F Marty Ytreberg - Related publications

Affiliations: 
Physics University of Idaho, Moscow, ID, United States 
Area:
Molecular Physics, General Biophysics
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50 most relevant papers in past 60 days:
Year Citation  Score
2020 Zhong S, Huang K, Luo S, Dong S, Duan L. Improving the performance of the MM/PBSA and MM/GBSA methods in recognizing the native structure of the Bcl-2 family using the interaction entropy method. Physical Chemistry Chemical Physics : Pccp. PMID 32043094 DOI: 10.1039/c9cp06459a   
2020 Gill M, McCully ME. Molecular dynamics simulations suggest stabilizing mutations in a de novo designed α/β protein. Protein Engineering, Design & Selection : Peds. PMID 32086513 DOI: 10.1093/protein/gzaa005   
2020 Sauer MF, Sevy AM, Crowe JE, Meiler J. Multi-state design of flexible proteins predicts sequences optimal for conformational change. Plos Computational Biology. 16: e1007339. PMID 32032348 DOI: 10.1371/journal.pcbi.1007339   
2020 Wu Y, Lou L, Xie ZR. A Pilot Study of All-Computational Drug Design Protocol-From Structure Prediction to Interaction Analysis. Frontiers in Chemistry. 8: 81. PMID 32117898 DOI: 10.3389/fchem.2020.00081   
2020 Sladek V, Harada R, Shigeta Y. Protein Dynamics and the Folding Degree. Journal of Chemical Information and Modeling. PMID 32090564 DOI: 10.1021/acs.jcim.9b00942   
2020 Tang Z, Chen SH, Chang CA. Transient states and barriers from molecular simulations and milestoning theory: kinetics in ligand-protein recognition and compound design. Journal of Chemical Theory and Computation. PMID 32031801 DOI: 10.1021/acs.jctc.9b01153   
2020 Nguyen LH, Tran TT, Truong LTN, Mai HH, Nguyen TT. Overcharging of zinc ion in the structure of zinc-finger protein is needed for DNA binding stability. Biochemistry. PMID 32043865 DOI: 10.1021/acs.biochem.9b01055   
2020 Allert MJ, Hellinga HW. Describing complex structure-function relationships in biomolecules at equilibrium. Journal of Molecular Biology. PMID 31940471 DOI: 10.1016/j.jmb.2019.12.039   
2020 Kim H, Kim JG, Muniyappan S, Kim TW, Lee SJ, Ihee H. Effect of Occluded Ligand Migration on the Kinetics and Structural Dynamics of Homodimeric Hemoglobin. The Journal of Physical Chemistry. B. PMID 32027135 DOI: 10.1021/acs.jpcb.9b11749   
2020 Láng A, Jákli I, Enyedi KN, Mező G, Menyhárd DK, Perczel A. Off-pathway 3D-structure provides protection against spontaneous Asn/Asp isomerization: shielding proteins Achilles heel. Quarterly Reviews of Biophysics. 53: e2. PMID 32000865 DOI: 10.1017/S003358351900009X   
2020 Bradshaw RT, Marinelli F, Faraldo-Gómez JD, Forrest LR. Interpretation of HDX Data by Maximum-Entropy Reweighting of Simulated Structural Ensembles. Biophysical Journal. PMID 32105651 DOI: 10.1016/j.bpj.2020.02.005   
2020 Jin Z, Wang Y, Yu XF, Tan QQ, Liang SS, Li T, Zhang H, Shaw PC, Wang J, Hu C. Structure-based virtual screening of influenza virus RNA polymerase inhibitors from natural compounds: Molecular dynamics simulation and MM-GBSA calculation. Computational Biology and Chemistry. 85: 107241. PMID 32120300 DOI: 10.1016/j.compbiolchem.2020.107241   
2020 Sasmal S, Gill SC, Lim NM, Mobley DL. Sampling conformational changes of bound ligands using Nonequilibrium Candidate Monte Carlo. Journal of Chemical Theory and Computation. PMID 32058713 DOI: 10.1021/acs.jctc.9b01066   
2020 Chen S, Gong X, Tan H, Liu Y, He L, Ouyang J. Study of the noncovalent interactions between phenolic acid and lysozyme by cold spray ionization mass spectrometry (CSI-MS), multi-spectroscopic and molecular docking approaches. Talanta. 211: 120762. PMID 32070628 DOI: 10.1016/j.talanta.2020.120762   
2020 Fine J, Konc J, Samudrala R, Chopra G. CANDOCK: Chemical Atomic Network-based Hierarchical Flexible Docking Algorithm using Generalized Statistical Potentials. Journal of Chemical Information and Modeling. PMID 32069042 DOI: 10.1021/acs.jcim.9b00686   
2020 Rangubpit W, Sompornpisut P, Pandey R. Structure and dynamics of aquaporin-1. Vitamins and Hormones. 112: 29-46. PMID 32061346 DOI: 10.1016/bs.vh.2019.09.001   
2020 Yeo J, Qiu Y, Jung GS, Zhang YW, Buehler MJ, Kaplan DL. Adverse effects of Alport syndrome-related Gly missense mutations on collagen type IV: Insights from molecular simulations and experiments. Biomaterials. 240: 119857. PMID 32085975 DOI: 10.1016/j.biomaterials.2020.119857   
2020 Li Y, Guo YC, Zhang XL, Deng L, Sang P, Yang LQ, Liu SQ. CD4-binding obstacles in conformational transitions and allosteric communications of HIV gp120. Biochimica Et Biophysica Acta. Biomembranes. 183217. PMID 32061646 DOI: 10.1016/j.bbamem.2020.183217   
2020 Yoo JI, Daugherty PS, O'Malley MA. Bridging non-overlapping reads illuminates high-order epistasis between distal protein sites in a GPCR. Nature Communications. 11: 690. PMID 32019920 DOI: 10.1038/s41467-020-14495-7   
2020 Heifetz A, James T, Southey M, Bodkin MJ, Bromidge S. Guiding Medicinal Chemistry with Fragment Molecular Orbital (FMO) Method. Methods in Molecular Biology (Clifton, N.J.). 2114: 37-48. PMID 32016885 DOI: 10.1007/978-1-0716-0282-9_3   
2020 Olanders G, Alogheli H, Brandt P, Karlén A. Conformational analysis of macrocycles: comparing general and specialized methods. Journal of Computer-Aided Molecular Design. PMID 31965404 DOI: 10.1007/s10822-020-00277-2   
2020 Alapati R, Shuvo MH, Bhattacharya D. SPECS: Integration of side-chain orientation and global distance-based measures for improved evaluation of protein structural models. Plos One. 15: e0228245. PMID 32053611 DOI: 10.1371/journal.pone.0228245   
2020 Zou R, Zhou Y, Wang Y, Kuang G, Agren H, Wu J, Tu Y. Free Energy Profile and Kinetics for Coupled Folding and Binding of the Intrinsically Disordered Protein p53 with MDM2. Journal of Chemical Information and Modeling. PMID 32053358 DOI: 10.1021/acs.jcim.9b00920   
2020 Islam SM, Havranek B, Ibnat Z, Roy PN. New Insights into the Role of Hydrogen Bonding in Furanoside Binding to Protein. The Journal of Physical Chemistry. B. PMID 32075374 DOI: 10.1021/acs.jpcb.9b11924   
2020 Purslow JA, Khatiwada B, Bayro MJ, Venditti V. NMR Methods for Structural Characterization of Protein-Protein Complexes. Frontiers in Molecular Biosciences. 7: 9. PMID 32047754 DOI: 10.3389/fmolb.2020.00009   
2020 Mondal SK, Sen MK. Loss of phosphatase activity in PTEN (phosphatase and tensin homolog deleted on chromosome ten) results in endometrial carcinoma in humans: An study. Heliyon. 6: e03106. PMID 32042934 DOI: 10.1016/j.heliyon.2019.e03106   
2020 Tang C, Gong Z. Integrating non-NMR distance restraints to augment NMR depiction of protein structure and dynamics. Journal of Molecular Biology. PMID 32044345 DOI: 10.1016/j.jmb.2020.01.023   
2020 Lindemann WR, Evans ED, Mijalis AJ, Saouaf OM, Pentelute BL, Ortony JH. Quantifying residue-specific conformational dynamics of a highly reactive 29-mer peptide. Scientific Reports. 10: 2597. PMID 32054898 DOI: 10.1038/s41598-020-59047-7   
2020 Heifetz A, Morao I, Babu MM, James T, Southey MW, Fedorov DG, Aldeghi M, Bodkin MJ, Townsend-Nicholson A. Characterising Inter-helical Interactions of G Protein-Coupled Receptors with the Fragment Molecular Orbital Method. Journal of Chemical Theory and Computation. PMID 32096994 DOI: 10.1021/acs.jctc.9b01136   
2020 Abramyan AM, Yano H, Xu M, Liu L, Naing S, Fant AD, Shi L. The Glu102 mutation disrupts higher-order oligomerization of the sigma 1 receptor. Computational and Structural Biotechnology Journal. 18: 199-206. PMID 32055286 DOI: 10.1016/j.csbj.2019.12.012   
2020 Yang H, Ahmad ZA, Song Y. Molecular insight for the role of key residues of calreticulin in its binding activities: A computational study. Computational Biology and Chemistry. 85: 107228. PMID 32062378 DOI: 10.1016/j.compbiolchem.2020.107228   
2020 Guéret SM, Thavam S, Carbajo RJ, Potowski M, Larsson N, Dahl G, Dells Eacute N A, Grossmann TN, Plowright AT, Valeur E, Lemurell M, Waldmann H. Macrocyclic Modalities Combining Peptide Epitopes and Natural Product Fragments. Journal of the American Chemical Society. PMID 32058716 DOI: 10.1021/jacs.0c00269   
2020 Bansal R, Haque A, Hassan I, Ethayathulla AS, Kaur P. Structural and conformational behavior of MurE ligase from Salmonella enterica serovar Typhi at different temperature and pH conditions. International Journal of Biological Macromolecules. PMID 32018007 DOI: 10.1016/j.ijbiomac.2020.01.306   
2020 Dash R, Choi HJ, Moon IS. Mechanistic insights into the deleterious roles of Nasu-Hakola disease associated TREM2 variants. Scientific Reports. 10: 3663. PMID 32107424 DOI: 10.1038/s41598-020-60561-x   
2020 Fleetwood O, Matricon P, Carlsson J, Delemotte L. Energy Landscapes Reveal Agonist Control of G Protein-Coupled Receptor Activation via Microswitches. Biochemistry. PMID 31999436 DOI: 10.1021/acs.biochem.9b00842   
2020 Fadilla RN, Rusydi F, Aisyah ND, Khoirunisa V, Dipojono HK, Ahmad F, Mudasir M, Puspitasari I. A Density-Functional Study of the Conformational Preference of Acetylcholine in the Neutral Hydrolysis. Molecules (Basel, Switzerland). 25. PMID 32033277 DOI: 10.3390/molecules25030670   
2020 Glöckner S, Ngo K, Sager CP, Hüfner-Wulsdorf T, Heine A, Klebe G. Conformational changes in alkyl chains determine the thermodynamic and kinetic binding profiles of Carbonic Anhydrase inhibitors. Acs Chemical Biology. PMID 32027480 DOI: 10.1021/acschembio.9b00895   
2020 Chakravarty D, McElfresh GW, Kundrotas PJ, Vakser IA. How to choose templates for modeling of protein complexes: Insights from benchmarking template-based docking. Proteins. PMID 31994759 DOI: 10.1002/prot.25875   
2020 Neira JL, Ortore MG, Florencio FJ, Muro-Pastor MI, Rizzuti B. Dynamics of the intrinsically disordered inhibitor IF7 of glutamine synthetase in isolation and in complex with its partner. Archives of Biochemistry and Biophysics. 108303. PMID 32074499 DOI: 10.1016/j.abb.2020.108303   
2020 Yazhini A, Srinivasan N. How good are comparative models in the understanding of protein dynamics? Proteins. PMID 31999374 DOI: 10.1002/prot.25879   
2020 Dang M, Song J. ALS-causing D169G mutation disrupts the ATP-binding capacity of TDP-43 RRM1 domain. Biochemical and Biophysical Research Communications. PMID 32007267 DOI: 10.1016/j.bbrc.2020.01.122   
2020 Vedithi SC, Rodrigues CHM, Portelli S, Skwark MJ, Das M, Ascher DB, Blundell TL, Malhotra S. Computational saturation mutagenesis to predict structural consequences of systematic mutations in the beta subunit of RNA polymerase in . Computational and Structural Biotechnology Journal. 18: 271-286. PMID 32042379 DOI: 10.1016/j.csbj.2020.01.002   
2020 Shi W, Lemoine JM, Shawky AA, Singha M, Pu L, Yang S, Ramanujam J, Brylinski M. BionoiNet: Ligand-binding site classification with off-the-shelf deep neural network. Bioinformatics (Oxford, England). PMID 32053156 DOI: 10.1093/bioinformatics/btaa094   
2020 Keiderling TA. Structure of Condensed Phase Peptides: Insights from Vibrational Circular Dichroism and Raman Optical Activity Techniques. Chemical Reviews. PMID 32101406 DOI: 10.1021/acs.chemrev.9b00636   
2020 Makarov AA, Iacob RE, Pirrone GF, Rodriguez-Granillo A, Joyce L, Mangion I, Moore JC, Sherer EC, Engen JR. Combination of HDX-MS and in silico modeling to study enzymatic reactivity and stereo-selectivity at different solvent conditions. Journal of Pharmaceutical and Biomedical Analysis. 182: 113141. PMID 32036298 DOI: 10.1016/j.jpba.2020.113141   
2020 Martin WR, Lightstone FC, Cheng F. In Silico Insights into Protein-protein Interaction Disruptive Mutations in the PCSK9-LDLR complex. International Journal of Molecular Sciences. 21. PMID 32106405 DOI: 10.3390/ijms21051550   
2020 Torabifard H, Panahi A, Brooks CL. M2 amphipathic helices facilitate pH-dependent conformational transition in influenza A virus. Proceedings of the National Academy of Sciences of the United States of America. PMID 32015120 DOI: 10.1073/pnas.1913385117   
2020 Konar M, Sahoo H. Tyrosine mediated conformational change in bone morphogenetic protein - 2: Biophysical implications of protein - Phytoestrogen interaction. International Journal of Biological Macromolecules. PMID 32061704 DOI: 10.1016/j.ijbiomac.2020.02.113   
2020 Kelly CM, Manukian S, Kim E, Gage MJ. Differences in stability and calcium sensitivity of the Ig Domains in Titin's N2A Region. Protein Science : a Publication of the Protein Society. PMID 32112607 DOI: 10.1002/pro.3848   
2020 Kumar A, Rai S, Rathi E, Agarwal P, Kini SG. Pharmacophore-guided fragment-based design of novel mammalian target of rapamycin inhibitors: Extra precision docking, fingerprint-based 2D and atom-based 3D-QSAR modelling. Journal of Biomolecular Structure & Dynamics. 1-29. PMID 32037974 DOI: 10.1080/07391102.2020.1726816