pypi: gmx | Projects | Ecosyste.ms: Papers

10.3389/fmolb.2019.00025

Anncolvar: Approximation of Complex Collective Variables by Artificial Neural Networks for Analysis and Biasing of Molecular Simulations
Cited by: 22
Author(s): Dalibor Trapl, Izabela Horvacanin, Václav Mareška, Furkan Özçelik, Gözde Ünal, Vojtěch Spiwok
Software Mentions: 11
Published: over 5 years ago

10.1371/journal.pcbi.1008807

Membrane-binding mechanism of the EEA1 FYVE domain revealed by multi-scale molecular dynamics simulations
Cited by: 7
Author(s): Andreas Haahr Larsen, Lilya Tata, Laura John, Mark S. P. Sansom
Software Mentions: 6
Published: about 3 years ago

10.1038/s41598-019-55777-5

Clustering of atomic displacement parameters in bovine trypsin reveals a distributed lattice of atoms with shared chemical properties
Cited by: 7
Author(s): Viktor Ahlberg Gagnér, Ida Lundholm, María-José García-Bonete, Helena Rodilla, Ran Friedman, Vitali Zhaunerchyk, Gleb Bourenkov, Thomas R. Schneider, Jan Stake, Gergely Katona
Software Mentions: 6
Published: about 5 years ago

10.3390/molecules26185574

Exploring EZH2-Proteasome Dual-Targeting Drug Discovery through a Computational Strategy to Fight Multiple Myeloma
Cited by: 2
Author(s): Filipe G A Estrada, Silvia Miccoli, Natália Aniceto, Alfonso T. García-Sosa, Rita C. Guedes
Software Mentions: 6
Published: over 3 years ago

10.3389/fcell.2020.601145

Spontaneous Membrane Nanodomain Formation in the Absence or Presence of the Neurotransmitter Serotonin
Cited by: 11
Author(s): Anna Bochicchio, Astrid F. Brandner, Oskar Engberg, Daniel Huster, Rainer A. Böckmann
Software Mentions: 5
Published: about 4 years ago

10.1107/S2052252518000519

Internal protein motions in molecular-dynamics simulations of Bragg and diffuse X-ray scattering
Cited by: 23
Author(s): Michael E. Wall
Software Mentions: 5
Published: almost 7 years ago

10.1126/sciadv.abh2217

Identification and assessment of cardiolipin interactions with E. coli inner membrane proteins
Cited by: 33
Author(s): Robin A. Corey, Wanling Song, Anna L. Duncan, T. Bertie Ansell, Mark S. P. Sansom, Phillip J. Stansfeld
Software Mentions: 4
Published: over 3 years ago

10.3390/molecules25184299

Impact of Cholesterol on the Stability of Monomeric and Dimeric Forms of the Translocator Protein TSPO: A Molecular Simulation Study
Cited by: 5
Author(s): Zeineb Si Chaib, Alessandro Marchetto, Klevia Dishnica, Paolo Carloni, Alejandro Giorgetti, Giulia Rossetti
Software Mentions: 4
Published: over 4 years ago

10.3389/fmolb.2020.00027

Conformational Changes Induced by S34Y and R98C Variants in the Death Domain of Myd88
Cited by: 2
Author(s): Vijayakumar Gosu, Kyeong-Hye Won, Jae-Don Oh, Donghyun Shin
Software Mentions: 4
Published: over 4 years ago

10.1063/1.5132692

Liquid-like and rigid-body motions in molecular-dynamics simulations of a crystalline protein
Cited by: 14
Author(s): David C. Wych, James S. Fraser, David L. Mobley, Michael E. Wall
Software Mentions: 4
Published: about 5 years ago

10.1021/acs.jctc.0c01308

Reconstruction of ARNT PAS-B Unfolding Pathways by Steered Molecular Dynamics and Artificial Neural Networks
Cited by: 12
Author(s): Stefano Motta, Alessandro Pandini, Arianna Fornili, Laura Bonati
Software Mentions: 3
Published: over 3 years ago

10.3390/molecules25092247

Conserved Dynamic Mechanism of Allosteric Response to L-arg in Divergent Bacterial Arginine Repressors
Cited by: 2
Author(s): Saurabh Pandey, Milan Melicherčík, David Rooney, Rüdiger Ettrich, Jannette Carey
Software Mentions: 3
Published: over 4 years ago

10.3390/ijms20225574

Establishing Computational Approaches Towards Identifying Malarial Allosteric Modulators: A Case Study of Plasmodium falciparum Hsp70s
Cited by: 10
Author(s): Arnold Amusengeri, Lindy Astl, Kevin A. Lobb, Gennady M. Verkhivker, Özlem Tastan Bishop
Software Mentions: 3
Published: about 5 years ago

10.3389/fpls.2019.00070

Mechanism Underlying Heat Stability of the Rice Endosperm Cytosolic ADP-Glucose Pyrophosphorylase
Cited by: 6
Author(s): Seon‐Kap Hwang, S. S. Singh, Jitendra Maharana, S. N. Kalita, Aytuğ Tuncel, Tanmayee Rath, Debashis Panda, Mahendra Kumar Modi, Thomas W. Okita
Software Mentions: 3
Published: almost 6 years ago

10.3390/ijms20040884

Identification and Evaluation of Inhibitors of Lipase from Malassezia restricta using Virtual High-Throughput Screening and Molecular Dynamics Studies
Cited by: 67
Author(s): Shahid Ali, Faez Iqbal Khan, Taj Mohammad, Dongming Lan, Md. Imtaiyaz Hassan, Yonghua Wang
Software Mentions: 3
Published: almost 6 years ago

10.1016/j.jsb.2021.107729

Structure of the cytoplasmic domain of SctV (SsaV) from the Salmonella SPI-2 injectisome and implications for a pH sensing mechanism
Cited by: 12
Author(s): Teige R. S. Matthews-Palmer, Nayim Gonzalez-Rodriguez, Thomas Calcraft, Signe Lagercrantz, Tobias Zachs, Xiu-Jun Yu, Grzegorz Grabe, David W. Holden, Andrea Nans, Peter B. Rosenthal, Sarah L. Rouse, Morgan Beeby
Software Mentions: 3
Published: over 3 years ago

10.1038/s41598-020-64088-z

Rational identification and characterisation of peptide ligands for targeting polysialic acid
Cited by: 1
Author(s): Divya G. Shastry, Flaviyan Jerome Irudayanathan, Arthur Robin Williams, Mattheos Koffas, Robert J. Linhardt, Shikha Nangia, Pankaj Karande
Software Mentions: 3
Published: over 4 years ago

10.1038/s41598-019-48849-z

Modelling of substrate access and substrate binding to cephalosporin acylases
Cited by: 6
Author(s): Virgilio F. Ferrario, Mona Fischer, Yushan Zhu, Jürgen Pleiss
Software Mentions: 3
Published: over 5 years ago

10.1038/s41598-019-40892-0

Steered molecular dynamic simulations of conformational lock of Cu, Zn-superoxide dismutase
Cited by: 11
Author(s): Bao-Lin Xiao, Yan-Na Ning, Nan-Nan Niu, Di Li, Ali Akbar Moosavi-Movahedi, Nader Sheibani, Jun Hong
Software Mentions: 3
Published: almost 6 years ago

10.3390/molecules25174016

Targeting the Initiator Protease of the Classical Pathway of Complement Using Fragment-Based Drug Discovery
Cited by: 8
Author(s): Blake R. Rushing, Denise L Rohlik, Sourav Roy, D. Andrew Skaff, Brandon L. Garcia
Software Mentions: 3
Published: over 4 years ago

10.1186/s12859-020-03575-6

Proteus: An algorithm for proposing stabilizing mutation pairs based on interactions observed in known protein 3D structures
Cited by: 5
Author(s): José Renato M. S. Barroso, Diego Mariano, Sandro Renato Dias, Rafael E. O. Rocha, Lucianna Helene Santos, R.A.P. Nagem, Raquel Cardoso de Melo‐Minardi
Software Mentions: 3
Published: over 4 years ago

10.1371/journal.pone.0221331

Identification of lead molecules against potential drug target protein MAPK4 from L. donovani: An in-silico approach using docking, molecular dynamics and binding free energy calculation
Cited by: 35
Author(s): Shweta Raj, Santanu Sasidharan, Vikash Kumar Dubey, Prakash Saudagar
Software Mentions: 3
Published: over 5 years ago

10.3390/biom10091286

Comparative Analysis of Bacteriophytochrome Agp2 and Its Engineered Photoactivatable NIR Fluorescent Proteins PAiRFP1 and PAiRFP2
Cited by: 13
Author(s): Faez Iqbal Khan, Fakhrul Hassan, Razique Anwer, Jia‐Xun Feng, Dakun Lai
Software Mentions: 3
Published: over 4 years ago

10.1038/s41598-021-83374-y

Effect of palmitoylation on the dimer formation of the human dopamine transporter
Cited by: 6
Author(s): Talia Zeppelin, Kasper B. Pedersen, Nils Berglund, Xavier Periole, Birgit Schiøtt
Software Mentions: 3
Published: almost 4 years ago

10.1038/s41598-019-40323-0

Molecular cloning, GTP recognition mechanism and tissue-specific expression profiling of myxovirus resistance (Mx) protein in Labeo rohita (Hamilton) after Poly I:C induction
Cited by: 14
Author(s): Basanta Kumar Das, Pragyan Roy, Ajaya Kumar Rout, Deepak Ranjan Sahoo, Soumya Prasad Panda, Sushmita Pattanaik, Budheswar Dehury, Bijay Kumar Behera, Sudhansu Sekhar Mishra
Software Mentions: 3
Published: almost 6 years ago

10.3390/molecules25040904

Understanding the Pyrimethamine Drug Resistance Mechanism via Combined Molecular Dynamics and Dynamic Residue Network Analysis
Cited by: 26
Author(s): Arnold Amusengeri, Rolland Bantar Tata, Özlem Tastan Bishop
Software Mentions: 3
Published: almost 5 years ago

10.1038/s41598-019-39984-8

Insights into the dynamic nature of the dsRNA-bound TLR3 complex
Cited by: 27
Author(s): Vijayakumar Gosu, Seung‐Woo Son, Donghyun Shin, Ki Duk Song
Software Mentions: 3
Published: almost 6 years ago

10.1038/s42003-020-01401-6

Structure-based dynamic analysis of the glycine cleavage system suggests key residues for control of a key reaction step
Cited by: 13
Author(s): Han Zhang, Yuchen Li, Jinglei Nie, Jie Ren, An‐Ping Zeng
Software Mentions: 3
Published: about 4 years ago

10.1016/j.dib.2020.106350

Data analysis of molecular dynamics simulation trajectories of β-sitosterol, sonidegib and cholesterol in smoothened protein with the CHARMM36 force field
Cited by: 7
Author(s): Che Omar
Software Mentions: 3
Published: about 4 years ago

10.1038/s41598-018-32040-x

The potential HLA Class I-restricted epitopes derived from LeIF and TSA of Leishmania donovani evoke anti-leishmania CD8+ T lymphocyte response
Cited by: 20
Author(s): Manas Ranjan Dikhit, Sushmita Das, Vijaya Mahantesh, Akhilesh Kumar, Ashish Kumar Singh, Budheswar Dehury, Ajaya Kumar Rout, Vahab Ali, Ganesh Chandra Sahoo, Roshan Kamal Topno, Krishna Pandey, Vidya Nand Rabi Das, Sanjiva Bimal, Pradeep Das
Software Mentions: 3
Published: over 6 years ago

10.3389/fcimb.2021.730288

Identification of Natural Inhibitors Against SARS-CoV-2 Drugable Targets Using Molecular Docking, Molecular Dynamics Simulation, and MM-PBSA Approach
Cited by: 35
Author(s): Prem Prakash Kushwaha, Atul Kumar Singh, Tanya Bansal, Akansha Yadav, Kumari Sunita Prajapati, Mohd Shuaib, Shashank Kumar
Software Mentions: 3
Published: over 3 years ago

10.1371/journal.pone.0223464

Molecular dynamic simulations to investigate the structural impact of known drug resistance mutations on HIV-1C Integrase-Dolutegravir binding
Cited by: 15
Author(s): Rumbidzai Chitongo, Adetayo Emmanuel Obasa, Sello Given Mikasi, Graeme Brendon Jacobs, Ruben Cloete
Software Mentions: 2
Published: over 4 years ago

10.3390/biom11081251

Computational Insights into the Structural Dynamics of MDA5 Variants Associated with Aicardi–Goutières Syndrome and Singleton–Merten Syndrome
Cited by: 12
Author(s): Vijayakumar Gosu, Santanu Sasidharan, Prakash Saudagar, Hak-Kyo Lee, Donghyun Shin
Software Mentions: 2
Published: over 3 years ago

10.3390/molecules26030697

Biochemical Characterization and Structural Insight into Interaction and Conformation Mechanisms of Serratia marcescens Lysine Decarboxylase (SmcadA)
Cited by: 2
Author(s): Tolbert Osire, Zhang Qiao, Taowei Yang, Meijuan Xu, Xian Zhang, Zhiming Rao
Software Mentions: 2
Published: almost 4 years ago

10.3390/molecules24010188

Discorhabdin N, a South African Natural Compound, for Hsp72 and Hsc70 Allosteric Modulation: Combined Study of Molecular Modeling and Dynamic Residue Network Analysis
Cited by: 22
Author(s): Arnold Amusengeri, Özlem Tastan Bishop
Software Mentions: 2
Published: almost 6 years ago

10.3390/molecules25092228

Reducing Ensembles of Protein Tertiary Structures Generated De Novo via Clustering
Cited by: 5
Author(s): Ahmed Bin Zaman, Parastoo Kamranfar, Carlotta Domeniconi, Amarda Shehu
Software Mentions: 2
Published: over 4 years ago

10.3390/ph14070669

New (Iso)quinolinyl-pyridine-2,6-dicarboxamide G-Quadruplex Stabilizers. A Structure-Activity Relationship Study
Cited by: 7
Author(s): Enrico Cadoni, Pedro R. Magalhães, Rita M. Emídio, Eduarda Mendes, Jorge M. B. Vítor, Josué Carvalho, Carla Cruz, Bruno L. Victor, Alexandra Paulo
Software Mentions: 2
Published: over 3 years ago

10.1371/journal.pcbi.1009232

Multi-scale simulations of the T cell receptor reveal its lipid interactions, dynamics and the arrangement of its cytoplasmic region
Cited by: 10
Author(s): Dheeraj Prakaash, Graham P. Cook, Oreste Acuto, Antreas C. Kalli
Software Mentions: 2
Published: over 3 years ago

10.1371/journal.pcbi.1005831

Concerted regulation of npc2 binding to endosomal/lysosomal membranes by bis(monoacylglycero)phosphate and sphingomyelin
Cited by: 26
Author(s): Giray Enkavi, Heikki Mikkolainen, Burçin Güngör, Elina Ikonen, Ilpo Vattulainen
Software Mentions: 2
Published: about 7 years ago

10.1371/journal.pcbi.1006900

Rapid interpretation of small-angle X-ray scattering data
Cited by: 20
Author(s): Marie Weiel, Ines Reinartz, Alexander Schug
Software Mentions: 2
Published: almost 6 years ago

10.1371/journal.pone.0257916

Comparative analysis of the unbinding pathways of antiviral drug Indinavir from HIV and HTLV1 proteases by supervised molecular dynamics simulation
Cited by: 4
Author(s): Farzin Sohraby, Hassan Aryapour
Software Mentions: 2
Published: about 3 years ago

10.1371/journal.pone.0258061

Molecular dynamics and protein frustration analysis of human fused in Sarcoma protein variants in Amyotrophic Lateral Sclerosis type 6: An In Silico approach
Cited by: 3
Author(s): Lizette Bonet, Joana Loureiro, Gabriel Rodrigues Coutinho Pereira, A. N. R. Da Silva, Joelma Freire De Mesquita
Software Mentions: 2
Published: about 3 years ago

10.1371/journal.pone.0209420

Deciphering the ATP-binding mechanism(s) in NLRP-NACHT 3D models using structural bioinformatics approaches
Cited by: 22
Author(s): Jitendra Maharana, Debashis Panda, Sachinandan De
Software Mentions: 2
Published: about 6 years ago

10.1371/journal.pone.0237884

The role of disulfide bonds in a Solanum tuberosum saposin-like protein investigated using molecular dynamics
Cited by: 1
Author(s): John H. Dupuis, Shenlin Wang, Chen Song, Rickey Y. Yada
Software Mentions: 2
Published: over 4 years ago

10.1371/journal.pone.0251910

Unraveling the unbinding pathways of SARS-CoV-2 Papain-like proteinase known inhibitors by Supervised Molecular Dynamics simulation
Cited by: 9
Author(s): Farzin Sohraby, Hassan Aryapour
Software Mentions: 2
Published: over 3 years ago

10.1371/journal.pone.0240653

Potential bioactive glycosylated flavonoids as SARS-CoV-2 main protease inhibitors: A molecular docking and simulation studies
Cited by: 105
Author(s): Sabri Cherrak, Hafida Merzouk, Nassima Mokhtari-Soulimane
Software Mentions: 2
Published: about 4 years ago

10.3390/cancers13153778

Targeting BRF2 in Cancer Using Repurposed Drugs
Cited by: 7
Author(s): Behnam Rashidieh, Maryam Molakarimi, Ammar Mohseni, Simon Manuel Tria, Hein Truong, Sriganesh Srihari, Ryan A. Adams, Jones Ma, Pascal H.G. Duijf, Murugan Kalimutho, Kum Kum Khanna
Software Mentions: 2
Published: over 3 years ago

10.3390/cells9041004

MiR193a Modulation and Podocyte Phenotype
Cited by: 4
Author(s): Alok Jha, Shourav Saha, Kamesh Ayasolla, Himanshu Vashistha, Ashwani Malhotra, Karl Skorecki, Pravin C. Singhal
Software Mentions: 2
Published: over 4 years ago

10.3389/fmolb.2021.631854

Multi-Scale Flexible Fitting of Proteins to Cryo-EM Density Maps at Medium Resolution
Cited by: 13
Author(s): Marta Kulik, Takaharu Mori, Yuji Sugita
Software Mentions: 2
Published: almost 4 years ago

10.3389/fmolb.2019.00041

Structural Analysis and Conformational Dynamics of STN1 Gene Mutations Involved in Coat Plus Syndrome
Cited by: 48
Author(s): Mohd. Amir, Taj Mohammad, Vijay Kumar, Mohamed F. Alajmi, Tabish Rehman, Afzal Hussain, Perwez Alam, Ravins Dohare, Asimul Islam, Faizan Ahmad, Md. Imtaiyaz Hassan
Software Mentions: 2
Published: over 5 years ago

10.1242/jcs.258399

Maintenance of complex I and its supercomplexes by NDUF-11 is essential for mitochondrial structure, function and health
Cited by: 13
Author(s): Amber Knapp-Wilson, Gonçalo C. Pereira, Emma Buzzard, Holly C Ford, A. Richardson, Robin A. Corey, Chris Neal, Paul Verkade, Andrew P. Halestrap, Vicki A. M. Gold, Patricia E. Kuwabara, Ian Collinson
Software Mentions: 2
Published: over 3 years ago

10.1038/s41598-017-17243-y

The orientation and stability of the GPCR-Arrestin complex in a lipid bilayer
Cited by: 10
Author(s): Dali Wang, Hua-Zhong Yu, Xiangdong Liu, Jianqiang Liu, Chen Song
Software Mentions: 2
Published: about 7 years ago

10.1038/s41598-018-20227-1

Communication between the leaflets of asymmetric membranes revealed from coarse-grain molecular dynamics simulations
Cited by: 23
Author(s): Jonathan Shearer, Syma Khalid
Software Mentions: 2
Published: almost 7 years ago

10.1038/s41598-018-29871-z

Insight into the molecular mechanism behind PEG-mediated stabilization of biofluid lipases
Cited by: 13
Author(s): Bianca Pérez, Andrea Coletta, Jannik Nedergaard Pedersen, Steen V. Petersen, Xavier Periole, Richard B. Sessions, Zheng Guo, Adam W. Perriman, Birgit Schiøtt
Software Mentions: 2
Published: over 6 years ago

10.1038/s41598-019-48940-5

Analysis of mutations leading to para-aminosalicylic acid resistance in Mycobacterium tuberculosis
Cited by: 15
Author(s): Bharati Pandey, Sonam Grover, Jagdeep Kaur, Abhinav Grover
Software Mentions: 2
Published: over 5 years ago

10.1038/s41598-020-77040-y

Effect of pH on the influenza fusion peptide properties unveiled by constant-pH molecular dynamics simulations combined with experiment
Cited by: 13
Author(s): Diana Lousa, A. M. P. Pinto, Sara R. R. Campos, António M. Baptista, Ana Salomé Veiga, Miguel A. R. B. Castanho, Cláudio M. Soares
Software Mentions: 2
Published: about 4 years ago

10.1107/S205225252100213X

Structural plasticity of the selectivity filter in a nonselective ion channel
Cited by: 13
Author(s): Raktim N Roy, Kitty Hendriks, Wojciech Kopeć, Saeid Abdolvand, Kevin L. Weiss, Bert L. de Groot, Adam Lange, Han Sun, Leighton Coates
Software Mentions: 2
Published: over 3 years ago

10.1186/s43141-021-00163-w

High-throughput screening of natural compounds and inhibition of a major therapeutic target HsGSK-3β for Alzheimer’s disease using computational approaches
Cited by: 9
Author(s): Rohit Shukla, Tiratha Raj Singh
Software Mentions: 2
Published: over 3 years ago

10.3390/ijms20030596

The Effect of FG-Nup Phosphorylation on NPC Selectivity: A One-Bead-Per-Amino-Acid Molecular Dynamics Study
Cited by: 14
Author(s): Ankur Mishra, Wouter Sipma, Liesbeth M. Veenhoff, E. van der Giessen, Patrick Onck
Software Mentions: 2
Published: almost 6 years ago

10.3390/ijms20071666

A Molecular Dynamics Approach to Explore the Intramolecular Signal Transduction of PPAR-α
Cited by: 17
Author(s): Shaherin Basith, Balachandran Manavalan, Tae Hwan Shin, Gwang Lee
Software Mentions: 2
Published: over 5 years ago

10.3390/ijms21082857

A Computational Probe into the Structure and Dynamics of the Full-Length Toll-Like Receptor 3 in a Phospholipid Bilayer
Cited by: 8
Author(s): Mahesh Chandra Patra, Maria Batool, Muhammad Haseeb, Sangdun Choi
Software Mentions: 2
Published: over 4 years ago

10.3390/ijms21113803

Identification of Selective Novel Hits against Plasmodium falciparum Prolyl tRNA Synthetase Active Site and a Predicted Allosteric Site Using In Silico Approaches
Cited by: 8
Author(s): Dorothy Wavinya Nyamai, Özlem Tastan Bishop
Software Mentions: 2
Published: over 4 years ago

10.3390/ijms22041643

Biochemical and Computational Studies of the Interaction between a Glucosamine Derivative, NAPA, and the IKKα Kinase
Cited by: 3
Author(s): Mariangela Lopreiato, Samuele Di Cristofano, Rossana Cocchiola, Alessia Mariano, Libera Guerrizio, Roberto Scandurra, Luciana Mosca, Domenico Raimondo, Anna Scotto d’Abusco
Software Mentions: 2
Published: almost 4 years ago

10.3390/ijms22157934

Simulations of Promising Indolizidine—α6-β2 Nicotinic Acetylcholine Receptor Complexes
Cited by: 1
Author(s): Francis A. Acquah, Matthew Paramel, Adama Kuta, Syed R. Hussaini, David R. Wallace, Blaine H. M. Mooers
Software Mentions: 2
Published: over 3 years ago

10.1021/acs.jpca.0c10845

Optimal Solution to the Torsional Coefficient Fitting Problem in Force Field Parametrization
Cited by: 4
Author(s): Adrian Kania, Krzysztof Sarapata, Michał Gucwa, Anna Wójcik-Augustyn
Software Mentions: 2
Published: over 3 years ago

10.1038/s42003-020-01260-1

Polyol and sugar osmolytes can shorten protein hydrogen bonds to modulate function
Cited by: 18
Author(s): Jingwen Li, Jingfei Chen, Liaoyuan An, Xiao Yuan, Lishan Yao
Software Mentions: 1
Published: about 4 years ago

10.15698/cst2017.11.111

The role of hydrophobic matching on transmembrane helix packing in cells
Cited by: 32
Author(s): Brayan Grau, Matti Javanainen, María Jesús García-Murria, Waldemar Kulig, Ilpo Vattulainen, Ismael Mingarro, Luis Martínez-Gil
Software Mentions: 1
Published: about 7 years ago

10.1371/journal.pone.0172947

Sox10 contributes to the balance of fate choice in dorsal root ganglion progenitors
Cited by: 21
Author(s): Mariana Delfino‐Machín, Romain Madelaine, Giorgia Busolin, Masataka Nikaido, Sarah Colanesi, Karen Camargo Sosa, Edward Law, Stefano Toppo, Patrick Blader, Natascia Tiso, Robert N. Kelsh
Software Mentions: 1
Published: almost 8 years ago

10.18632/aging.202301

Identification of a novel and potent small molecule inhibitor of SRPK1: mechanism of dual inhibition of SRPK1 for the inhibition of cancer progression
Cited by: 9
Author(s): Anshuman Chandra, Hanumappa Ananda, Nagendra Singh, Imteyaz Qamar
Software Mentions: 1
Published: about 4 years ago

10.3390/ijms22073299

Biological and Physico-Chemical Characteristics of Arginine-Rich Peptide Gemini Surfactants with Lysine and Cystine Spacers
Cited by: 10
Author(s): Damian Neubauer, Maciej Jaśkiewicz, Marta Bauer, Agata Olejniczak-Kęder, Emilia Sikorska, Karol Sikora, Wojciech Kamysz
Software Mentions: 1
Published: over 3 years ago

10.1371/journal.pone.0211381

Molecular dynamic (MD) studies on Gln233Arg (rs1137101) polymorphism of leptin receptor gene and associated variations in the anthropometric and metabolic profiles of Saudi women
Cited by: 15
Author(s): Maha H. Daghestani, Rituraj Purohit, Mazin H. Daghestani, Mamoon Daghistani, Arjumand S. Warsy
Software Mentions: 1
Published: almost 6 years ago

10.1038/s41598-020-60972-w

Purification, Characterization and Mechanistic Evaluation of Angiotensin Converting Enzyme Inhibitory Peptides Derived from Zizyphus Jujuba Fruit
Cited by: 16
Author(s): Mina Memarpoor-Yazdi, Hadi Zare‐Zardini, Navid Mogharrab, Leila Navapour
Software Mentions: 1
Published: almost 5 years ago

10.1371/journal.pcbi.1007033

Reduced level of docosahexaenoic acid shifts GPCR neuroreceptors to less ordered membrane regions
Cited by: 22
Author(s): Matti Javanainen, Giray Enkavi, Ramón Guixà-González, Waldemar Kulig, Hector Martinez‐Seara, Ilya Levental, Ilpo Vattulainen
Software Mentions: 1
Published: over 5 years ago

10.3390/ijms22094990

Assessing the Role of Calmodulin’s Linker Flexibility in Target Binding
Cited by: 7
Author(s): Bin Sun, Peter M. Kekenes‐Huskey
Software Mentions: 1
Published: over 3 years ago

10.1038/s41598-021-81592-y

Partridge and embryonated partridge egg as new preclinical models for candidiasis
Cited by: 2
Author(s): Hadi Tavakkoli, Ahmad Khosravi, Iraj Sharifi, Zahra Shahshahan, Ehsan Salarkia, Reza Kheirandish, Kazem Dehghantalebi, Maziar Jajarmi, Seyedeh Saedeh Mosallanejad, Shahriar Dabiri, Alireza Keyhani
Software Mentions: 1
Published: almost 4 years ago

10.3390/molecules26134002

In Silico Approach Using Free Software to Optimize the Antiproliferative Activity and Predict the Potential Mechanism of Action of Pyrrolizine-Based Schiff Bases
Cited by: 9
Author(s): Faisal A. Almalki, Ashraf N. Abdalla, Ahmed M. Shawky, Mahmoud A. El Hassab, Ahmed M. Gouda
Software Mentions: 1
Published: over 3 years ago

10.1038/s41598-021-83761-5

Serine 477 plays a crucial role in the interaction of the SARS-CoV-2 spike protein with the human receptor ACE2
Cited by: 76
Author(s): Amit Singh, Georg Steinkellner, Katharina Köchl, Karl Gruber, Christian Gruber
Software Mentions: 1
Published: almost 4 years ago

10.1038/s41598-021-93326-1

RETRACTED ARTICLE: New insights into the microscopic interactions associated with the physical mechanism of action of highly diluted biologics
Cited by: 15
Author(s): K. N. Woods
Software Mentions: 1
Published: over 3 years ago

10.3390/molecules25040902

Biophysical Characterization of Epigallocatechin-3-Gallate Effect on the Cardiac Sodium Channel Nav1.5
Cited by: 3
Author(s): Mohamed Yassine Amarouch, Han Kurt, Lucie Delemotte, Hugues Abriel
Software Mentions: 1
Published: almost 5 years ago

10.1128/mBio.02177-20

The Unconventional Cytoplasmic Sensing Mechanism for Ethanol Chemotaxis in Bacillus subtilis
Cited by: 15
Author(s): Payman Tohidifar, Girija A. Bodhankar, Sichong Pei, C. Keith Cassidy, Hanna E. Walukiewicz, George Ordal, Phillip J. Stansfeld, Christopher V. Rao
Software Mentions: 1
Published: about 4 years ago

10.1590/0074-02760160522

Structural insights into leishmanolysins encoded on chromosome 10 of Leishmania (Viannia) braziliensis
Cited by: 6
Author(s): A. Sutter, Deborah Antunes, Mariana Silva-Almeida, Maurício G. S. Costa, Ernesto R. Caffarena
Software Mentions: 1
Published: over 7 years ago

10.1128/JVI.01957-20

Capsid Structure of Leishmania RNA Virus 1
Cited by: 9
Author(s): Michaela Procházková, T. Füzik, Danyil Grybchuk, Francesco Luca Falginella, Lucie Podešvová, Vyacheslav Yurchenko, Robert Vácha, Pavel Plevka
Software Mentions: 1
Published: almost 4 years ago

10.1085/jgp.201912359

Conduction through a narrow inward-rectifier K+ channel pore
Cited by: 29
Author(s): Harald Bernsteiner, Eva-Maria Zangerl-Plessl, Xingyu Chen, Anna Stary-Weinzinger
Software Mentions: 1
Published: over 5 years ago

10.3390/ijms22169025

Decreased Interactions between Calmodulin and a Mutant Huntingtin Model Might Reduce the Cytotoxic Level of Intracellular Ca2+: A Molecular Dynamics Study
Cited by: 2
Author(s): Sanda Nastasia Moldovean, Vasile Chiş
Software Mentions: 1
Published: over 3 years ago

10.3390/ijms20020260

Effects of CD4 Binding on Conformational Dynamics, Molecular Motions, and Thermodynamics of HIV-1 gp120
Cited by: 9
Author(s): Yang Li, Lei Deng, Liquan Yang, Peng Sang, Shu-Qun Liu
Software Mentions: 1
Published: almost 6 years ago

10.3390/ijms20020370

A Hybrid Hamiltonian for the Accelerated Sampling along Experimental Restraints
Cited by: 5
Author(s): Emanuel K. Peter, Jiří Černý
Software Mentions: 1
Published: almost 6 years ago

10.3390/ijms221910423

Universal Properties and Specificities of the β2-Adrenergic Receptor-Gs Protein Complex Activation Mechanism Revealed by All-Atom Molecular Dynamics Simulations
Cited by: 2
Author(s): Argha Mitra, Arijit Sarkar, Attila Borics
Software Mentions: 1
Published: about 3 years ago

10.3390/ma13030710

Steered Pull Simulation to Determine Nanomechanical Properties of Cellulose Nanofiber
Cited by: 17
Author(s): Ruth M. Muthoka, Jaehwan Kim, Jung Woong Kim, Lindong Zhai, Pooja S. Panicker
Software Mentions: 1
Published: almost 5 years ago

10.1016/j.isci.2021.102542

Identification of binding sites for ivacaftor on the cystic fibrosis transmembrane conductance regulator
Cited by: 22
Author(s): Onofrio Laselva, Zafar Qureshi, Zhiwei Zeng, Evgeniy V. Petrotchenko, Mohabir Ramjeesingh, C. Michael Hamilton, Ling-Jun Huan, Christoph H. Borchers, Régis Pomès, Robert N. Young, Christine E. Bear
Software Mentions: 1
Published: over 3 years ago

10.3390/ijms20184493

Investigation into Early Steps of Actin Recognition by the Intrinsically Disordered N-WASP Domain V
Cited by: 3
Author(s): Maud Chan-Yao-Chong, Dominique Durand, Tâp Ha-Duong
Software Mentions: 1
Published: over 5 years ago

10.1016/j.bpj.2019.08.029

Molecular Simulations of Intact Anion Exchanger 1 Reveal Specific Domain and Lipid Interactions
Cited by: 16
Author(s): Dario De Vecchis, Reinhart A.F. Reithmeier, Antreas C. Kalli
Software Mentions: 1
Published: about 5 years ago

10.3390/ijms21031094

Aggregation Mechanism of Alzheimer’s Amyloid β-Peptide Mediated by α-Strand/α-Sheet Structure
Cited by: 10
Author(s): Anand Balupuri, Kwang-Eun Choi, Nam Sook Kang
Software Mentions: 1
Published: almost 5 years ago

10.18632/oncotarget.22343

Genetic identification and molecular modeling characterization reveal a novelPROM1mutation in Stargardt4-like macular dystrophy
Cited by: 29
Author(s): Saber Imani, Jingliang Cheng, Marzieh Dehghan Shasaltaneh, Chunli Wei, Lisha Yang, Shangyi Fu, Hui Zou, Md. Asaduzzaman Khan, Xianqin Zhang, Hanchun Chen, Dianzheng Zhang, Chengxia Duan, Hongbin Lv, Yumei Li, Rui Chen, Junjiang Fu
Software Mentions: 1
Published: about 7 years ago

10.3389/fphar.2020.607797

Hesperidin Interacts With CREB-BDNF Signaling Pathway to Suppress Pentylenetetrazole-Induced Convulsions in Zebrafish
Cited by: 22
Author(s): Pallavi Sharma, Savita Kumari, Jyoti Sharma, Rituraj Purohit, Damanpreet Singh
Software Mentions: 1
Published: almost 4 years ago

10.3389/fphar.2019.00953

Cell-Free Expression of Sodium Channel Domains for Pharmacology Studies. Noncanonical Spider Toxin Binding Site in the Second Voltage-Sensing Domain of Human Nav1.4 Channel
Cited by: 4
Author(s): Mikhail Yu. Myshkin, Roope Männikkö, Olesya A. Krumkacheva, Dmitrii S. Kulbatskii, Anton O. Chugunov, Antonina A. Berkut, Alexander S. Paramonov, Mikhail A. Shulepko, Matvey V. Fedin, Michael G. Hanna, Dimitri M. Kullmann, Elena G. Bagryanskaya, Alexander S. Arseniev, Mikhaǐl P. Kirpichnikov, Ekaterina N. Lyukmanova, Alexander A. Vassilevski, Захар О. Шенкарев
Software Mentions: 1
Published: over 5 years ago

10.3389/fmolb.2020.00114

Recent Developments in Linear Interaction Energy Based Binding Free Energy Calculations
Cited by: 10
Author(s): Eko Aditya Rifai, Marc van Dijk, Daan P. Geerke
Software Mentions: 1
Published: over 4 years ago

10.1155/2019/2930504

Transport of Reactive Oxygen and Nitrogen Species across Aquaporin: A Molecular Level Picture
Cited by: 30
Author(s): Maksudbek Yusupov, Jamoliddin Razzokov, Rodrigo M. Cordeiro, Annemie Bogaerts
Software Mentions: 1
Published: over 5 years ago

10.1021/acs.jctc.1c00322

Automated Coarse-Grained Mapping Algorithm for the Martini Force Field and Benchmarks for Membrane–Water Partitioning
Cited by: 26
Author(s): Thomas D. Potter, Elin L. Barrett, Mark A. Miller
Software Mentions: 1
Published: over 3 years ago

10.3389/fmicb.2021.660050

Genome-Wide Identification and Bioinformatics Characterization of Superoxide Dismutases in the Desiccation-Tolerant Cyanobacterium Chroococcidiopsis sp. CCMEE 029
Cited by: 3
Author(s): Alessandro Napoli, Federico Iacovelli, Claudia Fagliarone, Gianmarco Pascarella, Mattia Falconi, Daniela Billi
Software Mentions: 1
Published: over 3 years ago

10.1080/14756366.2019.1692828

Identifying novel sphingosine kinase 1 inhibitors as therapeutics against breast cancer
Cited by: 25
Author(s): Faez Iqbal Khan, Dakun Lai, Razique Anwer, Iffat Azim, Mohammad Kalim Ahmad Khan
Software Mentions: 1
Published: about 5 years ago

Projects: pypi: gmx

Papers Mentioning gmx 108