Chemistry. 100556. PMID 33744289 DOI: 10.1016/j.jbc.2021.100556   
2021 Di Rienzo L, Miotto M, Bò L, Ruocco G, Raimondo D, Milanetti E. Characterizing Hydropathy of Amino Acid Side Chain in a Protein Environment by Investigating the Structural Changes of Water Molecules Network. Frontiers in Molecular Biosciences. 8: 626837. PMID 33718433 DOI: 10.3389/fmolb.2021.626837   
2021 Bae JE, Kim IJ, Xu Y, Nam KH. Structural Flexibility of Peripheral Loops and Extended C-terminal Domain of Short Length Substrate Binding Protein from Rhodothermus marinus. The Protein Journal. PMID 33651244 DOI: 10.1007/s10930-021-09970-z   
2021 Dias D'Andréa É, Sebastian Retel J, Diehl A, Schmieder P, Oschkinat H, Ricardo Pires J. NMR structure and dynamics of Q4DY78, a conserved kinetoplasid-specific protein from Trypanosoma cruzi. Journal of Structural Biology. 107715. PMID 33705979 DOI: 10.1016/j.jsb.2021.107715   
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 Marzolf DR, Seffernick JT, Lindert S. Protein Structure Prediction from NMR Hydrogen-Deuterium Exchange Data. Journal of Chemical Theory and Computation. PMID 33780620 DOI: 10.1021/acs.jctc.1c00077   
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 Hong RS, Mattei A, Sheikh AY, Bhardwaj RM, Bellucci MA, McDaniel KF, Pierce MO, Sun G, Li S, Wang L, Mondal S, Ji J, Borchardt TB. Novel Physics-Based Ensemble Modeling Approach That Utilizes 3D Molecular Conformation and Packing to Access Aqueous Thermodynamic Solubility: A Case Study of Orally Available Bromodomain and Extraterminal Domain Inhibitor Lead Optimization Series. Journal of Chemical Information and Modeling. PMID 33661005 DOI: 10.1021/acs.jcim.0c01410   
2021 Cho SY, Yoon SI. Structural analysis of the activation and DNA interactions of the response regulator VbrR from Vibrio parahaemolyticus. Biochemical and Biophysical Research Communications. 555: 102-108. PMID 33813268 DOI: 10.1016/j.bbrc.2021.03.114   
2021 Monzon AM, Bonato P, Necci M, Tosatto SCE, Piovesan D. FLIPPER: Predicting and Characterizing Linear Interacting Peptides in the Protein Data Bank. Journal of Molecular Biology. 433: 166900. PMID 33647288 DOI: 10.1016/j.jmb.2021.166900   
2021 Wang L, Cao C, Zuo S. Protein secondary structure assignment using pc-polyline and convolutional neural network. Proteins. PMID 33780034 DOI: 10.1002/prot.26079   
2021 Wu X, Zhang M, Kuang Z, Yue J, Xue L, Zhu M, Zhu Z, Khan MH, Niu L. Crystal structures of anthranilate phosphoribosyltransferase from Saccharomyces cerevisiae. Acta Crystallographica. Section F, Structural Biology Communications. 77: 61-69. PMID 33682790 DOI: 10.1107/S2053230X21001989   
2021 Zhang S, Gong W, Han Z, Liu Y, Li C. Insight into Shared Properties and Differential Dynamics and Specificity of Secretory Phospholipase A Family Members. The Journal of Physical Chemistry. B. PMID 33780247 DOI: 10.1021/acs.jpcb.1c01315   
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 Gee CL, Holton JM, McPherson A. Structures of two novel crystal forms of Aspergillus oryzae alpha amylase (taka-amylase). Journal of Bioscience and Bioengineering. PMID 33814275 DOI: 10.1016/j.jbiosc.2021.02.008   
2021 Egelman EH, Wang F. Cryo-EM is a powerful tool, but helical applications can have pitfalls. Soft Matter. PMID 33729271 DOI: 10.1039/d1sm00282a   
2021 Akiyama T, Sasaki Y, Ito S, Yajima S. Structural basis of the conformational changes in Microbacterium hydrocarbonoxydans IclR transcription factor homolog due to ligand binding. Biochimica Et Biophysica Acta. Proteins and Proteomics. 1869: 140644. PMID 33716191 DOI: 10.1016/j.bbapap.2021.140644   
2021 Sagar A, Jeffries CM, Petoukhov MV, Svergun DI, Bernadó P. Comment on the Optimal Parameters to Derive Intrinsically Disordered Protein Conformational Ensembles from Small-Angle X-ray Scattering Data Using the Ensemble Optimization Method. Journal of Chemical Theory and Computation. PMID 33725442 DOI: 10.1021/acs.jctc.1c00014   
2021 Desiraju GR. Crystal engineering in IUCrJ: from 'the' crystal structure to 'a' crystal structure. Iucrj. 8: 148-149. PMID 33708389 DOI: 10.1107/S2052252521000993   
2021 Hernandes IS, Da Silva HC, Dos Santos HF, De Almeida WB. Unveiling the Molecular Structure of Antimalarial Drugs Chloroquine and Hydroxychloroquine in Solution through Analysis of H NMR Chemical Shifts. The Journal of Physical Chemistry. B. PMID 33760611 DOI: 10.1021/acs.jpcb.1c00609   
2021 Norn C, Wicky BIM, Juergens D, Liu S, Kim D, Tischer D, Koepnick B, Anishchenko I, , Baker D, Ovchinnikov S. Protein sequence design by conformational landscape optimization. Proceedings of the National Academy of Sciences of the United States of America. 118. PMID 33712545 DOI: 10.1073/pnas.2017228118   
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 Nath P, Goyal A. Structure and dynamics analysis of multi-domain putative β-1,4-glucosidase of family 3 glycoside hydrolase (PsGH3) from Pseudopedobacter saltans. Journal of Molecular Modeling. 27: 106. PMID 33694107 DOI: 10.1007/s00894-021-04721-4   
2021 Pinto SMV, Tasinato N, Barone V, Zanetti-Polzi L, Daidone I. A computational insight into the relationship between side chain IR line shapes and local environment in fibril-like structures. The Journal of Chemical Physics. 154: 084105. PMID 33639764 DOI: 10.1063/5.0038913   
2021 Miller EB, Murphy RB, Sindhikara D, Borrelli KW, Grisewood MJ, Ranalli F, Dixon SL, Jerome S, Boyles NA, Day T, Ghanakota P, Mondal S, Rafi SB, Troast DM, Abel R, et al. Reliable and Accurate Solution to the Induced Fit Docking Problem for Protein-Ligand Binding. Journal of Chemical Theory and Computation. PMID 33779166 DOI: 10.1021/acs.jctc.1c00136   
2021 Park SS, Lee S, Rhee DK. Crystal Structure of the Pneumococcal Vancomycin-Resistance Response Regulator DNA-Binding Domain. Molecules and Cells. 44: 179-185. PMID 33795535 DOI: 10.14348/molcells.2021.2235   
2021 Sanders JC, Holmstrom ED. Integrating single-molecule FRET and biomolecular simulations to study diverse interactions between nucleic acids and proteins. Essays in Biochemistry. PMID 33600559 DOI: 10.1042/EBC20200022   
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 van Zundert GCP, Moriarty NW, Sobolev OV, Adams PD, Borrelli KW. Macromolecular refinement of X-ray and cryoelectron microscopy structures with Phenix/OPLS3e for improved structure and ligand quality. Structure (London, England : 1993). PMID 33823127 DOI: 10.1016/j.str.2021.03.011   
2021 Niu C, Du Y, Kaltashov IA. Towards better understanding of the heparin role in NETosis: feasibility of using native mass spectrometry to monitor interactions of neutrophil elastase with heparin oligomers. International Journal of Mass Spectrometry. 463. PMID 33692650 DOI: 10.1016/j.ijms.2021.116550   
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 Fogarty CA, Fadda E. Oligomannose -Glycans 3D Architecture and Its Response to the FcγRIIIa Structural Landscape. The Journal of Physical Chemistry. B. PMID 33661628 DOI: 10.1021/acs.jpcb.1c00304   
2021 Leonardo DA, Cavini IA, Sala FA, Mendonça DC, V D Rosa H, Kumagai PS, Crusca E, Valadares NF, Marques IA, Brandão-Neto J, Munte CE, Kalbitzer HR, Soler N, Usón I, André I, et al. Orientational Ambiguity in Septin Coiled Coils and its Structural Basis. Journal of Molecular Biology. 166889. PMID 33639214 DOI: 10.1016/j.jmb.2021.166889   
2021 Dey S, Misra R, Saseendran A, Pahan S, Gopi H. Metal Coordinated Supramolecular Polymers from the Minimalistic Hybrid Peptide Foldamers. Angewandte Chemie (International Ed. in English). PMID 33543831 DOI: 10.1002/anie.202015838   
2021 Ahn J, Lee J, Jeong S, Kang SM, Park BJ, Ha NC. Beta-strand-mediated dimeric formation of the Ig-like domains of human lamin A/C and B1. Biochemical and Biophysical Research Communications. 550: 191-196. PMID 33706103 DOI: 10.1016/j.bbrc.2021.02.102   
2021 Chesterman C, Arnold E. Co-crystallization with diabodies: a case study for the introduction of synthetic symmetry. Structure (London, England : 1993). PMID 33636101 DOI: 10.1016/j.str.2021.02.001