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Subrata Dasgupta, Soumita Mukherjee, Bishnu P Mukhopadhyay, Avik Banerjee & Deepak K Mishra. (2018) Recognition dynamics of dopamine to human Monoamine oxidase B: role of Leu171/Gln206 and conserved water molecules in the active site cavity. Journal of Biomolecular Structure and Dynamics 36:6, pages 1439-1462.
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Hridoy R. Bairagya, Deepak K. Mishra, Bishnu P. Mukhopadhyay & K. Sekar. (2014) Conserved water-mediated recognition and dynamics of NAD+ (carboxamide group) to hIMPDH enzyme: water mimic approach toward the design of isoform-selective inhibitor. Journal of Biomolecular Structure and Dynamics 32:8, pages 1248-1262.
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Hridoy
R. Bairagya & Bishnu
P. Mukhopadhyay. (2013) Protein folding: challenge to chemistry. Journal of Biomolecular Structure and Dynamics 31:9, pages 993-994.
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Hridoy
R. Bairagya & Bishnu
P. Mukhopadhyay. (2013) An insight to the dynamics of conserved water-mediated salt bridge interaction and interdomain recognition in hIMPDH isoforms. Journal of Biomolecular Structure and Dynamics 31:7, pages 788-808.
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Deepak
K. Mishra, Hridoy
R. Bairagya & Bishnu
P. Mukhopadhyay. (2013) 172 Role of conserved water molecular triad in the recognition of IMP, NAD+ with Asp 274, Asn 303, Arg 322, and Asp 364 in both the isoform of hIMPDH. Journal of Biomolecular Structure and Dynamics 31:sup1, pages 111-111.
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Karina
S. Matos, Elaine
F.F. da Cunha, Arlan da Silva Gonçalves, Alan Wilter, Kamil Kuča, Tanos
C.C. França & Teodorico
C. Ramalho. (2012) First principles calculations of thermodynamics and kinetic parameters and molecular dynamics simulations of acetylcholinesterase reactivators: can mouse data provide new insights into humans?. Journal of Biomolecular Structure and Dynamics 30:5, pages 546-558.
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HridoyR. Bairagya, BishnuP. Mukhopadhyay & AsimK. Bera. (2011) Role of Salt Bridge Dynamics in Inter Domain Recognition of Human IMPDH Isoforms: An Insight to Inhibitor Topology for Isoform-II. Journal of Biomolecular Structure and Dynamics 29:3, pages 441-462.
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Esmaeil Behmard, Parviz Abdolmaleki, Ebrahim
Barzegari Asadabadi & Samad Jahandideh. (2011) Prevalent Mutations of Human Prion Protein: A Molecular Modeling and Molecular Dynamics Study. Journal of Biomolecular Structure and Dynamics 29:2, pages 379-389.
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AlineA. Oliveira, MagdalenaN. Rennó, César
A. S. de Matos, MorenaD. Bertuzzi, TeodoricoC. Ramalho, Carlos
A.M. Fraga & Tanos
C. C. França. (2011) Molecular Modeling Studies of Yersinia pestis Dihydrofolate Reductase. Journal of Biomolecular Structure and Dynamics 29:2, pages 351-367.
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Ping Li, Jian
Jun Tan, Ming Liu, Xiao
Yi Zhang, Wei
Zu Chen & Cun
Xin Wang. (2011) Insight into the Inhibitory Mechanism and Binding Mode Between D77 and HIV-1 Integrase by Molecular Modeling Methods. Journal of Biomolecular Structure and Dynamics 29:2, pages 311-323.
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Riddhi Majumder, Sujata Roy & Ashoke
Ranjan Thakur. (2011) Molecular Modeling and Molecular Dynamics Simulation Studies of Delta-Notch Complex. Journal of Biomolecular Structure and Dynamics 29:2, pages 297-310.
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Adeleh Divsalar, Ali
Akbar Saboury, Leila Ahadi, Elham Zemanatiyar, Hassan Mansouri-Torshizi, Davood Ajloo & RamaswamyH. Sarma. (2011) Biological Evaluation and Interaction of a Newly Designed Anti-cancer Pd(II) Complex and Human Serum Albumin. Journal of Biomolecular Structure and Dynamics 29:2, pages 283-296.
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Deok-Soo Kim, Chong-Min Kim, Chung-In Won, Jae-Kwan Kim, Joonghyun Ryu, Youngsong Cho, Changhee Lee & Jong Bhak. (2011) BetaDock: Shape-Priority Docking Method Based on Beta-Complex. Journal of Biomolecular Structure and Dynamics 29:1, pages 219-242.
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Zahra Omidvar, Kazem Parivar, Hamideh Sanee, Zeinab Amiri-Tehranizadeh, Ali Baratian, Mohammad
Reza Saberi, Ahmad Asoodeh & Jamshidkhan Chamani. (2011) Investigations with Spectroscopy, Zeta Potential and Molecular Modeling of the Non-Cooperative Behaviour Between Cyclophosphamide Hydrochloride and Aspirin upon Interaction with Human Serum Albumin: Binary and Ternary Systems from the View Point of Multi-Drug Therapy. Journal of Biomolecular Structure and Dynamics 29:1, pages 181-206.
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Sudipta Pal, Mili Das, Rahul Banerjee & Dipak Dasgupta. (2011) Biphasic Association of T7 RNA Polymerase and a Nucleotide Analogue, Cibacron Blue as a Model to Understand the Role of Initiating Nucleotide in the Mechanism of Enzyme Action. Journal of Biomolecular Structure and Dynamics 29:1, pages 153-164.
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Rituraj Purohit, Vidya Rajendran & Rao Sethumadhavan. (2011) Studies on Adaptability of Binding Residues Flap Region of TMC-114 Resistance HIV-1 Protease Mutants. Journal of Biomolecular Structure and Dynamics 29:1, pages 137-152.
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JaysonF. Varughese & Yumin Li. (2011) Molecular Dynamics and Docking Studies on Cardiac Troponin C. Journal of Biomolecular Structure and Dynamics 29:1, pages 123-135.
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Ji
Guo Su, Xian
Jin Xu, Chun
Hua Li, Wei
Zu Chen & Cun
Xin Wang. (2011) An Analysis of the Influence of Protein Intrinsic Dynamical Properties on its Thermal Unfolding Behavior. Journal of Biomolecular Structure and Dynamics 29:1, pages 105-121.
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AlexeiN. Pankratov, OlgaM. Tsivileva, BorisI. Drevko & ValentinaE. Nikitina. (2011) Compounds of the 1,5-di(4-R-phenyl)-3-selenopentanediones-1,5 series interaction with the Basidiomycete Lentinula edodes, lectins: Computations and Experiment. Journal of Biomolecular Structure and Dynamics 28:6, pages 969-974.
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MalihehS. Atri, AliA. Saboury, AliA. Moosavi-Movahedi, Bahram Goliaei, Yahya Sefidbakht, Hamid
Hadi Alijanvand, Ahmad Sharifzadeh & Amir Niasari-Naslaji. (2011) Structure and Stability Analysis of Cytotoxic Complex of Camel α-Lactalbumin and Unsaturated Fatty Acids Produced at High Temperature. Journal of Biomolecular Structure and Dynamics 28:6, pages 919-928.
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TeodoricoC. Ramalho, MelissaS. Caetano, Daniela Josa, GustavoP. Luz, ElisangelaA. Freitas & Elaine
F. F. da Cunha. (2011) Molecular Modeling of Mycobacterium Tuberculosis dUTpase: Docking and Catalytic Mechanism Studies. Journal of Biomolecular Structure and Dynamics 28:6, pages 907-917.
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Yue Wang, Fuyong Bian, Shengrong Deng, Qiang Shi, Maofa Ge, Shu Wang, Xingkang Zhang & Sichuan Xu. (2011) The Key Residues of Active Sites on the Catalytic Fragment for Paclitaxel Interacting with Poly (ADP-Ribose) Polymerase. Journal of Biomolecular Structure and Dynamics 28:6, pages 881-893.
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Mei Zhuohang, Liu Ji & Yu Hongwei. (2011) Modeling of Transition State by Molecular Dynamics. Prediction of Catalytic Efficiency of the Mutants of Mandelate Racemase. Journal of Biomolecular Structure and Dynamics 28:6, pages 871-879.
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Vinod Jani, UddhaveshB. Sonavane & Rajendra Joshi. (2011) Microsecond Scale Replica Exchange Molecular Dynamic Simulation of Villin Headpiece: An Insight into the Folding Landscape. Journal of Biomolecular Structure and Dynamics 28:6, pages 845-860.
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Yunjie Zhao, Zhou Gong & Yi Xiao. (2011) Improvements of the Hierarchical Approach for Predicting RNA Tertiary Structure. Journal of Biomolecular Structure and Dynamics 28:5, pages 815-826.
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EvandroP. Semighini, JonathanA. Resende, Peterson de Andrade, Pedro
A. B. Morais, Ivone Carvalho, CarltonA. Taft & Carlos
H. T. P. Silva. (2011) Using Computer-aided Drug Design and Medicinal Chemistry Strategies in the Fight Against Diabetes. Journal of Biomolecular Structure and Dynamics 28:5, pages 787-796.
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Zheng-Li Zhou, Jian-Hua Zhao, Hsuan-Liang Liu, JosephineW. Wu, Kung-Tien Liu, Chih-Kuang Chuang, Wei-Bor Tsai & Yih Ho. (2011) The Possible Structural Models for Polyglutamine Aggregation: A Molecular Dynamics Simulations Study. Journal of Biomolecular Structure and Dynamics 28:5, pages 743-758.
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Sujata Roy & Ashoke
Ranjan Thakur. (2011) Two models of Smad4 and Hoxa9 Complex are Proposed: Structural and Interactional Perspective. Journal of Biomolecular Structure and Dynamics 28:5, pages 729-742.
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Xianjin Xu, Jiguo Su, Weizu Chen & Cunxin Wang. (2011) Thermal Stability and Unfolding Pathways of Sso7d and its Mutant F31A: Insight from Molecular Dynamics Simulation. Journal of Biomolecular Structure and Dynamics 28:5, pages 717-727.
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Elif
Ozkirimli Olmez & Burak Alakent. (2011) Alpha7 Helix Plays an Important Role in the Conformational Stability of PTP1B. Journal of Biomolecular Structure and Dynamics 28:5, pages 675-693.
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H. Vahedian-Movahed, M.R. Saberi & J. Chamani. (2011) Comparison of Binding Interactions of Lomefloxacin to Serum Albumin and Serum Transferrin by Resonance Light Scattering and Fluorescence Quenching Methods. Journal of Biomolecular Structure and Dynamics 28:4, pages 483-502.
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Chia-Hui Lin, Tung-Ti Chang, Mao-Feng Sun, Hsin-Yi Chen, Fuu-Jen Tsai, Kun-Lung Chang, Mark Fisher & Calvin
Yu-Chian Chen. (2011) Potent Inhibitor Design Against H1N1 Swine Influenza: Structure-based and Molecular Dynamics Analysis for M2 Inhibitors from Traditional Chinese Medicine Database. Journal of Biomolecular Structure and Dynamics 28:4, pages 471-482.
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AnaP. Guimarães, AlineA. Oliveira, Elaine
F. F. da Cunha, TeodoricoC. Ramalho & Tanos
C. C. França. (2011) Design of New Chemotherapeutics Against the Deadly Anthrax Disease. Docking and Molecular Dynamics studies of Inhibitors Containing Pyrrolidine and Riboamidrazone Rings on Nucleoside Hydrolase from Bacillus anthracis
. Journal of Biomolecular Structure and Dynamics 28:4, pages 455-469.
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TeodoricoC. Ramalho & Elaine
F.F. da Cunha. (2011) Thermodynamic Framework of the Interaction between Protein and Solvent Drives Protein Folding. Journal of Biomolecular Structure and Dynamics 28:4, pages 645-646.
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Zhou Gong, Yunjie Zhao & Yi Xiao. (2010) RNA Stability Under Different Combinations of Amber Force Fields and Solvation Models. Journal of Biomolecular Structure and Dynamics 28:3, pages 431-441.
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Hyun
Mee Lee, Biao Jin, Sung
Wook Han & SeogK. Kim. (2010) Conformational Analysis of Genotoxic Benzo[a]pyrene-7,8-dione-Duplex DNA Adducts Using a Molecular Dynamics Method (II). Journal of Biomolecular Structure and Dynamics 28:3, pages 421-430.
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Jiří Wiesner, Zdeněk Kříž, Kamil Kuča, Daniel Jun & Jaroslav Koča. (2010) Influence of the Acetylcholinesterase Active Site Protonation on Omega Loop and Active Site Dynamics. Journal of Biomolecular Structure and Dynamics 28:3, pages 393-403.
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Linghao Zhong. (2010) Exposure of Hydrophobic Core in Human Prion Protein Pathogenic Mutant H187R. Journal of Biomolecular Structure and Dynamics 28:3, pages 355-361.
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Kumar Poddar, Z.A. Ansari, R.K. Brojen Singh, Ali
A. Moosavi Movahedi & Faizan Ahmad. (2010) Effect of Oligosaccharides and their Monosaccharide Mixtures on the Stability of Proteins: A Scaled Particle Study. Journal of Biomolecular Structure and Dynamics 28:3, pages 331-341.
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Zhiwei Yang, Nan Wu, Yujie Fu, Gang Yang, Wei Wang, Yuangang Zu & Thomas Efferth. (2010) Anti-Infectious Bronchitis Virus (IBV) Activity of 1,8-cineole: Effect on Nucleocapsid (N) Protein. Journal of Biomolecular Structure and Dynamics 28:3, pages 323-330.
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Sashikanth Banappagari, Sharon Ronald & D.
Seetharama Satyanarayanajois. (2010) A Conformationally Constrained Peptidomimetic Binds to the Extracellular Region of HER2 Protein. Journal of Biomolecular Structure and Dynamics 28:3, pages 289-308.
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Rasoul Nasiri, Homayoon Bahrami, Mansour Zahedi, Ali
Akbar Moosavi-Movahedi & Naghmeh Sattarahmady. (2010) A Theoretical Elucidation of Glucose Interaction with HSA's Domains. Journal of Biomolecular Structure and Dynamics 28:2, pages 211-226.
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Wei Yu, Hsin-Yi Chen, Fuu-Jen Tsai & Calvin
Yu-Chian Chen. (2010) A Novel Strategy for Designing the Selective PPAR Agonist by the “Sum of Activity” Model. Journal of Biomolecular Structure and Dynamics 28:2, pages 187-200.
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JaysonF. Varughese, JosephM. Chalovich & Yumin Lit. (2010) Molecular Dynamics Studies on Troponin (Tnl-TnT-TnC) Complexes: Insight into the Regulation of Muscle Contraction. Journal of Biomolecular Structure and Dynamics 28:2, pages 159-173.
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Yan Tao, Zi-He Rao & Shu-Qun Liu. (2010) Insight Derived from Molecular Dynamics Simulation into Substrate-Induced Changes in Protein Motions of Proteinase K. Journal of Biomolecular Structure and Dynamics 28:2, pages 143-157.
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Ye Yuan, MichaelH. Knaggs, LeslieB. Poole, JacquelynS. Fetrow & FreddieR. Salsbury$suffix/text()$suffix/text(). (2010) Conformational and Oligomeric Effects on the Cysteine pKa of Tryparedoxin Peroxidase. Journal of Biomolecular Structure and Dynamics 28:1, pages 51-70.
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Yu-Chian Chen. (2010) Structure-Based and Ligand-Based Drug Design for HER 2 Receptor. Journal of Biomolecular Structure and Dynamics 28:1, pages 23-37.
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Hridoy R. Bairagya, Alvea Tasneem, Gyan Prakash Rai & Saima Reyaz. (2020) Structural and Dynamical Impact of Water Molecules at Substrate- or Product-Binding Sites in Human GMPR Enzyme: A Study by Molecular Dynamics Simulations. The Journal of Physical Chemistry B 125:5, pages 1351-1362.
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Bornali Chakrabarti, Hridoy R Bairagya, Bishnu P Mukhopadhyay & K. Sekar. (2017) New biochemical insight of conserved water molecules at catalytic and structural Zn2+ ions in human matrix metalloproteinase-I: a study by MD-simulation. Journal of Molecular Modeling 23:2.
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Lei Zhang, Yantao Han, Qixiao Jiang, Chunbo Wang, Xuehong Chen, Xiaoguang Li, Fuming Xu, Yuqi Jiang, Qiang Wang & Wenfang Xu. (2015) Trend of Histone Deacetylase Inhibitors in Cancer Therapy: Isoform Selectivity or Multitargeted Strategy. Medicinal Research Reviews 35:1, pages 63-84.
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Tapas K. Nandi, Hridoy R. Bairagya, Bishnu P. Mukhopadhyay, Payel Mallik, Dipankar Sukul & Asim K. Bera. (2011) Conserved water-mediated H-bonding dynamics of catalytic His159 and Asp158: insight into a possible acid–base coupled mechanism in plant thiol protease. Journal of Molecular Modeling 18:6, pages 2633-2644.
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Teodorico C. Ramalho & Elaine F.F. da Cunha. (2011) Thermodynamic Framework of the Interaction between Protein and Solvent Drives Protein Folding. Journal of Biomolecular Structure and Dynamics 28:4, pages 645-646.
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Hridoy R. Bairagya, Bishnu P. Mukhopadhyay & Asim K. Bera. (2011) Conserved water mediated recognition and the dynamics of active site Cys 331 and Tyr 411 in hydrated structure of human IMPDH-II. Journal of Molecular Recognition 24:1, pages 35-44.
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Chien-Yu Chen & Calvin Yu-Chian Chen. (2010) Insights into designing the dual-targeted HER2/HSP90 inhibitors. Journal of Molecular Graphics and Modelling 29:1, pages 21-31.
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