Works matching DE "MOLECULAR dynamics"

Results: 5000

Virtual screening and molecular dynamics simulation study of approved drugs as a binder to the linoleic acid binding site on spike protein of SARS-CoV-2 and double mutant (E484Q and L452R).

Published in:

Indian Journal of Pharmacology, 2022, v. 54, n. 6, p. 431, doi. 10.4103/ijp.ijp_111_22

By:

Prajapat, Manisha;
Sarma, Phulen;
Shekhar, Nishant;
Chauhan, Arushi;
Kaur, Gurjeet;
Bhattacharyya, Anusuya;
Avti, Pramod;
Choudhary, Gajendra;
Bansal, Seema;
Sharma, Saurabh;
Kaur, Hardeep;
Kumar, Subodh;
Mann, Harvinder;
Raja, Anupam;
Singh, Ashutosh;
Singh, Rahul;
Sharma, Amit;
Prakash, Ajay;
Medhi, Bikash

Publication type:

Article

Positive list of antibiotics and food products: Current perspective in India and across the globe.

Published in:

Indian Journal of Pharmacology, 2019, v. 51, n. 4, p. 231, doi. 10.4103/ijp.IJP_548_19

By:

Mahalmani, Vidya;
Sarma, Phulen;
Prakash, Ajay;
Medhi, Bikash

Publication type:

Article

In silico analysis of potential inhibitors of Ca2+ activated K+ channel blocker, Charybdotoxin-C from Leiurus quinquestriatus hebraeus through molecular docking and dynamics studies.

Published in:

Indian Journal of Pharmacology, 2015, v. 47, n. 3, p. 280, doi. 10.4103/0253-7613.157123

By:

Baran Kumar, R.;
Shanmuga Priya, B.;
Xavier Suresh, M.

Publication type:

Article

Dihydrostreptomycin Directly Binds to, Modulates, and Passes through the MscL Channel Pore.

Published in:

PLoS Biology, 2016, v. 14, n. 6, p. 1, doi. 10.1371/journal.pbio.1002473

By:

Wray, Robin;
Iscla, Irene;
Gao, Ya;
Li, Hua;
Wang, Junmei;
Blount, Paul

Publication type:

Article

A High Precision Survey of the Molecular Dynamics of Mammalian Clathrin-Mediated Endocytosis.

Published in:

PLoS Biology, 2011, v. 9, n. 3, p. 1, doi. 10.1371/journal.pbio.1000604

By:

Taylor, Marcus J.;
Perrais, David;
Merrifield, Christien J.

Publication type:

Article

Crystal Structure of a Yeast Aquaporin at 1.15 Å Reveals a Novel Gating Mechanism.

Published in:

2009

By:

Fischer, Gerhard;
Kosinska-Eriksson, Urszula;
Aponte-Santamaría, Camilo;
Palmgren, Madelene;
Geijer, Cecilia;
Hedfalk, Kristina;
Hohmann, Stefan;
de Groot, Bert L.;
Neutze, Richard;
Lindkvist-Petersson, Karin

Publication type:

Bibliography

The Influence of Catalysis on Mad2 Activation Dynamics.

Published in:

PLoS Biology, 2009, v. 7, n. 1, p. e1000010, doi. 10.1371/journal.pbio.1000010

By:

Simonetta, Marco;
Manzoni, Romilde;
Mosca, Roberto;
Mapelli, Marina;
Massimiliano, Lucia;
Vink, Martin;
Novak, Bela;
Musacchio, Andrea;
Ciliberto, Andrea

Publication type:

Article

Recognizing Student Misconceptions through Ed's Tools and the Biology Concept Inventory.

Published in:

PLoS Biology, 2008, v. 6, n. 1, p. e3, doi. 10.1371/journal.pbio.0060003

By:

Klymkowsky, Michael W;
Garvin-Doxas, Kathy

Publication type:

Article

Modification of a Hydrophobic Layer by a Point Mutation in Syntaxin 1A Regulates the Rate of Synaptic Vesicle Fusion.

Published in:

PLoS Biology, 2007, v. 5, n. 4, p. 0800, doi. 10.1371/journal.pbio.0050072

By:

Lagow, Robert D.;
Hong Bao;
Cohen, Evan N.;
Daniels, Richard W.;
Zuzek, Aleksej;
Williams, Wade H.;
Macleod, Gregory T.;
Sutton, R. Bryan;
Bing Zhang

Publication type:

Article

Evolution, Interactions, and Biological Networks.

Published in:

PLoS Biology, 2007, v. 5, n. 1, p. 10, doi. 10.1371/journal.pbio.0050011

By:

Weitz, Joshua S.;
Benfey, Philip N.;
Wingreen, Ned S.

Publication type:

Article

Local Sharing as a Predominant Determinant of Synaptic Matrix Molecular Dynamics.

Published in:

PLoS Biology, 2006, v. 4, n. 9, p. 1572, doi. 10.1371/journal.pbio.0040271

By:

Tsuriel, Shlomo;
Geva, Ran;
Zamorano, Pedro;
Dresbach, Thomas;
Tobias Boeckers;
Eckart D. Gundelfinger;
Craig C. Garner;
Noam E. Ziv

Publication type:

Article

Nanomechanics of Single-Walled Carbon Nanotubes as Composite Reinforcement.

Published in:

Polymer Engineering & Science, 2006, v. 46, n. 8, p. 1051, doi. 10.1002/pen.20553

By:

Jia-Run Xiao;
Gillespie Jr., John W.

Publication type:

Article

Blends, Hydrogen Bonds, and Orientation: Understanding the Role of Interactions.

Published in:

Polymer Engineering & Science, 2004, v. 44, n. 2, p. 241, doi. 10.1002/pen.20023

By:

Brisson, Josée

Publication type:

Article

Applications of molecular dynamics to the study of thermal degradation in aromatic polymers. I...

Published in:

Polymer Engineering & Science, 1997, v. 37, n. 9, p. 1496, doi. 10.1002/pen.11798

By:

Nyden, Marc R.;
Coley, Terry R.

Publication type:

Article

Analysis of superhydrophobic material performance based on molecular dynamics simulations.

Published in:

Surface Engineering, 2016, v. 32, n. 2, p. 147, doi. 10.1179/1743294415Y.0000000110

By:

Yan, J.;
Liu, G.;
Wang, T.;
Zhao, J.;
Ding, Y.;
Chen, N.

Publication type:

Article

On the classical vibrational coherence of carbonyl groups in the selectivity filter backbone of the KcsA ion channel.

Published in:

Journal of Integrative Neuroscience, 2015, v. 14, n. 2, p. 195, doi. 10.1142/S0219635215500132

By:

Salari, V.;
Sajadi, M.;
Bassereh, H.;
Rezania, V.;
Alaei, M.;
Tuszynski, J. A.

Publication type:

Article

A quantum-mechanical description of ion motion within the confining potentials of voltage-gated ion channels.

Published in:

Journal of Integrative Neuroscience, 2012, v. 11, n. 2, p. 123, doi. 10.1142/S0219635212500094

By:

Summhammer, Johann;
Salari, Vahid;
Bernroider, Gustav

Publication type:

Article

DDINet: Drug–drug interaction prediction network based on multi-molecular fingerprint features and multi-head attention centered weighted autoencoder.

Published in:

Journal of Bioinformatics & Computational Biology, 2025, v. 23, n. 1, p. 1, doi. 10.1142/S0219720025500039

By:

Soni Sharmila, K.;
Revathi S., Thanga;
Sree, Pokkuluri Kiran

Publication type:

Article

Author index Volume 22 (2024).

Published in:: Journal of Bioinformatics & Computational Biology, 2024, v. 22, n. 6, p. 1, doi. 10.1142/S0219720024990014
Publication type:: Article

Molecular dynamics simulations of ribosome-binding sites in theophylline-responsive riboswitch associated with improving the gene expression regulation in chloroplasts.

Published in:

Journal of Bioinformatics & Computational Biology, 2024, v. 22, n. 5, p. 1, doi. 10.1142/S0219720024500239

By:

Berahmand, Rahim;
Emadpour, Masoumeh;
Javaran, Mokhtar Jalali;
Haji-Allahverdipoor, Kaveh;
Akbarabadi, Ali

Publication type:

Article

Construction of a multi-tissue compound–target interaction network of Qingfei Paidu decoction in COVID-19 treatment based on deep learning and transcriptomic analysis.

Published in:

Journal of Bioinformatics & Computational Biology, 2024, v. 22, n. 4, p. 1, doi. 10.1142/S0219720024500161

By:

Li, Xia;
Zhao, Xuetong;
Yu, Xinjian;
Zhao, Jianping;
Fang, Xiangdong

Publication type:

Article

ThermalProGAN: A sequence-based thermally stable protein generator trained using unpaired data.

Published in:

Journal of Bioinformatics & Computational Biology, 2023, v. 21, n. 1, p. 1, doi. 10.1142/S0219720023500087

By:

Huang, Hui-Ling;
Weng, Chong-Heng;
Nordling, Torbjörn E. M.;
Liou, Yi-Fan

Publication type:

Article

Author Index Volume 18 (2020).

Published in:: Journal of Bioinformatics & Computational Biology, 2020, v. 18, n. 6, p. N.PAG, doi. 10.1142/S0219720020990012
Publication type:: Article

EasyAmber: A comprehensive toolbox to automate the molecular dynamics simulation of proteins.

Published in:

Journal of Bioinformatics & Computational Biology, 2020, v. 18, n. 6, p. N.PAG, doi. 10.1142/S0219720020400119

By:

Suplatov, Dmitry;
Sharapova, Yana;
Švedas, Vytas

Publication type:

Article

From molecular energy landscapes to equilibrium dynamics via landscape analysis and markov state models.

Published in:

Journal of Bioinformatics & Computational Biology, 2019, v. 17, n. 6, p. N.PAG, doi. 10.1142/S0219720019400146

By:

Kabir, Kazi Lutful;
Akhter, Nasrin;
Shehu, Amarda

Publication type:

Article

Effect of mutant NMDA receptors on the oscillations in a model of hippocampus.

Published in:

Journal of Bioinformatics & Computational Biology, 2019, v. 17, n. 1, p. N.PAG, doi. 10.1142/S0219720019400031

By:

Batova, Anna Sergeevna;
Bugay, Aleksandr Nikolaevich;
Dushanov, Ermuhammad Berdimurodovich

Publication type:

Article

Investigation of non-hydroxamate scaffolds against HDAC6 inhibition: A pharmacophore modeling, molecular docking, and molecular dynamics simulation approach.

Published in:

Journal of Bioinformatics & Computational Biology, 2018, v. 16, n. 3, p. N.PAG, doi. 10.1142/S0219720018400152

By:

Zeb, Amir;
Park, Chanin;
Son, Minky;
Rampogu, Shailima;
Alam, Syed Ibrar;
Park, Seok Ju;
Lee, Keun Woo

Publication type:

Article

Potential HIV-1 fusion inhibitors mimicking gp41-specific broadly neutralizing antibody 10E8: In silico discovery and prediction of antiviral potency.

Published in:

Journal of Bioinformatics & Computational Biology, 2018, v. 16, n. 2, p. -1, doi. 10.1142/S0219720018400073

By:

Andrianov, Alexander M.;
Kashyn, Ivan A.;
Tuzikov, Alexander V.

Publication type:

Article

Molecular docking and molecular dynamics simulations of fumarate hydratase and its mutant H235N complexed with pyromellitic acid and citrate.

Published in:

Journal of Bioinformatics & Computational Biology, 2017, v. 15, n. 6, p. -1, doi. 10.1142/S0219720017500263

By:

Subasri, S.;
Chaudhary, Santosh Kumar;
Sekar, K.;
Kesherwani, Manish;
Velmurugan, D.

Publication type:

Article

Computational analysis and enzyme assay of inhibitor response to disease single nucleotide polymorphisms (SNPs) in lipoprotein lipase.

Published in:

Journal of Bioinformatics & Computational Biology, 2016, v. 14, n. 5, p. -1, doi. 10.1142/S0219720016500281

By:

He, Deyong;
Huang, Ling;
Xu, Yaping;
Pan, Xiaoliang;
Liu, Lijun

Publication type:

Article

Interaction sorting method for molecular dynamics on multi-core SIMD CPU architecture.

Published in:

Journal of Bioinformatics & Computational Biology, 2015, v. 13, n. 1, p. -1, doi. 10.1142/S0219720015400041

By:

Matvienko, Sergey;
Alemasov, Nikolay;
Fomin, Eduard

Publication type:

Article

Implementing a modeling software for animated protein-complex interactions using a physics simulation library.

Published in:

Journal of Bioinformatics & Computational Biology, 2014, v. 12, n. 6, p. -1, doi. 10.1142/S0219720014420037

By:

Ueno, Yutaka;
Ito, Shuntaro;
Konagaya, Akihiko

Publication type:

Article

Role of arginine 209 in the conformational transition of the protein kinase A regulatory subunit RIα A-domain.

Published in:

Journal of Bioinformatics & Computational Biology, 2014, v. 12, n. 2, p. -1, doi. 10.1142/S0219720014410054

By:

Rogacheva, Olga N.;
Stefanov, Vasiliy E.;
Shchegolev, Boris F.;
Vershinina, Elena A.;
Savvateeva-Popova, Elena V.

Publication type:

Article

FOUNDATIONS FOR MODELING THE DYNAMICS OF GENE REGULATORY NETWORKS: A MULTILEVEL-PERSPECTIVE REVIEW.

Published in:

Journal of Bioinformatics & Computational Biology, 2014, v. 12, n. 1, p. -1, doi. 10.1142/S0219720013300037

By:

SANCHEZ-OSORIO, ISMAEL;
RAMOS, FERNANDO;
MAYORGA, PEDRO;
DANTAN, EDGAR

Publication type:

Article

EVOLVING CONNECTIVITY BETWEEN GENETIC OSCILLATORS AND SWITCHES USING EVOLUTIONARY ALGORITHMS.

Published in:

Journal of Bioinformatics & Computational Biology, 2013, v. 11, n. 3, p. 1, doi. 10.1142/S0219720013410011

By:

THOMAS, SPENCER ANGUS;
JIN, YAOCHU

Publication type:

Article

CONFORMATIONAL DYNAMICS OF HIV-1 PROTEASE: A COMPARATIVE MOLECULAR DYNAMICS SIMULATION STUDY WITH MULTIPLE AMBER FORCE FIELDS.

Published in:

Journal of Bioinformatics & Computational Biology, 2012, v. 10, n. 6, p. -1, doi. 10.1142/S0219720012500187

By:

MEHER, BISWA RANJAN;
SATISH KUMAR, MATTAPARTHI VENKATA;
SHARMA, SMRITI;
BANDYOPADHYAY, PRADIPTA

Publication type:

Article

A SHORT INTRODUCTION TO SOME RECENT PROGRESS IN PHYLOGENETIC NETWORK RECONSTRUCTION, GENOME MAPPING, GENE EXPRESSION ANALYSIS, MOLECULAR DYNAMIC SIMULATION, AND OTHER PROBLEMS IN BIOINFORMATICS.

Published in:

Journal of Bioinformatics & Computational Biology, 2012, v. 10, n. 4, p. 1203002-1, doi. 10.1142/S0219720012030023

By:

WONG, LIMSOON

Publication type:

Article

A CHEMICAL GROUP GRAPH REPRESENTATION FOR EFFICIENT HIGH-THROUGHPUT ANALYSIS OF ATOMISTIC PROTEIN SIMULATIONS.

Published in:

Journal of Bioinformatics & Computational Biology, 2012, v. 10, n. 4, p. 1250008-1, doi. 10.1142/S0219720012500084

By:

BENSON, NOAH C.;
DAGGETT, VALERIE

Publication type:

Article

MODELING OF THREE DIMENSIONAL STRUCTURE OF HUMAN ALPHA-FETOPROTEIN COMPLEXED WITH DIETHYLSTILBESTROL:: DOCKING AND MOLECULAR DYNAMICS SIMULATION STUDY.

Published in:

Journal of Bioinformatics & Computational Biology, 2012, v. 10, n. 2, p. 1241012-1, doi. 10.1142/S0219720012410120

By:

TERENTIEV, ALEXANDER A.;
MOLDOGAZIEVA, NURBUBU T.;
LEVTSOVA, OLGA V.;
MAXIMENKO, DMITRY M.;
BOROZDENKO, DENIS A.;
SHAITAN, KONSTANTIN V.

Publication type:

Article

DISCOVERY AND EVALUATION OF POTENTIAL SONIC HEDGEHOG SIGNALING PATHWAY INHIBITORS USING PHARMACOPHORE MODELING AND MOLECULAR DYNAMICS SIMULATIONS.

Published in:

Journal of Bioinformatics & Computational Biology, 2011, v. 9, p. 15, doi. 10.1142/S0219720011005732

By:

HWANG, SWAN;
THANGAPANDIAN, SUNDARAPANDIAN;
LEE, YUNO;
SAKKIAH, SUGUNADEVI;
JOHN, SHALINI;
LEE, KEUN WOO

Publication type:

Article

FLEXIBILITY AND MOBILITY IN MESOPHILIC AND THERMOPHILIC HOMOLOGOUS PROTEINS FROM MOLECULAR DYNAMICS AND FOLDUNFOLD METHOD.

Published in:

Journal of Bioinformatics & Computational Biology, 2010, v. 8, n. 3, p. 377, doi. 10.1142/S0219720010004690

By:

MAMONOVA, TATYANA B.;
GLYAKINA, ANNA V.;
KURNIKOVA, MARIA G.;
GALZITSKAYA, OXANA V.

Publication type:

Article

Adsorption Effects of Isoniazid Drug Over Carbon Nanotube (C56H16) and Ab‐Initio Molecular Dynamics Simulation (ADMP) – A Computational Quantum Chemical Approach.

Published in:

Macromolecular Symposia, 2024, v. 413, n. 5, p. 1, doi. 10.1002/masy.202400047

By:

Pandey, Anoop Kumar;
Singh, Vijay;
Mishra, Gaurav;
Dwivedi, Apoorva

Publication type:

Article

Molecular Dynamics Simulation Insights into Hydrogen Bonding‐Mediated Conformational Changes Topoisomerase‐IB.

Published in:

Macromolecular Symposia, 2024, v. 413, n. 5, p. 1, doi. 10.1002/masy.202400036

By:

Dhar, Murali;
Tiwari, Rakesh Kumar

Publication type:

Article

Differential DNA Recognitions of Benzimidazole Based Astemizole, Omeprazole, Lansoprazole, and Thiabendazole.

Published in:

Macromolecular Symposia, 2024, v. 413, n. 1, p. 1, doi. 10.1002/masy.202300137

By:

Sur, Souvik

Publication type:

Article

Phase and Order Behavior of Charged Asymmetric Diblock‐Copolymer Melts in Bulk.

Published in:

Macromolecular Symposia, 2024, v. 413, n. 1, p. 1, doi. 10.1002/masy.202300028

By:

Moirangthem, Premjit M.;
Shagolsem, Lenin S.

Publication type:

Article

Different Conformational Properties and Frequencies of Periodic Motion in the β‐ and γ‐Cyclodextrin.

Published in:

Macromolecular Symposia, 2023, v. 411, n. 1, p. 1, doi. 10.1002/masy.202200160

By:

Raffaini, Giuseppina;
Ganazzoli, Fabio

Publication type:

Article

Benzoate‐Based Inhibitor Film to Prevent Chloride‐Induced Corrosion: Simulation Study of Efficiency of Dry or Hydrated Film.

Published in:

Macromolecular Symposia, 2023, v. 411, n. 1, p. 1, doi. 10.1002/masy.202200165

By:

Raffaini, Giuseppina;
Bolzoni, Fabio;
Ormellese, Marco

Publication type:

Article

Migration of Electroconductive Carbon Nanoparticles in Polymer Composites Melts.

Published in:

Macromolecular Symposia, 2022, v. 405, n. 1, p. 1, doi. 10.1002/masy.202100236

By:

Lebedev, Oleg V.;
Goncharuk, Galina P.;
Yablokov, Mikhail Yu.;
Kurkin, Tikhon S.;
Piskarev, Mikhail S.;
Golubev, Evgeny K.;
Ozerin, Alexander N.

Publication type:

Article

Vibrational Properties of (8,8) and (10,10) SWCNTs before and after Albumin Fragment Adsorption: A Molecular Dynamics Study.

Published in:: Macromolecular Symposia, 2022, v. 404, n. 1, p. 1, doi. 10.1002/masy.202100391
Publication type:: Article

Inclusion Complexes Between β‐cyclodextrin and the Anticancer Drug 5‐Fluorouracil for its Solubilization: a Molecular Dynamics Study at Different Stoichiometries.

Published in:

Macromolecular Symposia, 2022, v. 404, n. 1, p. 1, doi. 10.1002/masy.202100305

By:

Raffaini, Giuseppina;
Elli, Stefano;
Ganazzoli, Fabio;
Catauro, Michelina

Publication type:

Article