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Journal of Biomolecular Structure and Dynamics Volume 31, 2013 - Issue 1: Predictive biology using systems and integrative analysis and methods
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Articles

Relationship between helix stability and binding affinities: molecular dynamics simulations of Bfl-1/A1-binding pro-apoptotic BH3 peptide helices in explicit solvent

Vivek Modi Department of Biological Sciences and Bioengineering, Indian Institute of Technology Kanpur, Kanpur, 208016, India
,
Dilraj Lama Department of Biological Sciences and Bioengineering, Indian Institute of Technology Kanpur, Kanpur, 208016, India
&
Ramasubbu Sankararamakrishnan Department of Biological Sciences and Bioengineering, Indian Institute of Technology Kanpur, Kanpur, 208016, IndiaCorrespondence[email protected]
Pages 65-77 | Received 18 Apr 2011, Accepted 20 Jan 2012, Published online: 18 Jul 2012

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Mark Klein. (2017) Stabilized helical peptides: overview of the technologies and its impact on drug discovery. Expert Opinion on Drug Discovery 12:11, pages 1117-1125.
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Articles from other publishers (13)

Angelina T. Huynh, Thi-Tina N. Nguyen, Carina A. Villegas, Saira Montemorso, Benjamin Strauss, Richard A. Pearson, Jason G. Graham, Jonathan Oribello, Rohit Suresh, Brooke Lustig & Ningkun Wang. (2022) Prediction and confirmation of a switch-like region within the N-terminal domain of hSIRT1. Biochemistry and Biophysics Reports 30, pages 101275.
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Tomás Antonio Santa-Coloma. (2022) Overlapping synthetic peptides as a tool to map protein-protein interactions ̶ FSH as a model system of nonadditive interactions. Biochimica et Biophysica Acta (BBA) - General Subjects 1866:7, pages 130153.
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Chinthakunta Narendra Reddy & Ramasubbu Sankararamakrishnan. (2021) Designing BH3-Mimetic Peptide Inhibitors for the Viral Bcl-2 Homologues A179L and BHRF1: Importance of Long-Range Electrostatic Interactions. ACS Omega 6:41, pages 26976-26989.
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Xue Li, Junwei Dou, Qidong You & Zhengyu Jiang. (2021) Inhibitors of BCL2A1/Bfl-1 protein: Potential stock in cancer therapy. European Journal of Medicinal Chemistry 220, pages 113539.
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C. Narendra Reddy, Nishat Manzar, Bushra Ateeq & Ramasubbu Sankararamakrishnan. (2020) Computational Design of BH3-Mimetic Peptide Inhibitors That Can Bind Specifically to Mcl-1 or Bcl-X L : Role of Non-Hot Spot Residues . Biochemistry 59:45, pages 4379-4394.
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Parthiban Marimuthu, Jamoliddin Razzokov, Kalaimathy Singaravelu & Annemie Bogaerts. (2020) Predicted Hotspot Residues Involved in Allosteric Signal Transmission in Pro-Apoptotic Peptide—Mcl1 Complexes. Biomolecules 10:8, pages 1114.
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Vivek Modi & Ramasubbu Sankararamakrishnan. (2017) Binding affinity of pro-apoptotic BH3 peptides for the anti-apoptotic Mcl-1 and A1 proteins: Molecular dynamics simulations of Mcl-1 and A1 in complex with six different BH3 peptides. Journal of Molecular Graphics and Modelling 73, pages 115-128.
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Stefan M. Ivanov, Roland G. Huber, Jim Warwicker & Peter J. Bond. (2016) Energetics and Dynamics Across the Bcl-2-Regulated Apoptotic Pathway Reveal Distinct Evolutionary Determinants of Specificity and Affinity. Structure 24:11, pages 2024-2033.
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Bo LiXianfang ZhengChuancui HuYunxia Cao. (2015) Human Papillomavirus Genome-Wide Identification of T-Cell Epitopes for Peptide Vaccine Development Against Cervical Cancer: An Integration of Computational Analysis and Experimental Assay. Journal of Computational Biology 22:10, pages 962-974.
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Song Li, Huayan Hou, Takashi Mori, Darrell Sawmiller, Adam Smith, Jun Tian, Yanjiang Wang, Brian Giunta, Paul R. Sanberg, Sheqing Zhang & Jun Tan. (2015) Swedish mutant APP-based BACE1 binding site peptide reduces APP β-cleavage and cerebral Aβ levels in Alzheimer’s mice. Scientific Reports 5:1.
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Eol Han & Hwankyu Lee. (2014) Effect of the structural difference between Bax-α5 and Bcl-xL-α5 on their interactions with lipid bilayers. Phys. Chem. Chem. Phys. 16:3, pages 981-988.
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Laura Delgado-Soler, Maria del Mar Orzaez & Jaime Rubio-Martinez. (2013) Structure-based approach to the design of BakBH3 mimetic peptides with increased helical propensity. Journal of Molecular Modeling 19:10, pages 4305-4318.
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Dilraj Lama, Vivek Modi & Ramasubbu Sankararamakrishnan. (2013) Behavior of Solvent-Exposed Hydrophobic Groove in the Anti-Apoptotic Bcl-XL Protein: Clues for Its Ability to Bind Diverse BH3 Ligands from MD Simulations. PLoS ONE 8:2, pages e54397.
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