| Bridging the gap between atomistic and coarse-grained models of polymers: status and perspectives J Baschnagel, K Binder, P Doruker, AA Gusev, O Hahn, K Kremer, ... Viscoelasticity, atomistic models, statistical chemistry, 41-156, 2000 | 480 | 2000 |
| Dynamics of proteins predicted by molecular dynamics simulations and analytical approaches: Application to α‐amylase inhibitor P Doruker, AR Atilgan, I Bahar Proteins: Structure, Function, and Bioinformatics 40 (3), 512-524, 2000 | 401 | 2000 |
| Dynamics of large proteins through hierarchical levels of coarse‐grained structures P Doruker, RL Jernigan, I Bahar Journal of computational chemistry 23 (1), 119-127, 2002 | 279 | 2002 |
| Reverse mapping of coarse-grained polyethylene chains from the second nearest neighbor diamond lattice to an atomistic model in continuous space P Doruker, WL Mattice Macromolecules 30 (18), 5520-5526, 1997 | 136 | 1997 |
| ProDy 2.0: increased scale and scope after 10 years of protein dynamics modelling with Python S Zhang, JM Krieger, Y Zhang, C Kaya, B Kaynak, K Mikulska-Ruminska, ... Bioinformatics 37 (20), 3657-3659, 2021 | 133 | 2021 |
| Functional motions of influenza virus hemagglutinin: a structure-based analytical approach B Isin, P Doruker, I Bahar Biophysical journal 82 (2), 569-581, 2002 | 133 | 2002 |
| Mathematical description of ethanol fermentation by immobilised Saccharomyces cerevisiae G Birol, P Doruker, B Kirdar, Zİ Önsan, K Ülgen Process Biochemistry 33 (7), 763-771, 1998 | 132 | 1998 |
| Simulation of polyethylene thin films on a high coordination lattice P Doruker, WL Mattice Macromolecules 31 (4), 1418-1426, 1998 | 117 | 1998 |
| Intrinsic dynamics is evolutionarily optimized to enable allosteric behavior Y Zhang, P Doruker, B Kaynak, S Zhang, J Krieger, H Li, I Bahar Current opinion in structural biology 62, 14-21, 2020 | 101 | 2020 |
| Molecular simulations of small gas diffusion and solubility in copolymers of styrene E Kucukpinar, P Doruker Polymer 44 (12), 3607-3620, 2003 | 100 | 2003 |
| Effect of cooperative hydrogen bonding in azo− hydrazone tautomerism of azo dyes AS Özen, P Doruker, V Aviyente The Journal of Physical Chemistry A 111 (51), 13506-13514, 2007 | 94 | 2007 |
| Mobility of the surface and interior of thin films composed of amorphous polyethylene P Doruker, WL Mattice Macromolecules 32 (1), 194-198, 1999 | 93 | 1999 |
| Mixed levels of coarse-graining of large proteins using elastic network model succeeds in extracting the slowest motions O Kurkcuoglu, RL Jernigan, P Doruker Polymer 45 (2), 649-657, 2004 | 83 | 2004 |
| The ribosome structure controls and directs mRNA entry, translocation and exit dynamics O Kurkcuoglu, P Doruker, TZ Sen, A Kloczkowski, RL Jernigan Physical biology 5 (4), 046005, 2008 | 78 | 2008 |
| Molecular dynamics simulations on constraint metal binding peptides N Kantarci, C Tamerler, M Sarikaya, T Haliloglu, P Doruker Polymer 46 (12), 4307-4313, 2005 | 73 | 2005 |
| Conformational transition pathways explored by Monte Carlo simulation integrated with collective modes N Kantarci-Carsibasi, T Haliloglu, P Doruker Biophysical journal 95 (12), 5862-5873, 2008 | 72 | 2008 |
| Loop motions of triosephosphate isomerase observed with elastic networks O Kurkcuoglu, RL Jernigan, P Doruker Biochemistry 45 (4), 1173-1182, 2006 | 72 | 2006 |
| Functional motions can be extracted from on‐lattice construction of protein structures P Doruker, RL Jernigan Proteins: Structure, Function, and Bioinformatics 53 (2), 174-181, 2003 | 61 | 2003 |
| Focused functional dynamics of supramolecules by use of a mixed-resolution elastic network model O Kurkcuoglu, OT Turgut, S Cansu, RL Jernigan, P Doruker Biophysical journal 97 (4), 1178-1187, 2009 | 59 | 2009 |
| Coupling between catalytic loop motions and enzyme global dynamics Z Kurkcuoglu, A Bakan, D Kocaman, I Bahar, P Doruker Public Library of Science 8 (9), e1002705, 2012 | 58 | 2012 |
