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Ivet Bahar

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TOP 3
Elia Zomot; Ivet Bahar
Intracellular gating in an inward-facing state of aspartate transporter Glt(Ph) is regulated by the movements of the helical hairpin HP2.
Anindita Dutta; Ingo H Greger; Indira H Shrivastava; Madhav Sukumaran; Ivet Bahar
Comparative dynamics of NMDA- and AMPA-glutamate receptor N-terminal domains.
Divesh Bhatt; Ivet Bahar
An adaptive weighted ensemble procedure for efficient computation of free energies and first passage rates.

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All Publications

2013: Elia Zomot; Ivet Bahar
Intracellular gating in an inward-facing state of aspartate transporter Glt(Ph) is regulated by the movements of the helical hairpin HP2.
The Journal of biological chemistry 2013;288(12):8231-7.
2012: Anindita Dutta; Ingo H Greger; Indira H Shrivastava; Madhav Sukumaran; Ivet Bahar
Comparative dynamics of NMDA- and AMPA-glutamate receptor N-terminal domains.
Structure (London, England : 1993) 2012;20(11):1838-49.
2012: Divesh Bhatt; Ivet Bahar
An adaptive weighted ensemble procedure for efficient computation of free energies and first passage rates.
The Journal of chemical physics 2012;137(10):104101.
2012: Elia Zomot; Ivet Bahar
A conformational switch in a partially unwound helix selectively determines the pathway for substrate release from the carnitine/γ-butyrobetaine antiporter CaiT.
The Journal of biological chemistry 2012;287(38):31823-32.
2012: Ying Liu; Ivet Bahar
Sequence evolution correlates with structural dynamics.
Molecular biology and evolution 2012;29(9):2253-63.
2012: Timothy R Lezon; Ivet Bahar
Constraints imposed by the membrane selectively guide the alternating access dynamics of the glutamate transporter GltPh.
Biophysical journal 2012;102(6):1331-40.
2012: Lin Liu; Ivet Bahar; In-Ja L Byeon; Angela M Gronenborn
Domain swapping proceeds via complete unfolding: a 19F- and 1H-NMR study of the Cyanovirin-N protein.
Journal of the American Chemical Society 2012;134(9):4229-35.
2012: Zeynep Kurkcuoglu; Duygu Kocaman; Ivet Bahar; Ahmet Bakan; Pemra Doruker
Coupling between catalytic loop motions and enzyme global dynamics.
PLoS computational biology 2012;8(9):e1002705.
2012: Basak Isin; Judith Klein-Seetharaman; Zoltan N. Oltvai; Kalyan C Tirupula; Ivet Bahar
Identification of motions in membrane proteins by elastic network models and their experimental validation.
Methods in molecular biology (Clifton, N.J.) 2012;914():285-317.
2011: Lidio Meireles; Ahmet Bakan; Mert Gur; Ivet Bahar
Pre-existing soft modes of motion uniquely defined by native contact topology facilitate ligand binding to proteins.
Protein science : a publication of the Protein Society 2011;20(10):1645-58.
2011: Jie Jiang; Indira H Shrivastava; Spencer D Watts; Ivet Bahar; Susan Amara
Large collective motions regulate the functional properties of glutamate transporter trimers.
Proceedings of the National Academy of Sciences of the United States of America 2011;108(37):15141-6.
2011: Enrique Marcos; Ramon Crehuet; Ivet Bahar
Changes in dynamics upon oligomerization regulate substrate binding and allostery in amino acid kinase family members.
PLoS computational biology 2011;7(9):e1002201.
2011: Penelope A Morel; Rajan Munshi; Mangala Srinivas; Michael S Turner; Ivet Bahar; Maryam Feili-Hariri; Patrizia Fuschiotti; Eric T Ahrens
Gene expression analysis of dendritic cells that prevent diabetes in NOD mice: analysis of chemokines and costimulatory molecules.
Journal of leukocyte biology 2011;90(3):539-50.
2011: Elia Zomot; Ivet Bahar
Protonation of glutamate 208 induces the release of agmatine in an outward-facing conformation of an arginine/agmatine antiporter.
The Journal of biological chemistry 2011;286(22):19693-701.
2011: Ahmet Bakan; Lidio M Meireles; Ivet Bahar
ProDy: protein dynamics inferred from theory and experiments.
Bioinformatics (Oxford, England) 2011;27(11):1575-7.
2011: Madhav Sukumaran; Maxim Rossmann; Indira Shrivastava; Anindita Dutta; Ivet Bahar; Ingo H Greger
Dynamics and allosteric potential of the AMPA receptor N-terminal domain.
The EMBO journal 2011;30(5):972-82.
2011: Jason DeChancie; Indira H Shrivastava; Ivet Bahar
The mechanism of substrate release by the aspartate transporter GltPh: insights from simulations.
Molecular bioSystems 2011;7(3):832-42.
2011: Gabriela Mustata; Mei Li; Nicki Zevola; Ahmet Bakan; Lin Zhang; Michael Epperly; Joel S Greenberger; Jian Yu; Ivet Bahar
Development of small-molecule PUMA inhibitors for mitigating radiation-induced cell death.
Current topics in medicinal chemistry 2011;11(3):281-90.
2011: Ahmet Bakan; Ivet Bahar
Computational generation inhibitor-bound conformers of p38 map kinase and comparison with experiments.
Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing 2011;():181-92.
2010: Anindita Dutta; Ivet Bahar
Metal-binding sites are designed to achieve optimal mechanical and signaling properties.
Structure (London, England : 1993) 2010;18(9):1140-8.
2010: Timothy R Lezon; Ivet Bahar
Using entropy maximization to understand the determinants of structural dynamics beyond native contact topology.
PLoS computational biology 2010;6(6):e1000816.
2010: Ivet Bahar
On the functional significance of soft modes predicted by coarse-grained models for membrane proteins.
The Journal of general physiology 2010;135(6):563-73.
2010: Elia Zomot; Ivet Bahar
The sodium/galactose symporter crystal structure is a dynamic, not so occluded state.
Molecular bioSystems 2010;6(6):1040-6.
2010: Enrique Marcos; Ramon Crehuet; Ivet Bahar
On the conservation of the slow conformational dynamics within the amino acid kinase family: NAGK the paradigm.
PLoS computational biology 2010;6(4):e1000738.
2010: Ivet Bahar; Timothy R Lezon; Ahmet Bakan; Indira H Shrivastava
Normal mode analysis of biomolecular structures: functional mechanisms of membrane proteins.
Chemical reviews 2010;110(3):1463-97.
2010: Ying Liu; Lila M Gierasch; Ivet Bahar
Role of Hsp70 ATPase domain intrinsic dynamics and sequence evolution in enabling its functional interactions with NEFs.
PLoS computational biology 2010;6(9):.
2010: Ivet Bahar; Timothy R Lezon; Lee-Wei Yang; Eran Eyal
Global dynamics of proteins: bridging between structure and function.
Annual review of biophysics 2010;39():23-42.
2010: Ying Liu; Ivet Bahar
Toward understanding allosteric signaling mechanisms in the ATPase domain of molecular chaperones.
Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing 2010;():269-80.
2009: Lin Liu; Leonardus M I Koharudin; Angela M Gronenborn; Ivet Bahar
A comparative analysis of the equilibrium dynamics of a designed protein inferred from NMR, X-ray, and computations.
Proteins 2009;77(4):927-39.
2009: Timothy R Lezon; Andrej Sali; Ivet Bahar
Global motions of the nuclear pore complex: insights from elastic network models.
PLoS computational biology 2009;5(9):e1000496.
2009: Gabriela Molina; Andreas Vogt; Ahmet Bakan; Weixiang Dai; Pierre Queiroz de Oliveira; Wade Znosko; Thomas E Smithgall; Ivet Bahar; John Lazo; Billy W Day; Michael Tsang
Zebrafish chemical screening reveals an inhibitor of Dusp6 that expands cardiac cell lineages.
Nature chemical biology 2009;5(9):680-7.
2009: Ahmet Bakan; Ivet Bahar
The intrinsic dynamics of enzymes plays a dominant role in determining the structural changes induced upon inhibitor binding.
Proceedings of the National Academy of Sciences of the United States of America 2009;106(34):14349-54.
2009: Zheng Yang; Ivet Bahar; Michael Widom
Vibrational dynamics of icosahedrally symmetric biomolecular assemblies compared with predictions based on continuum elasticity.
Biophysical journal 2009;96(11):4438-48.
2009: Zheng Yang; Peter Májek; Ivet Bahar
Allosteric transitions of supramolecular systems explored by network models: application to chaperonin GroEL.
PLoS computational biology 2009;5(4):e1000360.
2009: Gabriela Mustata; Ariele Viacava Follis; Dalia I Hammoudeh; Steven J Metallo; Huabo Wang; Edward V Prochownik; John Lazo; Ivet Bahar
Discovery of novel Myc-Max heterodimer disruptors with a three-dimensional pharmacophore model.
Journal of medicinal chemistry 2009;52(5):1247-50.
2009: Lee-Wei Yang; Eran Eyal; Ivet Bahar; Akio Kitao
Principal component analysis of native ensembles of biomolecular structures (PCA_NEST): insights into functional dynamics.
Bioinformatics (Oxford, England) 2009;25(5):606-14.
2009: Yan Gu; Indira H Shrivastava; Susan Amara; Ivet Bahar
Molecular simulations elucidate the substrate translocation pathway in a glutamate transporter.
Proceedings of the National Academy of Sciences of the United States of America 2009;106(8):2589-94.
2008: Indira H Shrivastava; Jie Jiang; Susan Amara; Ivet Bahar
Time-resolved mechanism of extracellular gate opening and substrate binding in a glutamate transporter.
The Journal of biological chemistry 2008;283(42):28680-90.
2008: Basak Isin; Klaus Schulten; Emadeddin Emadeddin Tajkhorshid; Ivet Bahar
Mechanism of signal propagation upon retinal isomerization: insights from molecular dynamics simulations of rhodopsin restrained by normal modes.
Biophysical journal 2008;95(2):789-803.
2008: Ying Liu; Eran Eyal; Ivet Bahar
Analysis of correlated mutations in HIV-1 protease using spectral clustering.
Bioinformatics (Oxford, England) 2008;24(10):1243-50.
2008: Eran Eyal; Ivet Bahar
Toward a molecular understanding of the anisotropic response of proteins to external forces: insights from elastic network models.
Biophysical journal 2008;94(9):3424-35.
2008: Chakra Chennubhotla; Zheng Yang; Ivet Bahar
Coupling between global dynamics and signal transduction pathways: a mechanism of allostery for chaperonin GroEL.
Molecular bioSystems 2008;4(4):287-92.
2008: Ahmet Bakan; John Lazo; Peter Wipf; Kay M Brummond; Ivet Bahar
Toward a molecular understanding of the interaction of dual specificity phosphatases with substrates: insights from structure-based modeling and high throughput screening.
Current medicinal chemistry 2008;15(25):2536-44.
2008: Elife Z Bagci; Yoram Vodovotz; Timothy R Billiar; Bard Ermentrout; Ivet Bahar
Computational insights on the competing effects of nitric oxide in regulating apoptosis.
PloS one 2008;3(5):e2249.
2007: Ivet Bahar; Chakra Chennubhotla; Dror Tobi
Intrinsic dynamics of enzymes in the unbound state and relation to allosteric regulation.
Current opinion in structural biology 2007;17(6):633-40.
2007: Chakra Chennubhotla; Ivet Bahar
Signal propagation in proteins and relation to equilibrium fluctuations.
PLoS computational biology 2007;3(9):1716-26.
2007: John Lazo; John J Skoko; Stefan Werner; Branko Mitasev; Ahmet Bakan; Fumito Koizumi; Archibong Yellow-Duke; Ivet Bahar; Kay M Brummond
Structurally unique inhibitors of human mitogen-activated protein kinase phosphatase-1 identified in a pyrrole carboxamide library.
The Journal of pharmacology and experimental therapeutics 2007;322(3):940-7.
2007: John K Vries; Xiong Liu; Ivet Bahar
The relationship between n-gram patterns and protein secondary structure.
Proteins 2007;68(4):830-8.
2007: Eran Eyal; Shmuel Pietrokovski; Ivet Bahar
Rapid assessment of correlated amino acids from pair-to-pair (P2P) substitution matrices.
Bioinformatics (Oxford, England) 2007;23(14):1837-9.
2007: Chakra Chennubhotla; Ivet Bahar
Markov methods for hierarchical coarse-graining of large protein dynamics.
Journal of computational biology : a journal of computational molecular cell biology 2007;14(6):765-76.
2007: Eran Eyal; Chakra Chennubhotla; Lee-Wei Yang; Ivet Bahar
Anisotropic fluctuations of amino acids in protein structures: insights from X-ray crystallography and elastic network models.
Bioinformatics (Oxford, England) 2007;23(13):i175-84.
2007: Lee-Wei Yang; Eran Eyal; Chakra Chennubhotla; Jun-Goo Jee; Angela M Gronenborn; Ivet Bahar
Insights into equilibrium dynamics of proteins from comparison of NMR and X-ray data with computational predictions.
Structure (London, England : 1993) 2007;15(6):741-9.
2007: Anand Krishnan V Iyer; Kien T Tran; Christopher W Borysenko; Michael Cascio; Carlos J Camacho; Harry C Blair; Ivet Bahar; Alan Wells
Tenascin cytotactin epidermal growth factor-like repeat binds epidermal growth factor receptor with low affinity.
Journal of cellular physiology 2007;211(3):748-58.
2007: Dror Tobi; Ivet Bahar
Recruitment of rare 3-grams at functional sites: is this a mechanism for increasing enzyme specificity?
BMC bioinformatics 2007;8():226.
2006: Basak Isin; AJ Rader; Harpreet Kaur Dhiman; Judith Klein-Seetharaman; Ivet Bahar
Predisposition of the dark state of rhodopsin to functional changes in structure.
Proteins 2006;65(4):970-83.
2006: Eran Eyal; Lee-Wei Yang; Ivet Bahar
Anisotropic network model: systematic evaluation and a new web interface.
Bioinformatics (Oxford, England) 2006;22(21):2619-27.
2006: Lee-Wei Yang; AJ Rader; Xiong Liu; Christopher Jon Jursa; Shann-Ching Chen; Hassan A Karimi; Ivet Bahar
oGNM: online computation of structural dynamics using the Gaussian Network Model.
Nucleic acids research 2006;34(Web Server issue):W24-31.
2006: Indira H Shrivastava; Ivet Bahar
Common mechanism of pore opening shared by five different potassium channels.
Biophysical journal 2006;90(11):3929-40.
2006: Dror Tobi; Ivet Bahar
Optimal design of protein docking potentials: efficiency and limitations.
Proteins 2006;62(4):970-81.
2006: E Z Bagci; Yoram Vodovotz; T R Billiar; G Bard Ermentrout; Ivet Bahar
Bistability in apoptosis: roles of bax, bcl-2, and mitochondrial permeability transition pores.
Biophysical journal 2006;90(5):1546-59.
2006: Illés J Farkas; Chuang Wu; Chakra Chennubhotla; Ivet Bahar; Zoltan N. Oltvai
Topological basis of signal integration in the transcriptional-regulatory network of the yeast, Saccharomyces cerevisiae.
BMC bioinformatics 2006;7():478.
2006: Chakra Chennubhotla; Ivet Bahar
Markov propagation of allosteric effects in biomolecular systems: application to GroEL-GroES.
Molecular systems biology 2006;2():36.
2006: Rajan Munshi; Rob D Coalson; G Bard Ermentrout; Jeffry D Madura; Hagai Meirovitch; Joel R Stiles; Ivet Bahar
An introduction to simulation and visualization of biological systems at multiple scales: a summer training program for interdisciplinary research.
Biotechnology progress 2006;22(1):179-85.
2005: Dror Tobi; Ivet Bahar
Structural changes involved in protein binding correlate with intrinsic motions of proteins in the unbound state.
Proceedings of the National Academy of Sciences of the United States of America 2005;102(52):18908-13.
2005: Chakra Chennubhotla; AJ Rader; Lee-Wei Yang; Ivet Bahar
Elastic network models for understanding biomolecular machinery: from enzymes to supramolecular assemblies.
Physical biology 2005;2(4):S173-80.
2005: Ivet Bahar; AJ Rader
Coarse-grained normal mode analysis in structural biology.
Current opinion in structural biology 2005;15(5):586-92.
2005: Lee-Wei Yang; Xiong Liu; Christopher Jon Jursa; Mark Holliman; AJ Rader; Hassan A Karimi; Ivet Bahar
iGNM: a database of protein functional motions based on Gaussian Network Model.
Bioinformatics (Oxford, England) 2005;21(13):2978-87.
2005: Lee-Wei Yang; Ivet Bahar
Coupling between catalytic site and collective dynamics: a requirement for mechanochemical activity of enzymes.
Structure (London, England : 1993) 2005;13(6):893-904.
2005: Jason A Berberich; Lee-Wei Yang; Ivet Bahar; Alan Russell
A stable three enzyme creatinine biosensor. 2. Analysis of the impact of silver ions on creatine amidinohydrolase.
Acta biomaterialia 2005;1(2):183-91.
2005: Jason A Berberich; Lee-Wei Yang; Jeff Madura; Ivet Bahar; Alan Russell
A stable three-enzyme creatinine biosensor. 1. Impact of structure, function and environment on PEGylated and immobilized sarcosine oxidase.
Acta biomaterialia 2005;1(2):173-81.
2005: AJ Rader; Daniel H Vlad; Ivet Bahar
Maturation dynamics of bacteriophage HK97 capsid.
Structure (London, England : 1993) 2005;13(3):413-21.
2005: Amutha Ramaswamy; Ivet Bahar; Ilya P Ioshikhes
Structural dynamics of nucleosome core particle: comparison with nucleosomes containing histone variants.
Proteins 2005;58(3):683-96.
2004: N Alpay Temiz; Eva Meirovitch; Ivet Bahar
Escherichia coli adenylate kinase dynamics: comparison of elastic network model modes with mode-coupling (15)N-NMR relaxation data.
Proteins 2004;57(3):468-80.
2004: Mineaki Seki; Chikahide Masutani; Lee-Wei Yang; Anthony Schuffert; Shigenori Iwai; Ivet Bahar; Richard D Wood
High-efficiency bypass of DNA damage by human DNA polymerase Q.
The EMBO journal 2004;23(22):4484-94.
2004: Yoram Vodovotz; Peter K M Kim; Elife Zerrin Bagci; G Bard Ermentrout; Carson C Chow; Ivet Bahar; Timothy R Billiar
Inflammatory modulation of hepatocyte apoptosis by nitric oxide: in vivo, in vitro, and in silico studies.
Current molecular medicine 2004;4(7):753-62.
2004: Nicolas Sluis-Cremer; N Alpay Temiz; Ivet Bahar
Conformational changes in HIV-1 reverse transcriptase induced by nonnucleoside reverse transcriptase inhibitor binding.
Current HIV research 2004;2(4):323-32.
2004: Marni Brisson; Theresa Nguyen; Andreas Vogt; Jack C Yalowich; Angela Giorgianni; Dror Tobi; Ivet Bahar; Corey R J Stephenson; Peter Wipf; John Lazo
Discovery and characterization of novel small molecule inhibitors of human Cdc25B dual specificity phosphatase.
Molecular pharmacology 2004;66(4):824-33.
2004: Yongmei Wang; A J Rader; Ivet Bahar; Robert L Jernigan
Global ribosome motions revealed with elastic network model.
Journal of structural biology 2004;147(3):302-14.
2004: Shann-Ching Chen; Ivet Bahar
Mining frequent patterns in protein structures: a study of protease families.
Bioinformatics (Oxford, England) 2004;20 Suppl 1():i77-85.
2004: AJ Rader; Gülsüm Anderson; Basak Isin; H Gobind Khorana; Ivet Bahar; Judith Klein-Seetharaman
Identification of core amino acids stabilizing rhodopsin.
Proceedings of the National Academy of Sciences of the United States of America 2004;101(19):7246-51.
2004: John K Vries; Rajan Munshi; Dror Tobi; Judith Klein-Seetharaman; Panayiotis V Benos; Ivet Bahar
A sequence alignment-independent method for protein classification.
Applied bioinformatics 2004;3(2-3):137-48.
2003: Chunyan Xu; Dror Tobi; Ivet Bahar
Allosteric changes in protein structure computed by a simple mechanical model: hemoglobin T<-->R2 transition.
Journal of molecular biology 2003;333(1):153-68.
2003: Zerrin Bagci; Andrzej Kloczkowski; Robert L Jernigan; Ivet Bahar
The origin and extent of coarse-grained regularities in protein internal packing.
Proteins 2003;53(1):56-67.
2003: S Banu Ozkan; Ken A Dill; Ivet Bahar
Computing the transition state populations in simple protein models.
Biopolymers 2003;68(1):35-46.
2002: N Alpay Temiz; Ivet Bahar
Inhibitor binding alters the directions of domain motions in HIV-1 reverse transcriptase.
Proteins 2002;49(1):61-70.
2002: S Banu Ozkan; Ken A Dill; Ivet Bahar
Fast-folding protein kinetics, hidden intermediates, and the sequential stabilization model.
Protein science : a publication of the Protein Society 2002;11(8):1958-70.
2002: ozlem keskin; Stewart R Durell; Ivet Bahar; Robert L Jernigan; David G Covell
Relating molecular flexibility to function: a case study of tubulin.
Biophysical journal 2002;83(2):663-80.
2002: Basak Isin; Pemra Doruker; Ivet Bahar
Functional motions of influenza virus hemagglutinin: a structure-based analytical approach.
Biophysical journal 2002;82(2):569-81.
2002: Pemra Doruker; Robert L Jernigan; Ivet Bahar
Dynamics of large proteins through hierarchical levels of coarse-grained structures.
Journal of computational chemistry 2002;23(1):119-27.
2002: ozlem keskin; Ivet Bahar; D Flatow; David G Covell; Robert L Jernigan
Molecular mechanisms of chaperonin GroEL-GroES function.
Biochemistry 2002;41(2):491-501.
2001: S Banu Ozkan; Ivet Bahar; Ken A Dill
Transition states and the meaning of Phi-values in protein folding kinetics.
Nature structural biology 2001;8(9):765-9.
2001: AR Atilgan; Stewart R Durell; Robert L Jernigan; Melik C Demirel; ozlem keskin; Ivet Bahar
Anisotropy of fluctuation dynamics of proteins with an elastic network model.
Biophysical journal 2001;80(1):505-15.
2000: Pemra Doruker; AR Atilgan; Ivet Bahar
Dynamics of proteins predicted by molecular dynamics simulations and analytical approaches: application to alpha-amylase inhibitor.
Proteins 2000;40(3):512-24.
2000: ozlem keskin; Ivet Bahar; Robert L Jernigan; J A Beutler; R H Shoemaker; Edward A Sausville; D G Covell
Characterization of anticancer agents by their growth inhibitory activity and relationships to mechanism of action and structure.
Anti-cancer drug design 2000;15(2):79-98.
2000: ozlem keskin; Robert L Jernigan; Ivet Bahar
Proteins with similar architecture exhibit similar large-scale dynamic behavior.
Biophysical journal 2000;78(4):2093-106.
1999: Turkan Haliloglu; Ivet Bahar
Structure-based analysis of protein dynamics: comparison of theoretical results for hen lysozyme with X-ray diffraction and NMR relaxation data.
Proteins 1999;37(4):654-67.
1999: Ivet Bahar; Robert L Jernigan
Cooperative fluctuations and subunit communication in tryptophan synthase.
Biochemistry 1999;38(12):3478-90.
1999: Ivet Bahar; Batu Erman; Robert L Jernigan; AR Atilgan; D G Covell
Collective motions in HIV-1 reverse transcriptase: examination of flexibility and enzyme function.
Journal of molecular biology 1999;285(3):1023-37.
1998: ozlem keskin; Ivet Bahar; A Y Badretdinov; O B Ptitsyn; Robert L Jernigan
Empirical solvent-mediated potentials hold for both intra-molecular and inter-molecular inter-residue interactions.
Protein science : a publication of the Protein Society 1998;7(12):2578-86.
1998: Melik C Demirel; AR Atilgan; Robert L Jernigan; Batu Erman; Ivet Bahar
Identification of kinetically hot residues in proteins.
Protein science : a publication of the Protein Society 1998;7(12):2522-32.
1998: Ivet Bahar; Robert L Jernigan
Vibrational dynamics of transfer RNAs: comparison of the free and synthetase-bound forms.
Journal of molecular biology 1998;281(5):871-84.
1998: B Ozkan; Ivet Bahar
Recognition of native structure from complete enumeration of low-resolution models with constraints.
Proteins 1998;32(2):211-22.
1998: Turkan Haliloglu; Ivet Bahar
Coarse-grained simulations of conformational dynamics of proteins: application to apomyoglobin.
Proteins 1998;31(3):271-81.
1998: Ivet Bahar; Anders Wallqvist; David G Covell; Robert L Jernigan
Correlation between native-state hydrogen exchange and cooperative residue fluctuations from a simple model.
Biochemistry 1998;37(4):1067-75.
1998: ozlem keskin; Ivet Bahar
Packing of sidechains in low-resolution models for proteins.
Folding & design 1998;3(6):469-79.
1997: Ivet Bahar; Batu Erman; Turkan Haliloglu; Robert L Jernigan
Efficient characterization of collective motions and interresidue correlations in proteins by low-resolution simulations.
Biochemistry 1997;36(44):13512-23.
1997: Ivet Bahar; M Kaplan; Robert L Jernigan
Short-range conformational energies, secondary structure propensities, and recognition of correct sequence-structure matches.
Proteins 1997;29(3):292-308.
1997: Ivet Bahar; AR Atilgan; Robert L Jernigan; Batu Erman
Understanding the recognition of protein structural classes by amino acid composition.
Proteins 1997;29(2):172-85.
1997: Pemra Doruker; Ivet Bahar
Role of water on unfolding kinetics of helical peptides studied by molecular dynamics simulations.
Biophysical journal 1997;72(6):2445-56.
1997: Ivet Bahar; Robert L Jernigan
Inter-residue potentials in globular proteins and the dominance of highly specific hydrophilic interactions at close separation.
Journal of molecular biology 1997;266(1):195-214.
1997: Ivet Bahar; AR Atilgan; Batu Erman
Direct evaluation of thermal fluctuations in proteins using a single-parameter harmonic potential.
Folding & design 1997;2(3):173-81.
1996: Robert L Jernigan; Ivet Bahar
Structure-derived potentials and protein simulations.
Current opinion in structural biology 1996;6(2):195-209.
1996: Ivet Bahar; Robert L Jernigan
Coordination geometry of nonbonded residues in globular proteins.
Folding & design 1996;1(5):357-70.
1994: Ivet Bahar; Robert L Jernigan
Cooperative structural transitions induced by non-homogeneous intramolecular interactions in compact globular proteins.
Biophysical journal 1994;66(2 Pt 1):467-81.
1994: Ivet Bahar; Robert L Jernigan
Stabilization of intermediate density states in globular proteins by homogeneous intramolecular attractive interactions.
Biophysical journal 1994;66(2 Pt 1):454-66.