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Ivet Bahar
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2020 – today
- 2022
- [j42]Iris N. Smith, Jennifer E. Dawson, James Krieger, Stetson Thacker, Ivet Bahar
, Charis Eng
Structural and Dynamic Effects of PTEN C-Terminal Tail Phosphorylation. J. Chem. Inf. Model. 62(17): 4175-4190 (2022) - [j41]Omer Acar
Elastic network modeling of cellular networks unveils sensor and effector genes that control information flow. PLoS Comput. Biol. 18(5) (2022) - 2021
- [j40]She Zhang
ProDy 2.0: increased scale and scope after 10 years of protein dynamics modelling with Python. Bioinform. 37(20): 3657-3659 (2021) - [j39]Burak T. Kaynak
ClustENMD: efficient sampling of biomolecular conformational space at atomic resolution. Bioinform. 37(21): 3956-3958 (2021) - [j38]Haohan Wang, Fen Pei, Michael M. Vanyukov, Ivet Bahar, Wei Wu, Eric P. Xing:
Coupled mixed model for joint genetic analysis of complex disorders with two independently collected data sets. BMC Bioinform. 22(1): 50 (2021) - [j37]Fen Pei
Predicting Protein-Protein Interactions Using Symmetric Logistic Matrix Factorization. J. Chem. Inf. Model. 61(4): 1670-1682 (2021) - 2020
- [j36]Luca Ponzoni
Rhapsody: predicting the pathogenicity of human missense variants. Bioinform. 36(10): 3084-3092 (2020) - [j35]Hongchun Li, Fen Pei, D. Lansing Taylor, Ivet Bahar
QuartataWeb: Integrated Chemical-Protein-Pathway Mapping for Polypharmacology and Chemogenomics. Bioinform. 36(12): 3935-3937 (2020) - [j34]Luca Ponzoni
Complementary computational and experimental evaluation of missense variants in the ROMK potassium channel. PLoS Comput. Biol. 16(4) (2020)
2010 – 2019
- 2019
- [j33]Karolina Mikulska-Ruminska
Characterization of Differential Dynamics, Specificity, and Allostery of Lipoxygenase Family Members. J. Chem. Inf. Model. 59(5): 2496-2508 (2019) - 2017
- [j32]Hongchun Li, Yuan-Yu Chang, Ji Young Lee, Ivet Bahar, Lee-Wei Yang
DynOmics: dynamics of structural proteome and beyond. Nucleic Acids Res. 45(Webserver-Issue): W374-W380 (2017) - 2016
- [j31]Hongchun Li, Yuan-Yu Chang, Lee-Wei Yang
iGNM 2.0: the Gaussian network model database for biomolecular structural dynamics. Nucleic Acids Res. 44(Database-Issue): 415-422 (2016) - 2015
- [j30]Murat Can Cobanoglu, Zoltán N. Oltvai, D. Lansing Taylor
BalestraWeb: efficient online evaluation of drug-target interactions. Bioinform. 31(1): 131-133 (2015) - [j29]Eran Eyal, Gengkon Lum, Ivet Bahar:
The anisotropic network model web server at 2015 (ANM 2.0). Bioinform. 31(9): 1487-1489 (2015) - [j28]Wenzhi Mao
Comparative study of the effectiveness and limitations of current methods for detecting sequence coevolution. Bioinform. 31(12): 1929-1937 (2015) - [j27]Gregory F. Cooper, Ivet Bahar, Michael J. Becich, Panayiotis V. Benos
The center for causal discovery of biomedical knowledge from big data. J. Am. Medical Informatics Assoc. 22(6): 1132-1136 (2015) - 2014
- [j26]Ahmet Bakan, Anindita Dutta, Wenzhi Mao
Evol and ProDy for bridging protein sequence evolution and structural dynamics. Bioinform. 30(18): 2681-2683 (2014) - [j25]Avisek Das, Mert Gur
Exploring the Conformational Transitions of Biomolecular Systems Using a Simple Two-State Anisotropic Network Model. PLoS Comput. Biol. 10(4) (2014) - [j24]Ignacio J. General, Ying Liu, Mandy E. Blackburn, Wenzhi Mao
ATPase Subdomain IA Is a Mediator of Interdomain Allostery in Hsp70 Molecular Chaperones. PLoS Comput. Biol. 10(5) (2014) - [j23]Mary Hongying Cheng, Ivet Bahar:
Complete Mapping of Substrate Translocation Highlights the Role of LeuT N-terminal Segment in Regulating Transport Cycle. PLoS Comput. Biol. 10(10) (2014) - 2013
- [j22]Murat Can Cobanoglu, Chang Liu, Feizhuo Hu, Zoltán N. Oltvai, Ivet Bahar:
Predicting Drug-Target Interactions Using Probabilistic Matrix Factorization. J. Chem. Inf. Model. 53(12): 3399-3409 (2013) - 2012
- [j21]Zeynep Kurkcuoglu, Ahmet Bakan, Duygu Kocaman, Ivet Bahar, Pemra Doruker
Coupling between Catalytic Loop Motions and Enzyme Global Dynamics. PLoS Comput. Biol. 8(9) (2012) - 2011
- [j20]Ahmet Bakan, Lidio M. C. Meireles, Ivet Bahar:
ProDy: Protein Dynamics Inferred from Theory and Experiments. Bioinform. 27(11): 1575-1577 (2011) - [j19]Enrique Marcos
Changes in Dynamics upon Oligomerization Regulate Substrate Binding and Allostery in Amino Acid Kinase Family Members. PLoS Comput. Biol. 7(9) (2011) - [c6]Ahmet Bakan, Ivet Bahar:
Computational Generation inhibitor-Bound Conformers of P38 Map Kinase and Comparison with Experiments. Pacific Symposium on Biocomputing 2011: 181-192 - 2010
- [j18]Enrique Marcos
On the Conservation of the Slow Conformational Dynamics within the Amino Acid Kinase Family: NAGK the Paradigm. PLoS Comput. Biol. 6(4) (2010) - [j17]Timothy R. Lezon
Using Entropy Maximization to Understand the Determinants of Structural Dynamics beyond Native Contact Topology. PLoS Comput. Biol. 6(6) (2010) - [j16]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 Comput. Biol. 6(9) (2010) - [c5]Ying Liu, Ivet Bahar:
Toward Understanding Allosteric Signaling Mechanisms in the ATPase Domain of Molecular Chaperones. Pacific Symposium on Biocomputing 2010: 269-280
2000 – 2009
- 2009
- [j15]Lee-Wei Yang, Eran Eyal, Ivet Bahar, Akio Kitao
Principal component analysis of native ensembles of biomolecular structures (PCA_NEST): insights into functional dynamics. Bioinform. 25(5): 606-614 (2009) - [j14]Lee-Wei Yang, Eran Eyal, Ivet Bahar, Akio Kitao
Principal component analysis of native ensembles of biomolecular structures (PCA_NEST): insights into functional dynamics. Bioinform. 25(16): 2147 (2009) - [j13]Zheng Yang, Peter Májek, Ivet Bahar:
Allosteric Transitions of Supramolecular Systems Explored by Network Models: Application to Chaperonin GroEL. PLoS Comput. Biol. 5(4) (2009) - [j12]Timothy R. Lezon
Global Motions of the Nuclear Pore Complex: Insights from Elastic Network Models. PLoS Comput. Biol. 5(9) (2009) - 2008
- [j11]Ying Liu, Eran Eyal, Ivet Bahar:
Analysis of correlated mutations in HIV-1 protease using spectral clustering. Bioinform. 24(10): 1243-1250 (2008) - 2007
- [j10]Eran Eyal, Shmuel Pietrokovski
Rapid assessment of correlated amino acids from pair-to-pair (P2P) substitution matrices. Bioinform. 23(14): 1837-1839 (2007) - [j9]Dror Tobi
Recruitment of rare 3-grams at functional sites: Is this a mechanism for increasing enzyme specificity? BMC Bioinform. 8 (2007) - [j8]Chakra Chennubhotla, Ivet Bahar:
Markov Methods for Hierarchical Coarse-Graining of Large Protein Dynamics. J. Comput. Biol. 14(6): 765-776 (2007) - [j7]Chakra Chennubhotla, Ivet Bahar:
Signal Propagation in Proteins and Relation to Equilibrium Fluctuations. PLoS Comput. Biol. 3(9) (2007) - [j6]Chakra Chennubhotla, Ivet Bahar:
Correction: Signal Propagation in Proteins and Relation to Equilibrium Fluctuations. PLoS Comput. Biol. 3(10) (2007) - [c4]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. ISMB/ECCB (Supplement of Bioinformatics) 2007: 175-184 - 2006
- [j5]Eran Eyal, Lee-Wei Yang, Ivet Bahar:
Anisotropic network model: systematic evaluation and a new web interface. Bioinform. 22(21): 2619-2627 (2006) - [j4]Illés J. Farkas, Chuang Wu, Chakra Chennubhotla, Ivet Bahar, Zoltán N. Oltvai:
Topological basis of signal integration in the transcriptional-regulatory network of the yeast, Saccharomyces cerevisiae. BMC Bioinform. 7: 478 (2006) - [j3]Lee-Wei Yang, A. J. Rader, Xiong Liu
oGNM: online computation of structural dynamics using the Gaussian Network Model. Nucleic Acids Res. 34(Web-Server-Issue): 24-31 (2006) - [c3]Chakra Chennubhotla, Ivet Bahar:
Markov Methods for Hierarchical Coarse-Graining of Large Protein Dynamics. RECOMB 2006: 379-393 - 2005
- [j2]Lee-Wei Yang, Xiong Liu
iGNM: a database of protein functional motions based on Gaussian Network Model. Bioinform. 21(13): 2978-2987 (2005) - 2004
- [c2]Xiong Liu
Protein Functional Motion Query and Visualization. COMPSAC Workshops 2004: 86-89 - [c1]Shann-Ching Chen, Ivet Bahar:
Mining frequent patterns in protein structures: a study of protease families. ISMB/ECCB (Supplement of Bioinformatics) 2004: 77-85 - 2002
- [j1]Pemra Doruker
Dynamics of large proteins through hierarchical levels of coarse-grained structures. J. Comput. Chem. 23(1): 119-127 (2002)
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