| Year |
Citation |
Score |
| 2023 |
Franke L, Peter C. Visualizing the Residue Interaction Landscape of Proteins by Temporal Network Embedding. Journal of Chemical Theory and Computation. PMID 37122117 DOI: 10.1021/acs.jctc.2c01228 |
0.314 |
|
| 2023 |
Hunkler S, Buhl T, Kukharenko O, Peter C. Generating a conformational landscape of ubiquitin chains at atomistic resolution by back-mapping based sampling. Frontiers in Chemistry. 10: 1087963. PMID 36704619 DOI: 10.3389/fchem.2022.1087963 |
0.302 |
|
| 2021 |
Saini R, Globisch C, Franke L, Peter C, Debnath A. Interactions Determining the Structural Integrity of the Trimer of Plant Light Harvesting Complex in Lipid Membranes. The Journal of Membrane Biology. PMID 33427943 DOI: 10.1007/s00232-020-00162-x |
0.71 |
|
| 2020 |
Berg A, Franke L, Scheffner M, Peter C. Correction to Machine Learning Driven Analysis of Large Scale Simulations Reveals Conformational Characteristics of Ubiquitin Chains. Journal of Chemical Theory and Computation. PMID 33064468 DOI: 10.1021/acs.jctc.0c00992 |
0.77 |
|
| 2020 |
Peter C, Delle Site L, Kremer K. Classical simulations from the atomistic to the mesoscale and back: coarse graining an liquid crystal. Soft Matter. 4: 859-869. PMID 32907192 DOI: 10.1039/B717324E |
0.579 |
|
| 2020 |
Gkeka P, Stoltz G, Barati Farimani A, Belkacemi Z, Ceriotti M, Chodera JD, Dinner AR, Ferguson AL, Maillet JB, Minoux H, Peter C, Pietrucci F, Silveira A, Tkatchenko A, Trstanova Z, et al. Machine learning force fields and coarse-grained variables in molecular dynamics: application to materials and biological systems. Journal of Chemical Theory and Computation. PMID 32559068 DOI: 10.1021/Acs.Jctc.0C00355 |
0.316 |
|
| 2020 |
Berg A, Franke L, Scheffner M, Peter C. Machine Learning Driven Analysis of Large Scale Simulations Reveals Conformational Characteristics of Ubiquitin Chains. Journal of Chemical Theory and Computation. PMID 32196332 DOI: 10.1021/Acs.Jctc.0C00045 |
0.803 |
|
| 2020 |
Mark AE, Peter C. Editorial overview: Theory and simulation: Progress, yes; revolutions, no. Current Opinion in Structural Biology. PMID 32146080 DOI: 10.1016/J.Sbi.2020.02.001 |
0.313 |
|
| 2020 |
Schneider T, Berg A, Peter C, Kovermann M. Exploring Artificially Conjugated Ubiquitin Dimers by Means of NMR Spectroscopy and MD Simulations Biophysical Journal. 118. DOI: 10.1016/J.Bpj.2019.11.2783 |
0.411 |
|
| 2019 |
Schneider T, Berg A, Ulusoy Z, Gamerdinger M, Peter C, Kovermann M. Conformational and functional characterization of artificially conjugated non-canonical ubiquitin dimers. Scientific Reports. 9: 19991. PMID 31882959 DOI: 10.1038/S41598-019-56458-Z |
0.794 |
|
| 2019 |
Lemke T, Berg A, Jain A, Peter C. EncoderMap(II): Visualizing important molecular motions with improved generation of protein conformations. Journal of Chemical Information and Modeling. PMID 31647645 DOI: 10.1021/Acs.Jcim.9B00675 |
0.775 |
|
| 2019 |
Hunkler S, Lemke T, Peter C, Kukharenko O. Back-mapping based sampling: Coarse grained free energy landscapes as a guideline for atomistic exploration. The Journal of Chemical Physics. 151: 154102. PMID 31640363 DOI: 10.1063/1.5115398 |
0.37 |
|
| 2019 |
Berg A, Peter C. Simulating and analysing configurational landscapes of protein-protein contact formation. Interface Focus. 9: 20180062. PMID 31065336 DOI: 10.1098/Rsfs.2018.0062 |
0.788 |
|
| 2019 |
Jain A, Globisch C, Verma S, Peter C. Coarse grained simulations of peptide nanoparticle formation - the role of local structure and nonbonded interactions. Journal of Chemical Theory and Computation. PMID 30633860 DOI: 10.1021/Acs.Jctc.8B01138 |
0.369 |
|
| 2019 |
Lemke T, Peter C. EncoderMap: Dimensionality Reduction and Generation of Molecule Conformations. Journal of Chemical Theory and Computation. PMID 30632745 DOI: 10.1021/Acs.Jctc.8B00975 |
0.34 |
|
| 2019 |
Chaimovich A, Kremer K, Peter C. Relative Resolution: A multipole approximation at appropriate distances Physical Review Research. 1. DOI: 10.1103/Physrevresearch.1.023034 |
0.579 |
|
| 2019 |
King M, Pasler S, Peter C. Coarse-Grained Simulation of CaCO3 Aggregation and Crystallization Made Possible by Nonbonded Three-Body Interactions Journal of Physical Chemistry C. 123: 3152-3160. DOI: 10.1021/Acs.Jpcc.8B09604 |
0.376 |
|
| 2018 |
Berg A, Kukharenko O, Scheffner M, Peter C. Towards a molecular basis of ubiquitin signaling: A dual-scale simulation study of ubiquitin dimers. Plos Computational Biology. 14: e1006589. PMID 30444864 DOI: 10.1371/Journal.Pcbi.1006589 |
0.802 |
|
| 2018 |
Aichem A, Anders S, Catone N, Rößler P, Stotz S, Berg A, Schwab R, Scheuermann S, Bialas J, Schütz-Stoffregen MC, Schmidtke G, Peter C, Groettrup M, Wiesner S. Author Correction: The structure of the ubiquitin-like modifier FAT10 reveals an alternative targeting mechanism for proteasomal degradation. Nature Communications. 9: 4646. PMID 30389928 DOI: 10.1038/S41467-018-07183-0 |
0.743 |
|
| 2018 |
Lemke T, Peter C, Kukharenko O. Efficient sampling and characterization of free energy landscapes of ion-peptide systems. Journal of Chemical Theory and Computation. PMID 30240208 DOI: 10.1021/Acs.Jctc.8B00560 |
0.342 |
|
| 2018 |
Aichem A, Anders S, Catone N, Rößler P, Stotz S, Berg A, Schwab R, Scheuermann S, Bialas J, Schütz-Stoffregen MC, Schmidtke G, Peter C, Groettrup M, Wiesner S. The structure of the ubiquitin-like modifier FAT10 reveals an alternative targeting mechanism for proteasomal degradation. Nature Communications. 9: 3321. PMID 30127417 DOI: 10.1038/S41467-018-05776-3 |
0.745 |
|
| 2017 |
Lemke T, Peter C. Neural network based prediction of conformational free energies - a new route towards coarse-grained simulation models. Journal of Chemical Theory and Computation. PMID 29120633 DOI: 10.1021/Acs.Jctc.7B00864 |
0.438 |
|
| 2017 |
Poon GG, Lemke T, Peter C, Molinero V, Peters B. Oligomeric Nucleants: Simulations of Chain Length, Binding Strength, and Volume Fraction Effects. The Journal of Physical Chemistry Letters. PMID 29116791 DOI: 10.1021/Acs.Jpclett.7B02651 |
0.379 |
|
| 2017 |
Berg A, Peter C, Johnston K. Evaluation and Optimisation of Interface Force Fields for Water on Gold Surfaces. Journal of Chemical Theory and Computation. PMID 28992416 DOI: 10.1021/Acs.Jctc.7B00612 |
0.759 |
|
| 2017 |
Mukherjee B, Peter C, Kremer K. Single molecule translocation in smectics illustrates the challenge for time-mapping in simulations on multiple scales. The Journal of Chemical Physics. 147: 114501. PMID 28938812 DOI: 10.1063/1.5001482 |
0.567 |
|
| 2017 |
Mishra NK, Jain A, Peter C, Verma S. Combining Experimental and Simulation Techniques to Understand Morphology Control in Pentapeptide Nanostructures. The Journal of Physical Chemistry. B. PMID 28774171 DOI: 10.1021/Acs.Jpcb.7B06005 |
0.339 |
|
| 2016 |
Hanebuth MA, Kityk R, Fries SJ, Jain A, Kriel A, Albanese V, Frickey T, Peter C, Mayer MP, Frydman J, Deuerling E. Multivalent contacts of the Hsp70 Ssb contribute to its architecture on ribosomes and nascent chain interaction. Nature Communications. 7: 13695. PMID 27917864 DOI: 10.1038/Ncomms13695 |
0.339 |
|
| 2016 |
Xiao S, Peter C, Kremer K. Systematic comparison of model polymer nanocomposite mechanics. Bioinspiration & Biomimetics. 11: 055008. PMID 27623170 DOI: 10.1088/1748-3190/11/5/055008 |
0.471 |
|
| 2016 |
Kukharenko O, Sawade K, Steuer J, Peter C. Using Dimensionality Reduction to Systematically Expand Conformational Sampling of Intrinsically Disordered Peptides. Journal of Chemical Theory and Computation. 12: 4726-4734. PMID 27588692 DOI: 10.1021/Acs.Jctc.6B00503 |
0.389 |
|
| 2016 |
Site LD, Deserno M, Dünweg B, Holm C, Peter C, Pleiner H. Editorial The European Physical Journal Special Topics. 225: 1317-1321. DOI: 10.1140/Epjst/E2016-60242-X |
0.542 |
|
| 2016 |
Dalgicdir C, Globisch C, Sayar M, Peter C. Representing environment-induced helix-coil transitions in a coarse grained peptide model European Physical Journal-Special Topics. 225: 1463-1481. DOI: 10.1140/Epjst/E2016-60147-8 |
0.387 |
|
| 2016 |
Krishnamani V, Globisch C, Peter C, Deserno M. Breaking a virus: Identifying molecular level failure modes of a viral capsid by multiscale modeling The European Physical Journal Special Topics. 225: 1757-1774. DOI: 10.1140/Epjst/E2016-60141-2 |
0.665 |
|
| 2015 |
Chaimovich A, Peter C, Kremer K. Relative resolution: A hybrid formalism for fluid mixtures. The Journal of Chemical Physics. 143: 243107. PMID 26723592 DOI: 10.1063/1.4929834 |
0.531 |
|
| 2015 |
Schmidt MJ, Fedoseev A, Bücker D, Borbas J, Peter C, Drescher M, Summerer D. EPR Distance Measurements in Native Proteins with Genetically Encoded Spin Labels. Acs Chemical Biology. PMID 26421438 DOI: 10.1021/Acschembio.5B00512 |
0.349 |
|
| 2015 |
Dalgicdir C, Globisch C, Peter C, Sayar M. Tipping the Scale from Disorder to Alpha-helix: Folding of Amphiphilic Peptides in the Presence of Macroscopic and Molecular Interfaces. Plos Computational Biology. 11: e1004328. PMID 26295346 DOI: 10.1371/Journal.Pcbi.1004328 |
0.392 |
|
| 2015 |
Debnath A, Wiegand S, Paulsen H, Kremer K, Peter C. Derivation of coarse-grained simulation models of chlorophyll molecules in lipid bilayers for applications in light harvesting systems. Physical Chemistry Chemical Physics : Pccp. 17: 22054-63. PMID 26235608 DOI: 10.1039/C5Cp01140J |
0.771 |
|
| 2014 |
Schach D, Globisch C, Roeters SJ, Woutersen S, Fuchs A, Weiss CK, Backus EH, Landfester K, Bonn M, Peter C, Weidner T. Sticky water surfaces: helix-coil transitions suppressed in a cell-penetrating peptide at the air-water interface. The Journal of Chemical Physics. 141: 22D517. PMID 25494788 DOI: 10.1063/1.4898711 |
0.369 |
|
| 2014 |
Jain A, Jochum M, Peter C. Molecular dynamics simulations of peptides at the air-water interface: influencing factors on peptide-templated mineralization. Langmuir : the Acs Journal of Surfaces and Colloids. 30: 15486-95. PMID 25470652 DOI: 10.1021/La503549Q |
0.354 |
|
| 2014 |
Potestio R, Peter C, Kremer K. Computer Simulations of Soft Matter: Linking the Scales Entropy. 16: 4199-4245. DOI: 10.3390/E16084199 |
0.592 |
|
| 2014 |
Krishnamani V, Globisch C, Peter C, Deserno M. Breaking a Virus: Identifying Molecular Level Failure Modes of Viral Capsid Compression through Multi-Scale Simulation Techniques Biophysical Journal. 106: 61a-62a. DOI: 10.1016/J.Bpj.2013.11.419 |
0.647 |
|
| 2013 |
Dalgicdir C, Sensoy O, Peter C, Sayar M. A transferable coarse-grained model for diphenylalanine: how to represent an environment driven conformational transition. The Journal of Chemical Physics. 139: 234115. PMID 24359360 DOI: 10.1063/1.4848675 |
0.427 |
|
| 2013 |
Mukherjee B, Peter C, Kremer K. Dual translocation pathways in smectic liquid crystals facilitated by molecular flexibility. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 88: 010502. PMID 23944395 DOI: 10.1103/Physreve.88.010502 |
0.508 |
|
| 2013 |
Globisch C, Krishnamani V, Deserno M, Peter C. Optimization of an elastic network augmented coarse grained model to study CCMV capsid deformation. Plos One. 8: e60582. PMID 23613730 DOI: 10.1016/J.Bpj.2012.11.2301 |
0.653 |
|
| 2013 |
Shen JW, Li C, Van Der Vegt NFA, Peter C. Understanding the control of mineralization by polyelectrolyte additives: Simulation of preferential binding to calcite surfaces Journal of Physical Chemistry C. 117: 6904-6913. DOI: 10.1021/Jp402341W |
0.328 |
|
| 2013 |
Globisch C, Jochum M, Peter C. Molecular Dynamics of Peptide Folding and Aggregation at the Vapor-Water Interface Biophysical Journal. 104: 688a. DOI: 10.1016/J.Bpj.2012.11.3800 |
0.378 |
|
| 2013 |
Schach D, Weiss C, Peter C, Bonn M, Weidner T. Folding and Unfolding of pH Sensitive Peptides: The Role of Interfaces Biophysical Journal. 104: 394a. DOI: 10.1016/J.Bpj.2012.11.2199 |
0.377 |
|
| 2012 |
Bereau T, Globisch C, Deserno M, Peter C. Coarse-Grained and Atomistic Simulations of the Salt-Stable Cowpea Chlorotic Mottle Virus (SS-CCMV) Subunit 26-49: β-Barrel Stability of the Hexamer and Pentamer Geometries. Journal of Chemical Theory and Computation. 8: 3750-8. PMID 26593018 DOI: 10.1021/Ct200888U |
0.673 |
|
| 2012 |
Jochum M, Andrienko D, Kremer K, Peter C. Structure-based coarse-graining in liquid slabs. The Journal of Chemical Physics. 137: 064102. PMID 22897250 DOI: 10.1063/1.4742067 |
0.527 |
|
| 2012 |
Mukherjee B, Delle Site L, Kremer K, Peter C. Derivation of coarse grained models for multiscale simulation of liquid crystalline phase transitions. The Journal of Physical Chemistry. B. 116: 8474-84. PMID 22475134 DOI: 10.1021/Jp212300D |
0.562 |
|
| 2012 |
Bezkorovaynaya O, Lukyanov A, Kremer K, Peter C. Multiscale simulation of small peptides: consistent conformational sampling in atomistic and coarse-grained models. Journal of Computational Chemistry. 33: 937-49. PMID 22298285 DOI: 10.1002/Jcc.22915 |
0.576 |
|
| 2012 |
Li C, Shen J, Peter C, Vegt NFAvd. A Chemically Accurate Implicit-Solvent Coarse-Grained Model for Polystyrenesulfonate Solutions Macromolecules. 45: 2551-2561. DOI: 10.1021/Ma202490H |
0.402 |
|
| 2011 |
Shen JW, Li C, van der Vegt NF, Peter C. Transferability of Coarse Grained Potentials: Implicit Solvent Models for Hydrated Ions. Journal of Chemical Theory and Computation. 7: 1916-27. PMID 26596452 DOI: 10.1021/Ct2001396 |
0.375 |
|
| 2011 |
Rzepiela AJ, Louhivuori M, Peter C, Marrink SJ. Hybrid simulations: combining atomistic and coarse-grained force fields using virtual sites. Physical Chemistry Chemical Physics : Pccp. 13: 10437-48. PMID 21494747 DOI: 10.1039/C0Cp02981E |
0.395 |
|
| 2011 |
Böckmann M, Marx D, Peter C, Site LD, Kremer K, Doltsinis NL. Multiscale modelling of mesoscopic phenomena triggered by quantum events: light-driven azo-materials and beyond. Physical Chemistry Chemical Physics : Pccp. 13: 7604-21. PMID 21267491 DOI: 10.1039/C0Cp01661F |
0.561 |
|
| 2010 |
Villa A, Peter C, van der Vegt NF. Transferability of Nonbonded Interaction Potentials for Coarse-Grained Simulations: Benzene in Water. Journal of Chemical Theory and Computation. 6: 2434-44. PMID 26613497 DOI: 10.1021/Ct100228T |
0.411 |
|
| 2010 |
Peter C, Kremer K. Multiscale simulation of soft matter systems. Faraday Discussions. 144: 9-24. PMID 20158020 DOI: 10.1039/B919800H |
0.511 |
|
| 2009 |
Villa A, Peter C, van der Vegt NF. Self-assembling dipeptides: conformational sampling in solvent-free coarse-grained simulation. Physical Chemistry Chemical Physics : Pccp. 11: 2077-86. PMID 19280018 DOI: 10.1039/B818144F |
0.441 |
|
| 2009 |
Villa A, van der Vegt NF, Peter C. Self-assembling dipeptides: including solvent degrees of freedom in a coarse-grained model. Physical Chemistry Chemical Physics : Pccp. 11: 2068-76. PMID 19280017 DOI: 10.1039/B818146M |
0.415 |
|
| 2009 |
Peter C, Kremer K. Multiscale simulation of soft matter systems – from the atomistic to the coarse-grained level and back Soft Matter. 5: 4357. DOI: 10.1039/B912027K |
0.602 |
|
| 2008 |
Özal TA, Peter C, Hess B, Vegt NFAvd. Modeling Solubilities of Additives in Polymer Microstructures: Single-Step Perturbation Method Based on a Soft-Cavity Reference State Macromolecules. 41: 5055-5061. DOI: 10.1021/Ma702329Q |
0.374 |
|
| 2007 |
Böckmann M, Peter C, Site LD, Doltsinis NL, Kremer K, Marx D. Atomistic Force Field for Azobenzene Compounds Adapted for QM/MM Simulations with Applications to Liquids and Liquid Crystals. Journal of Chemical Theory and Computation. 3: 1789-802. PMID 26627622 DOI: 10.1021/Ct7000733 |
0.56 |
|
| 2005 |
Christen M, Hünenberger PH, Bakowies D, Baron R, Bürgi R, Geerke DP, Heinz TN, Kastenholz MA, Kräutler V, Oostenbrink C, Peter C, Trzesniak D, van Gunsteren WF. The GROMOS software for biomolecular simulation: GROMOS05. Journal of Computational Chemistry. 26: 1719-51. PMID 16211540 DOI: 10.1002/Jcc.20303 |
0.653 |
|
| 2005 |
Peter C, Hummer G. Ion transport through membrane-spanning nanopores studied by molecular dynamics simulations and continuum electrostatics calculations. Biophysical Journal. 89: 2222-34. PMID 16006629 DOI: 10.1529/Biophysj.105.065946 |
0.52 |
|
| 2005 |
Hsu ST, Peter C, van Gunsteren WF, Bonvin AM. Entropy calculation of HIV-1 Env gp120, its receptor CD4, and their complex: an analysis of configurational entropy changes upon complexation. Biophysical Journal. 88: 15-24. PMID 15489307 DOI: 10.1529/Biophysj.104.044933 |
0.489 |
|
| 2004 |
Peter C, Oostenbrink C, van Dorp A, van Gunsteren WF. Estimating entropies from molecular dynamics simulations. The Journal of Chemical Physics. 120: 2652-61. PMID 15268408 DOI: 10.1063/1.1636153 |
0.645 |
|
| 2003 |
Peter C, Rueping M, Wörner HJ, Jaun B, Seebach D, van Gunsteren WF. Molecular dynamics simulations of small peptides: can one derive conformational preferences from ROESY spectra? Chemistry (Weinheim An Der Bergstrasse, Germany). 9: 5838-49. PMID 14673855 DOI: 10.1002/Chem.200305147 |
0.576 |
|
| 2003 |
Peter C, van Gunsteren WF, Hünenberger PH. A fast-Fourier transform method to solve continuum-electrostatics problems with truncated electrostatic interactions: Algorithm and application to ionic solvation and ion–ion interaction The Journal of Chemical Physics. 119: 12205-12223. DOI: 10.1063/1.1624054 |
0.514 |
|
| 2003 |
Bergdorf M, Peter C, Hünenberger PH. Influence of cut-off truncation and artificial periodicity of electrostatic interactions in molecular simulations of solvated ions: A continuum electrostatics study Journal of Chemical Physics. 119: 9129-9144. DOI: 10.1063/1.1614202 |
0.368 |
|
| 2002 |
Daura X, Glättli A, Gee P, Peter C, van Gunsteren WF. Unfolded state of peptides. Advances in Protein Chemistry. 62: 341-60. PMID 12418109 DOI: 10.1016/S0065-3233(02)62013-3 |
0.529 |
|
| 2002 |
Feenstra KA, Peter C, Scheek RM, van Gunsteren WF, Mark AE. A comparison of methods for calculating NMR cross-relaxation rates (NOESY and ROESY intensities) in small peptides. Journal of Biomolecular Nmr. 23: 181-94. PMID 12238590 DOI: 10.1023/A:1019854626147 |
0.565 |
|
| 2002 |
Peter C, Daura X, van Gunsteren WF. Calculation of NMR-relaxation parameters for flexible molecules from molecular dynamics simulations. Journal of Biomolecular Nmr. 20: 297-310. PMID 11563554 DOI: 10.1023/A:1011241030461 |
0.553 |
|
| 2002 |
Peter C, van Gunsteren WF, Hünenberger PH. Solving the Poisson equation for solute–solvent systems using fast Fourier transforms The Journal of Chemical Physics. 116: 7434-7451. DOI: 10.1063/1.1465396 |
0.466 |
|
| 2001 |
van Gunsteren WF, Bürgi R, Peter C, Daura X. The Key to Solving the Protein-Folding Problem Lies in an Accurate Description of the Denatured State. Angewandte Chemie (International Ed. in English). 40: 351-355. PMID 29712400 DOI: 10.1002/1521-3773(20010119)40:2<351::Aid-Anie351>3.0.Co;2-6 |
0.531 |
|
| 2001 |
Van Gunsteren WF, Bürgi R, Peter C, Daura X. Reply. Angewandte Chemie (International Ed. in English). 40: 4616-4618. PMID 12404365 DOI: 10.1002/1521-3773(20011217)40:24<4616::AID-ANIE4616>3.0.CO;2-B |
0.304 |
|
| 2001 |
van Gunsteren WF, Bürgi R, Peter C, Daura X. The Key to Solving the Protein-Folding Problem Lies in an Accurate Description of the Denatured State Financial support from the Schweizerischer Nationalfonds (Project no. 21-50929.97) is gratefully acknowledged. Angewandte Chemie (International Ed. in English). 40: 351-355. PMID 11180322 DOI: 10.1002/1521-3773(20010119)40:2<351::AID-ANIE351>3.0.CO;2-6 |
0.402 |
|
| 2001 |
Hamprecht FA, Peter C, Daura X, Thiel W, van Gunsteren WF. A strategy for analysis of (molecular) equilibrium simulations: Configuration space density estimation, clustering, and visualization The Journal of Chemical Physics. 114: 2079-2089. DOI: 10.1063/1.1330216 |
0.515 |
|
| 2001 |
van Gunsteren WF, Bürgi R, Peter C, Daura X. Der Schlüssel zum Verständnis des Proteinfaltungsproblems liegt in der richtigen Beschreibung des denaturierten Zustandes Angewandte Chemie. 113: 363-367. DOI: 10.1002/1521-3757(20010119)113:2<363::Aid-Ange363>3.0.Co;2-J |
0.422 |
|
| 2000 |
Peter C, Daura X, van Gunsteren WF. Peptides of Aminoxy Acids: A Molecular Dynamics Simulation Study of Conformational Equilibria under Various Conditions Journal of the American Chemical Society. 122: 7461-7466. DOI: 10.1021/Ja000873T |
0.556 |
|
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