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Pieter G. Bolhuis - Related publications

University of Amsterdam, Amsterdam, Netherlands 
Computational Chemistry
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50 most relevant papers in past 60 days:
Year Citation  Score
2020 Ferreira PHB, Freitas FC, McCully ME, Slade GG, Oliveira RJ. The Role of Electrostatics and Folding Kinetics on the Thermostability of Homologous Cold Shock Proteins. Journal of Chemical Information and Modeling. PMID 31910002 DOI: 10.1021/acs.jcim.9b00797   
2020 Paul S, Hossain SS, Samanta A. Insights into the Folding Pathway of a c-MYC Promoter based i-Motif DNA in Crowded Environments at the Single-Molecule Level. The Journal of Physical Chemistry. B. PMID 31917565 DOI: 10.1021/acs.jpcb.9b10633   
2020 Srivastava R, Chattopadhyaya M, Bandyopadhyay P. Calculation of salt-dependent free energy of binding of β-lactoglobulin homodimer formation and mechanism of dimer formation using molecular dynamics simulation and three-dimensional reference interaction site model (3D-RISM): diffuse salt ions and non-polar interactions between the monomers favor the dimer formation. Physical Chemistry Chemical Physics : Pccp. PMID 31912070 DOI: 10.1039/c9cp05578a   
2020 Srivastava R, Chattopadhyaya M, Bandyopadhyay P. Calculation of salt-dependent free energy of binding of β-lactoglobulin homodimer formation and mechanism of dimer formation using molecular dynamics simulation and three-dimensional reference interaction site model (3D-RISM): diffuse salt ions and non-polar interactions between the monomers favor the dimer formation. Physical Chemistry Chemical Physics : Pccp. PMID 31912070 DOI: 10.1039/c9cp05578a   
2020 Chu X, Suo Z, Wang J. Confinement and Crowding Effects on Folding of a Multi-domain Y-family DNA Polymerase. Journal of Chemical Theory and Computation. PMID 31972079 DOI: 10.1021/acs.jctc.9b01146   
2020 Li W. Residue-Residue Mutual Work Analysis of Retinal-Opsin Interaction in Rhodopsin: Implications for Protein-Ligand Binding. Journal of Chemical Theory and Computation. PMID 31972074 DOI: 10.1021/acs.jctc.9b01035   
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 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 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 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 Di Natale C, La Manna S, Avitabile C, Florio D, Morelli G, Netti PA, Marasco D. Engineered β-hairpin scaffolds from human prion protein regions: Structural and functional investigations of aggregates. Bioorganic Chemistry. 96: 103594. PMID 31991323 DOI: 10.1016/j.bioorg.2020.103594   
2020 Nouchikian L, Lento C, Donovan K, Dobson R, Wilson DJ. Comparing the Conformational Stability of Pyruvate Kinase in the Gas Phase and in Solution. Journal of the American Society For Mass Spectrometry. PMID 31951698 DOI: 10.1021/jasms.9b00130   
2020 Robinson PJ, Kanemura S, Cao X, Bulleid NJ. Protein secondary structure determines the temporal relationship between folding and disulfide formation. The Journal of Biological Chemistry. PMID 31953323 DOI: 10.1074/jbc.RA119.011983   
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 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 Wu MT, D'Souza V. Alternate RNA Structures. Cold Spring Harbor Perspectives in Biology. 12. PMID 31896543 DOI: 10.1101/cshperspect.a032425   
2020 Ghosh C, Jana B. Inter-Subunit Assisted Folding of DNA Binding Domains in Dimeric Catabolite Activator Protein. The Journal of Physical Chemistry. B. PMID 31999927 DOI: 10.1021/acs.jpcb.9b10941   
2020 Frelih T, Wang B, Plavec J, Šket P. Pre-folded structures govern folding pathways of human telomeric G-quadruplexes. Nucleic Acids Research. PMID 31950178 DOI: 10.1093/nar/gkz1235   
2020 Al-Maharik N, Cordes DB, Slawin AMZ, Bühl M, O'Hagan D. Probing the helical integrity of multivicinal all-syn-fluoro alkanes. Organic & Biomolecular Chemistry. PMID 31942902 DOI: 10.1039/c9ob02647a   
2020 Wang J, Peng C, Yu Y, Chen Z, Xu Z, Cai T, Shao Q, Shi J, Zhu W. Exploring Conformational Change of Adenylate Kinase by Replica Exchange Molecular Dynamic Simulation. Biophysical Journal. PMID 31995738 DOI: 10.1016/j.bpj.2020.01.001   
2020 Migliore M, Bonvicini A, Tognetti V, Guilhaudis L, Baaden M, Oulyadi H, Joubert L, Ségalas-Milazzo I. Characterization of β-turns by electronic circular dichroism spectroscopy: a coupled molecular dynamics and time-dependent density functional theory computational study. Physical Chemistry Chemical Physics : Pccp. PMID 31894790 DOI: 10.1039/c9cp05776e   
2020 Mouro PR, Povinelli APR, Leite VBP, Chahine J. Exploring Folding Aspects of Monomeric Superoxide Dismutase. The Journal of Physical Chemistry. B. PMID 31898906 DOI: 10.1021/acs.jpcb.9b09640   
2020 Ratha BN, Kar RK, Bednarikova Z, Gazova Z, Kotler SA, Raha S, De S, Maiti NC, Bhunia A. Molecular Details of A Salt-Bridge and Its Role in Insulin Fibrillation by NMR and Raman Spectroscopic Analysis. The Journal of Physical Chemistry. B. PMID 31958230 DOI: 10.1021/acs.jpcb.9b10349   
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 Murray DT, Tycko R. Side Chain Hydrogen-Bonding Interactions within Amyloid-like Fibrils Formed by the Low-Complexity Domain of FUS: Evidence from Solid State Nuclear Magnetic Resonance Spectroscopy. Biochemistry. PMID 31895552 DOI: 10.1021/acs.biochem.9b00892   
2020 Kimura N, Mochizuki K, Umezawa K, Hecht MH, Arai R. Hyperstable Protein with a Dimeric Bisecting Topology. Acs Synthetic Biology. PMID 31951376 DOI: 10.1021/acssynbio.9b00501   
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 Gupta P, Khan FI, Ambreen D, Lai D, Alajmi MF, Hussain A, Islam A, Ahmad F, Hassan MI. Investigation of guanidinium chloride-induced unfolding pathway of sphingosine kinase 1. International Journal of Biological Macromolecules. PMID 31917989 DOI: 10.1016/j.ijbiomac.2020.01.023   
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 Wang K, Ning S, Guo Y, Duan M, Yang M. The regulation mechanism of phosphorylation and mutations in intrinsically disordered protein 4E-BP2. Physical Chemistry Chemical Physics : Pccp. PMID 31951234 DOI: 10.1039/c9cp05888e   
2020 Li X, Lee KH, Shorkey S, Chen J, Chen M. Different Anomeric Sugar Bound States of MBP Resolved by a Cytolysin A Nanopore Tweezer. Acs Nano. PMID 31995359 DOI: 10.1021/acsnano.9b07385   
2020 Barnes CA, Shen Y, Ying J, Bax A. Modulating the Stiffness of the Myosin VI Single α-Helical Domain. Biophysical Journal. PMID 32049057 DOI: 10.1016/j.bpj.2020.01.003   
2020 Nacar C. Propensities of Amino Acid Pairings in Secondary Structure of Globular Proteins. The Protein Journal. PMID 31933010 DOI: 10.1007/s10930-020-09880-6   
2020 Taylor WR. Exploring Protein Fold Space. Biomolecules. 10. PMID 32012781 DOI: 10.3390/biom10020193   
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 Shamsi A, Mohammad T, Anwar S, Alajmi MF, Hussain A, Hassan MI, Ahmad F, Islam A. Probing the interaction of Rivastigmine Tartrate, an important Alzheimer's drug, with serum albumin: Attempting treatment of Alzheimer's disease. International Journal of Biological Macromolecules. PMID 31954794 DOI: 10.1016/j.ijbiomac.2020.01.134   
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 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 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 Jewel Y, Van Dinh Q, Liu J, Dutta P. Substrate Dependent Transport Mechanism in AcrB of Multidrug Resistance Bacteria. Proteins. PMID 31998988 DOI: 10.1002/prot.25877   
2020 Ganguly HK, Basu G. Conformational landscape of substituted prolines. Biophysical Reviews. PMID 31953795 DOI: 10.1007/s12551-020-00621-8   
2020 Su W, Zhang Y, Liu J, Ma M, Guo P, Liu X, Wang H, Li C. Molecular Dynamic Simulation of D-mannitol Polymorphs in Solid State and in Solution Relating with Spontaneous Nucleation. Journal of Pharmaceutical Sciences. PMID 31981595 DOI: 10.1016/j.xphs.2020.01.012   
2020 Pillai M, Jha SK. Early metastable assembly during the stress-induced formation of worm-like amyloid fibrils of nucleic acid binding domains of TDP-43. Biochemistry. PMID 31898895 DOI: 10.1021/acs.biochem.9b00780   
2020 Sharma R, Sagurthi SR, Narahari Sastry G. Elucidating the preference of dimeric over monomeric form for thermal stability of Thermus thermophilus isopropylmalate dehydrogenase: A molecular dynamics perspective. Journal of Molecular Graphics & Modelling. 96: 107530. PMID 31986322 DOI: 10.1016/j.jmgm.2020.107530   
2020 Klykov O, van der Zwaan C, Heck AJR, Meijer AB, Scheltema RA. Missing regions within the molecular architecture of human fibrin clots structurally resolved by XL-MS and integrative structural modeling. Proceedings of the National Academy of Sciences of the United States of America. 117: 1976-1987. PMID 31924745 DOI: 10.1073/pnas.1911785117   
2020 Sternisha SM, Whittington AC, Martinez Fiesco JA, Porter C, McCray MM, Logan T, Olivieri C, Veglia G, Steinbach PJ, Miller BG. Nanosecond-Timescale Dynamics and Conformational Heterogeneity in Human GCK Regulation and Disease. Biophysical Journal. PMID 32023434 DOI: 10.1016/j.bpj.2019.12.036   
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 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 Imbernón B, Serrano A, Bueno-Crespo A, Abellán JL, Pérez-Sánchez H, Cecilia JM. METADOCK 2: A high-throughput parallel metaheuristic scheme for molecular docking. Bioinformatics (Oxford, England). PMID 31960899 DOI: 10.1093/bioinformatics/btz958