Frederic M. Richards - Related publications

Molecular Biophysics and Biochemistry Yale University, New Haven, CT 
protein structure and function
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50 most relevant papers in past 60 days:
Year Citation  Score
2021 Jedhe GS, Arora PS. Hydrogen bond surrogate helices as minimal mimics of protein α-helices. Methods in Enzymology. 656: 1-25. PMID 34325784 DOI: 10.1016/bs.mie.2021.04.007   
2021 Halder P, Mitra P. Human prion protein: exploring the thermodynamic stability and structural dynamics of its pathogenic mutants. Journal of Biomolecular Structure & Dynamics. 1-17. PMID 34338141 DOI: 10.1080/07391102.2021.1957715   
2021 Li J, Hou C, Ma X, Guo S, Zhang H, Shi L, Liao C, Zheng B, Ye L, Yang L, He X. Entropy-Enthalpy Compensations Fold Proteins in Precise Ways. International Journal of Molecular Sciences. 22. PMID 34502559 DOI: 10.3390/ijms22179653   
2021 Zweckstetter M. NMR hawk-eyed view of AlphaFold2 structures. Protein Science : a Publication of the Protein Society. PMID 34469019 DOI: 10.1002/pro.4175   
2021 Bie LH, Fei JW, Gao J. Molecular mechanism of methyl-dependent and spatial-specific DNA recognition of c-Jun homodimer. Journal of Molecular Modeling. 27: 227. PMID 34264385 DOI: 10.1007/s00894-021-04840-y   
2021 Sato Y, Matsugami A, Watanabe S, Hayashi F, Arai M, Kigawa T, Nishimura C. Changes in dynamic and static structures of the HIV-1 p24 capsid protein N-domain caused by amino-acid substitution are associated with its viral viability. Protein Science : a Publication of the Protein Society. PMID 34523753 DOI: 10.1002/pro.4184   
2021 Mir S, Ashraf S, Saeed M, Rahman AU, Ul-Haq Z. Protonation states at different pH, conformational changes and impact of glycosylation in synapsin Ia. Physical Chemistry Chemical Physics : Pccp. PMID 34318818 DOI: 10.1039/d1cp00531f   
2021 Dass R, Corlianò E, Mulder FAA. The contribution of electrostatics to hydrogen exchange in the unfolded protein state. Biophysical Journal. PMID 34370996 DOI: 10.1016/j.bpj.2021.08.003   
2021 Florio G, Pugno NM, Buehler MJ, Puglisi G. A coarse-grained mechanical model for folding and unfolding of tropoelastin with possible mutations. Acta Biomaterialia. PMID 34303013 DOI: 10.1016/j.actbio.2021.07.032   
2021 Poghosyan AH, Shahinyan AA, Kirakosyan GR, Ayvazyan NM, Mamasakhlisov YS, Papoian GA. A molecular dynamics study of protein denaturation induced by sulfonate-based surfactants. Journal of Molecular Modeling. 27: 261. PMID 34432183 DOI: 10.1007/s00894-021-04882-2   
2021 Boucher L, Somani S, Negron C, Ma W, Jacobs S, Chan W, Malia T, Obmolova G, Teplyakov A, Gilliland GL, Luo J. Surface Salt bridges Contribute to the Extreme Thermal Stability of an FN3-like domain from a thermophilic bacterium. Proteins. PMID 34405904 DOI: 10.1002/prot.26218   
2021 Schwarz D, Georges G, Kelm S, Shi J, Vangone A, Deane CM. Co-evolutionary Distance Predictions Contain Flexibility Information. Bioinformatics (Oxford, England). PMID 34383892 DOI: 10.1093/bioinformatics/btab562   
2021 Seong K, Krasileva K. Computational structural genomics unravels common folds and novel families in the secretome of fungal phytopathogen . Molecular Plant-Microbe Interactions : Mpmi. PMID 34415195 DOI: 10.1094/MPMI-03-21-0071-R   
2021 Mishra S, Looger LL, Porter LL. A sequence-based method for predicting extant fold switchers that undergo α-helix ↔ β-strand transitions. Biopolymers. e23471. PMID 34498740 DOI: 10.1002/bip.23471   
2021 Fellows AP, Casford MTL, Davies PB. Using hybrid atomic force microscopy and infrared spectroscopy (AFM-IR) to identify chemical components of the hair medulla on the nanoscale. Journal of Microscopy. PMID 34313326 DOI: 10.1111/jmi.13052   
2021 Pan CY, Chou CC. Molecular origin of the effects of mutation on the structure and mechanical properties of human epithelial keratin K5/K14. Journal of the Mechanical Behavior of Biomedical Materials. 124: 104798. PMID 34509171 DOI: 10.1016/j.jmbbm.2021.104798   
2021 Liu Y, Shao X, Wang T, Wang X, Li N, Zhao Y, Xia W, Sun L. [Structure prediction and biological activity analysis of dybowskin-1ST antimicrobial peptide in Rana dybowskii]. Sheng Wu Gong Cheng Xue Bao = Chinese Journal of Biotechnology. 37: 2890-2902. PMID 34472306 DOI: 10.13345/j.cjb.200564   
2021 Zhao J, Liu M, Zang J, Yang S, Chen R, Zhao X, Ding L. Molecular docking, 3D-QASR and molecular dynamics simulations of thiazoles Pin1 inhibitors. Journal of Biomolecular Structure & Dynamics. 1-15. PMID 34499020 DOI: 10.1080/07391102.2021.1975568   
2021 Medeiros Almeida V, Chaudhuri A, Cangussu Cardoso MV, Matsuyama BY, Monteiro Ferreira G, Goulart Trossini GH, Salinas RK, Loria JP, Marana SR. Role of a high centrality residue in protein dynamics and thermal stability. Journal of Structural Biology. 213: 107773. PMID 34320379 DOI: 10.1016/j.jsb.2021.107773   
2021 Breunig SL, Tirrell DA. Incorporation of proline analogs into recombinant proteins expressed in Escherichia coli. Methods in Enzymology. 656: 545-571. PMID 34325798 DOI: 10.1016/bs.mie.2021.05.008   
2021 Papp D, Szigyártó IC, Nordén B, Perczel A, Beke-Somfai T. Structural Water Stabilizes Protein Motifs in Liquid Protein Phase: The Folding Mechanism of Short β-Sheets Coupled to Phase Transition. International Journal of Molecular Sciences. 22. PMID 34445303 DOI: 10.3390/ijms22168595   
2021 Santhouse JR, Rao SR, Horne WS. Analysis of folded structure and folding thermodynamics in heterogeneous-backbone proteomimetics. Methods in Enzymology. 656: 93-122. PMID 34325801 DOI: 10.1016/bs.mie.2021.04.009   
2021 Verburgt J, Kihara D. Benchmarking of structure refinement methods for protein complex models. Proteins. PMID 34309909 DOI: 10.1002/prot.26188   
2021 Miao Z, Wang Q, Xiao X, Kamal GM, Song L, Zhang X, Li C, Zhou X, Jiang B, Liu M. CSI-LSTM: a web server to predict protein secondary structure using bidirectional long short term memory and NMR chemical shifts. Journal of Biomolecular Nmr. PMID 34510297 DOI: 10.1007/s10858-021-00383-9   
2021 Ahammad T, Khan RH, Sahu ID, Drew DL, Faul E, Li T, McCarrick RM, Lorigan GA. Pinholin S mutations induce structural topology and conformational changes. Biochimica Et Biophysica Acta. Biomembranes. 183771. PMID 34499883 DOI: 10.1016/j.bbamem.2021.183771   
2021 Cymer F, Schneider D. Small Residues Inhibit Homo-Dimerization of the Human Carbonic Anhydrase XII Transmembrane Domain. Membranes. 11. PMID 34357162 DOI: 10.3390/membranes11070512   
2021 Kondra S, Chen F, Chen Y, Chen Y, Collette CJ, Xu W. A study of a hierarchical structure of proteins and ligand binding sites of receptors using the TSR-based structure comparison method and development of a size-filtering feature designed for comparing different sizes of protein structures. Proteins. PMID 34392570 DOI: 10.1002/prot.26215   
2021 Dongre AV, Das S, Bellur A, Kumar S, Chandrashekarmath A, Karmakar T, Balaram P, Balasubramanian S, Balaram H. Structural basis for the hyperthermostability of an archaeal enzyme induced by succinimide formation. Biophysical Journal. PMID 34302792 DOI: 10.1016/j.bpj.2021.07.014   
2021 Dongre AV, Das S, Bellur A, Kumar S, Chandrashekarmath A, Karmakar T, Balaram P, Balasubramanian S, Balaram H. Structural basis for the hyperthermostability of an archaeal enzyme induced by succinimide formation. Biophysical Journal. PMID 34302792 DOI: 10.1016/j.bpj.2021.07.014   
2021 Dash R, Mitra S, Munni YA, Choi HJ, Ali MC, Barua L, Jang TJ, Moon IS. Computational Insights into the Deleterious Impacts of Missense Variants on -Acetyl-d-glucosamine Kinase Structure and Function. International Journal of Molecular Sciences. 22. PMID 34360815 DOI: 10.3390/ijms22158048   
2021 Yan B, Ran X, Jiang Y, Torrence SK, Yuan L, Shao Q, Yang ZJ. Rate-Perturbing Single Amino Acid Mutation for Hydrolases: A Statistical Profiling. The Journal of Physical Chemistry. B. PMID 34524819 DOI: 10.1021/acs.jpcb.1c05901   
2021 Shmool TA, Martin LK, Bui-Le L, Moya-Ramirez I, Kotidis P, Matthews RP, Venter GA, Kontoravdi C, Polizzi KM, Hallett JP. An experimental approach probing the conformational transitions and energy landscape of antibodies: a glimmer of hope for reviving lost therapeutic candidates using ionic liquid. Chemical Science. 12: 9528-9545. PMID 34349928 DOI: 10.1039/d1sc02520a   
2021 Van Deuren V, Yang YS, de Guillen K, Dubois C, Royer CA, Roumestand C, Barthe P. Comparative Assessment of NMR Probes for the Experimental Description of Protein Folding Pathways with High-Pressure NMR. Biology. 10. PMID 34356511 DOI: 10.3390/biology10070656   
2021 Mule SN, Rosa-Fernandes L, Coutinho JVP, Gomes VM, Macedo-da-Silva J, Santiago VF, Quina D, de Oliveira GS, Thaysen-Andersen M, Larsen MR, Labriola L, Palmisano G. Systems-wide analysis of glycoprotein conformational changes by limited deglycosylation assay. Journal of Proteomics. 248: 104355. PMID 34450331 DOI: 10.1016/j.jprot.2021.104355   
2021 Tan KP, Singh K, Hazra A, Madhusudhan MS. Peptide bond planarity constrains hydrogen bond geometry and influences secondary structure conformations. Current Research in Structural Biology. 3: 1-8. PMID 34382009 DOI: 10.1016/j.crstbi.2020.11.002   
2021 Aguirre-Cardenas MI, Geddes-Buehre DH, Crowhurst KA. Removal of disulfide from acid stress chaperone HdeA does not wholly eliminate structure or function at low pH. Biochemistry and Biophysics Reports. 27: 101064. PMID 34307907 DOI: 10.1016/j.bbrep.2021.101064   
2021 Yang J, Zhang P, Cheng WX, Lu Y, Gang W, Ren G. Exposing Structural Variations in SARS-CoV-2 Evolution. Research Square. PMID 34545355 DOI: 10.21203/   
2021 Gupta C, Khaniya U, Vant JW, Shekhar M, Mao J, Gunner MR, Singharoy A. Poor Person's pH Simulation of Membrane Proteins. Methods in Molecular Biology (Clifton, N.J.). 2315: 197-217. PMID 34302678 DOI: 10.1007/978-1-0716-1468-6_12   
2021 Gupta C, Khaniya U, Vant JW, Shekhar M, Mao J, Gunner MR, Singharoy A. Poor Person's pH Simulation of Membrane Proteins. Methods in Molecular Biology (Clifton, N.J.). 2315: 197-217. PMID 34302678 DOI: 10.1007/978-1-0716-1468-6_12   
2021 Mortuza SM, Zheng W, Zhang C, Li Y, Pearce R, Zhang Y. Improving fragment-based ab initio protein structure assembly using low-accuracy contact-map predictions. Nature Communications. 12: 5011. PMID 34408149 DOI: 10.1038/s41467-021-25316-w   
2021 Gupta A, Vijayan V, Pant P, Kaur P, Singh TP, Sharma P, Sharma S. Structure prediction and discovery of inhibitors against phosphopantothenoyl cysteine synthetase of . Journal of Biomolecular Structure & Dynamics. 1-13. PMID 34348086 DOI: 10.1080/07391102.2021.1958699   
2021 Song KC, Molina AV, Chen R, Gagnon IA, Koh YH, Roux B, Sosnick TR. Folding and misfolding of potassium channel monomers during assembly and tetramerization. Proceedings of the National Academy of Sciences of the United States of America. 118. PMID 34413192 DOI: 10.1073/pnas.2103674118   
2021 Gu J, Isozumi N, Yuan S, Jin L, Gao B, Ohki S, Zhu S. Evolution-Based Protein Engineering for Antifungal Peptide Improvement. Molecular Biology and Evolution. PMID 34320203 DOI: 10.1093/molbev/msab224   
2021 Cucuzza S, Güntert P, Plückthun A, Zerbe O. An automated iterative approach for protein structure refinement using pseudocontact shifts. Journal of Biomolecular Nmr. PMID 34338940 DOI: 10.1007/s10858-021-00376-8   
2021 Peterson TA, Piper RC. Deconvolution of Multiple Rab Binding Domains Using the Batch Yeast 2-Hybrid Method DEEPN. Methods in Molecular Biology (Clifton, N.J.). 2293: 117-141. PMID 34453714 DOI: 10.1007/978-1-0716-1346-7_9   
2021 Voith von Voithenberg L, Barth A, Trauschke V, Demarco B, Tyagi S, Koehler C, Lemke EA, Lamb DC. Comparative analysis of the coordinated motion of Hsp70s from different organelles observed by single-molecule three-color FRET. Proceedings of the National Academy of Sciences of the United States of America. 118. PMID 34389669 DOI: 10.1073/pnas.2025578118   
2021 Volkov VV, Heinz H, Perry CC. Anchoring of a hydrophobic heptapeptide (AFILPTG) on silica facilitates peptide unfolding at the abiotic-biotic interface. Physical Chemistry Chemical Physics : Pccp. PMID 34382985 DOI: 10.1039/d1cp02072b   
2021 Si W, Yang H, Wu G, Zhang Y, Sha J. Velocity control of protein translocation through a nanopore by tuning the fraction of benzenoid residues. Nanoscale. PMID 34498657 DOI: 10.1039/d1nr04492c   
2021 Shen R, Crean RM, Johnson SJ, Kamerlin SCL, Hengge AC. Single Residue on the WPD-Loop Affects the pH Dependency of Catalysis in Protein Tyrosine Phosphatases. Jacs Au. 1: 646-659. PMID 34308419 DOI: 10.1021/jacsau.1c00054   
2021 Quadir F, Roy RS, Soltanikazemi E, Cheng J. DeepComplex: A Web Server of Predicting Protein Complex Structures by Deep Learning Inter-chain Contact Prediction and Distance-Based Modelling. Frontiers in Molecular Biosciences. 8: 716973. PMID 34497831 DOI: 10.3389/fmolb.2021.716973