pypi: ProDy | Projects | Ecosyste.ms: Papers

10.1371/journal.pone.0153680

Viral Evolved Inhibition Mechanism of the RNA Dependent Protein Kinase PKR's Kinase Domain, a Structural Perspective
Cited by: 4
Author(s): K. Hari Krishna, Yallamandayya Vadlamudi, Mithilesh Kumar
Software Mentions: 9
Published: over 8 years ago

10.1186/s12859-014-0399-6

Integrating protein structural dynamics and evolutionary analysis with Bio3D
Cited by: 279
Author(s): Lars Skjærven, Xin‐Qiu Yao, Guido Scarabelli, Barry J. Grant
Software Mentions: 6
Published: almost 10 years ago

10.1186/1471-2105-15-324

Polyphony: superposition independent methods for ensemble-based drug discovery
Cited by: 8
Author(s): William R. Pitt, Rinaldo W. Montalvão, Tom L. Blundell
Software Mentions: 6
Published: about 10 years ago

10.1371/journal.pone.0183057

Data-driven coarse graining of large biomolecular structures
Cited by: 11
Author(s): Yi‐Ling Chen, Michael Habeck
Software Mentions: 5
Published: over 7 years ago

10.12688/f1000research.17456.1

pdb-tools: a swiss army knife for molecular structures
Cited by: 81
Author(s): João P. G. L. M. Rodrigues, João M.C. Teixeira, Mikaël Trellet, Alexandre M. J. J. Bonvin
Software Mentions: 5
Published: almost 6 years ago

10.1186/s13321-021-00522-2

GNINA 1.0: molecular docking with deep learning
Cited by: 131
Author(s): Andrew T. McNutt, Paul Francoeur, Rishal Aggarwal, Takuya Masuda, Rocco Meli, Matthew Ragoza, Jocelyn Sunseri
Software Mentions: 4
Published: over 3 years ago

10.1186/s12859-018-2150-1

Identification of residue pairing in interacting β-strands from a predicted residue contact map
Cited by: 4
Author(s): Wenzhi Mao, Tong Wang, Wenxuan Zhang, H. Gong
Software Mentions: 4
Published: over 6 years ago

10.1371/journal.pone.0178931

In silico discovery of substituted pyrido[2,3-d]pyrimidines and pentamidine-like compounds with biological activity in myotonic dystrophy models
Cited by: 10
Author(s): Àlex L. González, Piotr Konieczny, Beatriz Llamusí, Estefanía Delgado‐Pinar, José I. Borrell, Jordi Teixidó, Enrique García‐España, Manuel Pérez-Alonso, Roger Estrada‐Tejedor, Rubén Artero
Software Mentions: 4
Published: over 7 years ago

10.7717/peerj.266

Analyzing machupo virus-receptor binding by molecular dynamics simulations
Cited by: 9
Author(s): Austin G. Meyer, Sara L. Sawyer, Andrew D. Ellington, Claus O. Wilke
Software Mentions: 4
Published: over 10 years ago

10.1007/s10295-019-02189-z

Structural insights into dehydratase substrate selection for the borrelidin and fluvirucin polyketide synthases
Cited by: 6
Author(s): Jesus F. Barajas, R.P. McAndrew, Mitchell G. Thompson, Tyler W. H. Backman, Bo Pang, Tristan de Rond, J.H. Pereira, Veronica T. Benites, Héctor García Martín, Edward E. K. Baidoo, Nathan J. Hillson, Paul D. Adams, Jay D. Keasling
Software Mentions: 4
Published: over 5 years ago

10.1021/acs.jcim.1c00362

Data-Driven Ensemble Docking to Map Molecular Interactions of Steroid Analogs with Hepatic Organic Anion Transporting Polypeptides
Cited by: 5
Author(s): Alzbeta Tuerkova, Orsolya Ungvári, Réka Laczkó-Rigó, Erzsébet Mernyák, Gergely Szakács, Csilla Özvegy‐Laczka, Barbara Zdrazil
Software Mentions: 4
Published: over 3 years ago

10.3390/ijms20133155

GPathFinder: Identification of Ligand-Binding Pathways by a Multi-Objective Genetic Algorithm
Cited by: 13
Author(s): José-Emilio Sánchez-Aparicio, Giuseppe Sciortino, Daniel Viladrich Herrmannsdoerfer, Pablo Orenes Chueca, Jaime Rodríguez-Guerra Pedregal, Jean‐Didier Maréchal
Software Mentions: 3
Published: over 5 years ago

10.3389/fchem.2020.597495

Exploring the Allosteric Mechanism of Src Homology-2 Domain-Containing Protein Tyrosine Phosphatase 2 (SHP2) by Molecular Dynamics Simulations
Cited by: 4
Author(s): Quan Wang, Wencheng Zhao, Xueqi Fu, Qing‐Chuan Zheng
Software Mentions: 3
Published: almost 4 years ago

10.1371/journal.pone.0054178

Evolutionary, Structural and Functional Interplay of the IκB Family Members
Cited by: 22
Author(s): Shaherin Basith, Balachandran Manavalan, Vijayakumar Gosu, Sangdun Choi
Software Mentions: 3
Published: almost 12 years ago

10.1371/journal.pone.0183889

Elastic network model of learned maintained contacts to predict protein motion
Cited by: 13
Author(s): Ines Putz, Oliver Brock
Software Mentions: 3
Published: about 7 years ago

10.1186/s12918-016-0271-6

Systems biology of the structural proteome
Cited by: 47
Author(s): Elizabeth Brunk, Nathan Mih, Jonathan M. Monk, Zhen Zhang, Edward J. O’Brien, Spencer Bliven, Ke Chen, Roger L. Chang, Philip E. Bourne, Bernhard Ø. Palsson
Software Mentions: 3
Published: over 8 years ago

10.1371/journal.pcbi.1008197

Integrating structure-based machine learning and co-evolution to investigate specificity in plant sesquiterpene synthases
Cited by: 8
Author(s): Janani Durairaj, Elena Melillo, Harro J. Bouwmeester, Jules Beekwilder, Dick de Ridder, Aalt D. J. van Dijk
Software Mentions: 3
Published: over 3 years ago

10.1371/journal.pntd.0004710

Cholesterol Corrects Altered Conformation of MHC-II Protein in Leishmania donovani Infected Macrophages: Implication in Therapy
Cited by: 22
Author(s): Koushik Roy, Sapan Mandloi, Saikat Chakrabarti, Syamal Roy
Software Mentions: 3
Published: over 8 years ago

10.1371/journal.pcbi.1008719

Mechanical coupling in the nitrogenase complex
Cited by: 6
Author(s): Qi Huang, Monika Tokmina‐Lukaszewska, Lewis E. Johnson, Hayden Kallas, Bojana Ginovska, John W. Peters, Lance C. Seefeldt, Brian Bothner, Simone Raugei
Software Mentions: 3
Published: over 3 years ago

10.1186/s12859-019-3097-6

Glycosylator: a Python framework for the rapid modeling of glycans
Cited by: 16
Author(s): Thomas Lemmin, Cinque Soto
Software Mentions: 3
Published: about 5 years ago

10.1371/journal.pcbi.1007970

Real time structural search of the Protein Data Bank
Cited by: 36
Author(s): Dmytro Guzenko, S.K. Burley, José M. Duarte
Software Mentions: 3
Published: over 4 years ago

10.3390/ijms19030916

Site-Mutation of Hydrophobic Core Residues Synchronically Poise Super Interleukin 2 for Signaling: Identifying Distant Structural Effects through Affordable Computations
Cited by: 2
Author(s): Long‐Can Mei, Yanping Zhou, Lizhe Zhu, Changlin Liu, Zhuo Wu, Fangkui Wang, Ge‐Fei Hao, Di Yu, Hong Yuan, Yanfang Cui
Software Mentions: 3
Published: over 6 years ago

10.1038/s41598-018-36041-8

Characterizing early drug resistance-related events using geometric ensembles from HIV protease dynamics
Cited by: 20
Author(s): Olivier Sheik Amamuddy, Nigel T. Bishop, Özlem Tastan Bishop
Software Mentions: 3
Published: almost 6 years ago

10.3389/fmolb.2020.575196

Probing the Structural Dynamics of the Plasmodium falciparum Tunneling-Fold Enzyme 6-Pyruvoyl Tetrahydropterin Synthase to Reveal Allosteric Drug Targeting Sites
Cited by: 2
Author(s): Afrah Khairallah, Caroline Jane Ross, Özlem Tastan Bishop
Software Mentions: 3
Published: about 4 years ago

10.3389/fchem.2020.00107

Exploring the RNA-Recognition Mechanism Using Supervised Molecular Dynamics (SuMD) Simulations: Toward a Rational Design for Ribonucleic-Targeting Molecules?
Cited by: 14
Author(s): Maicol Bissaro, Mattia Sturlese, Stefano Moro
Software Mentions: 3
Published: over 4 years ago

10.1038/srep44504

Fine-tuning the extent and dynamics of binding cleft opening as a potential general regulatory mechanism in parvulin-type peptidyl prolyl isomerases
Cited by: 7
Author(s): András Czajlik, Bertalan Kovács, Perttu Permi, Zoltán Gáspári
Software Mentions: 2
Published: over 7 years ago

10.1186/s12859-018-2373-1

Diverse dynamics features of novel protein kinase C (PKC) isozymes determine the selectivity of a fluorinated balanol analogue for PKCε
Cited by: 4
Author(s): Ari Hardianto, Varun Khanna, Fei Liu, Shoba Ranganathan
Software Mentions: 2
Published: almost 6 years ago

10.1186/s12859-018-2348-2

Molecular dynamics and structure function analysis show that substrate binding and specificity are major forces in the functional diversification of Eqolisins
Cited by: 2
Author(s): Nicolás Stocchi, María V. Revuelta, Priscila Ailín Lanza Castronuovo, D. Mariano A. Vera, Arjen ten Have
Software Mentions: 2
Published: about 6 years ago

10.1186/1756-0500-5-391

BetaSearch: a new method for querying β-residue motifs
Cited by: 1
Author(s): Hui Kian Ho, Graeme Gange, Michael J. Kuiper, Kotagiri Ramamohanarao
Software Mentions: 2
Published: over 12 years ago

10.1093/bioinformatics/btx515

<i>In silico</i> identification of rescue sites by double force scanning
Cited by: 10
Author(s): Matteo Tiberti, Alessandro Pandini, Franca Fraternali, Arianna Fornili
Software Mentions: 2
Published: over 7 years ago

10.1093/bioinformatics/btw482

Online interactive analysis of protein structure ensembles with Bio3D-web
Cited by: 29
Author(s): Lars Skjærven, Shashank Jariwala, Xin‐Qiu Yao, Barry J. Grant
Software Mentions: 2
Published: over 8 years ago

10.1016/j.bpj.2015.06.061

Structure, Dynamics, and Allosteric Potential of Ionotropic Glutamate Receptor N-Terminal Domains
Cited by: 26
Author(s): James Krieger, İvet Bahar, Ingo H. Greger
Software Mentions: 2
Published: about 9 years ago

10.3390/molecules24010142

Identification of Novel Potential Inhibitors of Pteridine Reductase 1 in Trypanosoma brucei via Computational Structure-Based Approaches and in Vitro Inhibition Assays
Cited by: 19
Author(s): Magambo Phillip Kimuda, Dustin Laming, Özlem Tastan Bishop
Software Mentions: 2
Published: almost 6 years ago

10.3390/molecules25204623

In Silico Molecular Study of Tryptophan Bitterness
Cited by: 8
Author(s): Antonella Di Pizio, Alessandro Nicoli
Software Mentions: 2
Published: about 4 years ago

10.3390/molecules26040837

Exploring the Distinct Binding and Activation Mechanisms for Different CagA Oncoproteins and SHP2 by Molecular Dynamics Simulations
Cited by: 3
Author(s): Quan Wang, Wencheng Zhao, Xueqi Fu, Qing‐Chuan Zheng
Software Mentions: 2
Published: almost 4 years ago

10.1371/journal.pcbi.1002705

Coupling between Catalytic Loop Motions and Enzyme Global Dynamics
Cited by: 43
Author(s): Zeynep Kurkcuoglu, Ahmet Bakan, Duygu Kocaman, İvet Bahar, Pemra Doruker
Software Mentions: 2
Published: about 12 years ago

10.1371/journal.pone.0211043

Repository of Enriched Structures of Proteins Involved in the Red Blood Cell Environment (RESPIRE)
Cited by: 5
Author(s): Stéphane Teletchea, Hubert Santuz, Sylvain Léonard, Catherine Etchebest
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pone.0191882

The reliability of molecular dynamics simulations of the multidrug transporter P-glycoprotein in a membrane environment
Cited by: 31
Author(s): Karmen Čondić‐Jurkić, Nandhitha Subramanian, Alan E. Mark, Megan L. O’Mara
Software Mentions: 2
Published: almost 7 years ago

10.1371/journal.pone.0145142

How Intrinsic Molecular Dynamics Control Intramolecular Communication in Signal Transducers and Activators of Transcription Factor STAT5
Cited by: 7
Author(s): Florent Langenfeld, Yann Guarracino, Michel Arock, Alain Trouvé, Luba Tchertanov
Software Mentions: 2
Published: almost 9 years ago

10.1371/journal.pone.0119771

Structure, Dynamics, and Interaction of Mycobacterium tuberculosis (Mtb) DprE1 and DprE2 Examined by Molecular Modeling, Simulation, and Electrostatic Studies
Cited by: 34
Author(s): Isha Bhutani, Saurabh Loharch, Pawan Gupta, Rethi Madathil, Raman Parkesh
Software Mentions: 2
Published: over 9 years ago

10.1371/journal.pone.0118684

How Structural and Physicochemical Determinants Shape Sequence Constraints in a Functional Enzyme
Cited by: 42
Author(s): Luciano A. Abriata, Timothy Palzkill, Matteo Dal Peraro
Software Mentions: 2
Published: over 9 years ago

10.1371/journal.pone.0152049

On the Applicability of Elastic Network Models for the Study of RNA CUG Trinucleotide Repeat Overexpansion
Cited by: 8
Author(s): Àlex L. González, Jordi Teixidó, José I. Borrell, Roger Estrada‐Tejedor
Software Mentions: 2
Published: over 8 years ago

10.1016/j.csbj.2020.03.011

Caretta – A multiple protein structure alignment and feature extraction suite
Cited by: 18
Author(s): Mehmet Akdel, Janani Durairaj, Dick de Ridder, Aalt D. J. van Dijk
Software Mentions: 2
Published: almost 5 years ago

10.3389/fmolb.2021.614443

Non-RBM Mutations Impaired SARS-CoV-2 Spike Protein Regulated to the ACE2 Receptor Based on Molecular Dynamic Simulation
Cited by: 5
Author(s): Yaoqiang Du, Hao Wang, Linjie Chen, Quan Fang, Biqin Zhang, Jiang Lei, Zhaoyu Wu, Yuanhong Yang, Ying Zhou, Bingyu Chen, Jianxin Lyu, Zhen Wang
Software Mentions: 2
Published: over 3 years ago

10.1080/14756366.2021.1954919

Supervised Molecular Dynamics (SuMD) Insights into the mechanism of action of SARS-CoV-2 main protease inhibitor PF-07321332
Cited by: 55
Author(s): Matteo Pavan, Giovanni Bolcato, Davide Bassani, Mattia Sturlese, Stefano Moro
Software Mentions: 2
Published: almost 4 years ago

10.1002/pro.3732

Pharmmaker: Pharmacophore modeling and hit identification based on druggability simulations
Cited by: 17
Author(s): Ji Young Lee, James Krieger, Hongchun Li, İvet Bahar
Software Mentions: 2
Published: almost 5 years ago

10.1038/srep34984

Structural insights into conformational stability of both wild-type and mutant EZH2 receptor
Cited by: 179
Author(s): Imlimaong Aier, Pritish Kumar Varadwaj, Utkarsh Raj
Software Mentions: 2
Published: about 8 years ago

10.1038/s41598-018-32815-2

Allosteric Role of Substrate Occupancy Toward the Alignment of P-glycoprotein Nucleotide Binding Domains
Cited by: 13
Author(s): Lurong Pan, Stephen G. Aller
Software Mentions: 2
Published: about 6 years ago

10.1007/s00894-016-2982-4

Improvements in GROMACS plugin for PyMOL including implicit solvent simulations and displaying results of PCA analysis
Cited by: 17
Author(s): Tomasz Makarewicz, Rajmund Kaźmierkiewicz
Software Mentions: 2
Published: over 8 years ago

10.1016/j.yjsbx.2020.100038

Structures and dynamics of the novel S1/S2 protease cleavage site loop of the SARS-CoV-2 spike glycoprotein
Cited by: 33
Author(s): Thomas Lemmin, David Kalbermatter, Daniel Harder, Philippe Plattet, Dimitrios Fotiadis
Software Mentions: 2
Published: almost 5 years ago

10.1016/j.jmb.2020.08.023

Transglutaminase-Mediated Cross-Linking of Tropoelastin to Fibrillin Stabilises the Elastin Precursor Prior to Elastic Fibre Assembly
Cited by: 14
Author(s): Michael P. Lockhart-Cairns, Helena Newandee, Jennifer M. Thomson, Anthony S. Weiss, Clair Baldock, Anna Tarakanova
Software Mentions: 1
Published: about 4 years ago

10.18632/oncotarget.14517

Molecular dynamics simulation reveals how phosphorylation of tyrosine 26 of phosphoglycerate mutase 1 upregulates glycolysis and promotes tumor growth
Cited by: 12
Author(s): Yan Wang, Wensheng Cai, Luonan Chen, Guanyu Wang
Software Mentions: 1
Published: almost 8 years ago

10.1371/journal.pone.0080261

TAL Effectors Specificity Stems from Negative Discrimination
Cited by: 17
Author(s): Basile I. M. Wicky, Marco Stenta, Matteo Dal Peraro
Software Mentions: 1
Published: almost 11 years ago

10.1371/journal.pone.0138118

Comparison of the Internal Dynamics of Metalloproteases Provides New Insights on Their Function and Evolution
Cited by: 7
Author(s): Henrique F. Carvalho, Ana C. A. Roque, Olga Iranzo, Ricardo Branco
Software Mentions: 1
Published: about 9 years ago

10.3390/molecules26175153

Insights into Conformational Dynamics and Allostery in DNMT1-H3Ub/USP7 Interactions
Cited by: 5
Author(s): Yu Zhu, Fei Ye, Ziyun Zhou, Wanlin Liu, Zhongjie Liang, Guang Hu
Software Mentions: 1
Published: about 3 years ago

10.7554/eLife.34353

Microtubule assembly governed by tubulin allosteric gain in flexibility and lattice induced fit
Cited by: 42
Author(s): Maxim Igaev, Helmut Grubmüller
Software Mentions: 1
Published: over 6 years ago

10.3390/molecules25071522

Disordered Residues and Patterns in the Protein Data Bank
Cited by: 7
Author(s): М. Л. Лобанов, Ilya V. Likhachev, Oxana V. Galzitskaya
Software Mentions: 1
Published: over 4 years ago

10.1111/febs.15268

Breaking a single hydrogen bond in the mitochondrial tRNA<sup>Phe</sup>‐PheRS complex leads to phenotypic pleiotropy of human disease
Cited by: 4
Author(s): Moshe Peretz, Dmitry Tworowski, Ekaterine Kartvelishvili, John H. Livingston, Zofia M.A. Chrzanowska-Lightowlers, Mark Safro
Software Mentions: 1
Published: over 4 years ago

10.3390/molecules22010145

Intrinsic Dynamics Analysis of a DNA Octahedron by Elastic Network Model
Cited by: 9
Author(s): Guang Hu, Lei He, Federico Iacovelli, Mattia Falconi
Software Mentions: 1
Published: almost 8 years ago

10.3390/molecules24183293

Normal Mode Analysis as a Routine Part of a Structural Investigation
Cited by: 42
Author(s): Jacob Bauer, Jelena Pavlović, Vladena Bauerová-Hlinková
Software Mentions: 1
Published: about 5 years ago

10.3389/fmolb.2021.654164

Comparative Analysis of Structural and Dynamical Features of Ribosome Upon Association With mRNA Reveals Potential Role of Ribosomal Proteins
Cited by: 3
Author(s): Sneha Bheemireddy, Sankaran Sandhya
Software Mentions: 1
Published: over 3 years ago

10.3389/fmolb.2020.586075

Exploring Allosteric Signaling in the Exit Tunnel of the Bacterial Ribosome by Molecular Dynamics Simulations and Residue Network Model
Cited by: 8
Author(s): Pelin Güzel, Hatice Zeynep Yildirim, Merve Yuce, Özge Kürkçüoğlu
Software Mentions: 1
Published: about 4 years ago

10.7554/eLife.34186

Free-energy simulations reveal molecular mechanism for functional switch of a DNA helicase
Cited by: 14
Author(s): Wen Ma, Kevin D. Whitley, Yann R. Chemla, Zaida Luthey‐Schulten, Klaus Schulten
Software Mentions: 1
Published: over 6 years ago

10.1093/molbev/msz102

Shared Signature Dynamics Tempered by Local Fluctuations Enables Fold Adaptability and Specificity
Cited by: 42
Author(s): She Zhang, Hongchun Li, James Krieger, İvet Bahar
Software Mentions: 1
Published: over 5 years ago

10.1016/j.jbc.2021.100430

Direct coupling of oligomerization and oligomerization-driven endocytosis of the dopamine transporter to its conformational mechanics and activity
Cited by: 8
Author(s): Tatiana Sorkina, Mary Hongying Cheng, Tarique Rajasaheb Bagalkot, Callen T. Wallace, Simon C. Watkins, İvet Bahar, Alexander Sorkin
Software Mentions: 1
Published: almost 4 years ago

10.1186/1754-6834-7-83

Molecular dynamics study of enhanced Man5B enzymatic activity
Cited by: 33
Author(s): Rafael C. Bernardi, Isaac Cann, Klaus Schulten
Software Mentions: 1
Published: over 10 years ago

10.1042/BSR20180609

Water structure changes in oxime-mediated reactivation process of phosphorylated human acetylcholinesterase
Cited by: 5
Author(s): Irina V. Zueva, Sofya V. Lushchekina, Patrick Masson
Software Mentions: 1
Published: over 6 years ago

10.3390/biology1020222

Global Conformational Dynamics of HIV-1 Reverse Transcriptase Bound to Non-Nucleoside Inhibitors
Cited by: 7
Author(s): David W. Wright, Benjamin A. Hall, Paul Kellam, Peter V. Coveney
Software Mentions: 1
Published: over 12 years ago

10.1371/journal.ppat.1002667

The Lipopolysaccharide from Capnocytophaga canimorsus Reveals an Unexpected Role of the Core-Oligosaccharide in MD-2 Binding
Cited by: 32
Author(s): Simon Ittig, Buko Lindner, Marco Stenta, Pablo Manfredi, Evelina L. Zdorovenko, Yuriy A. Knirel, Matteo Dal Peraro, Guy R. Cornelis, Ulrich Zähringer
Software Mentions: 1
Published: over 12 years ago

10.1186/s13628-017-0034-9

Native flexibility of structurally homologous proteins: insights from anisotropic network model
Cited by: 5
Author(s): Ranja Sarkar
Software Mentions: 1
Published: almost 8 years ago

10.3390/ijms21218348

Ensemble-Based Analysis of the Dynamic Allostery in the PSD-95 PDZ3 Domain in Relation to the General Variability of PDZ Structures
Cited by: 4
Author(s): Dániel Dudola, Anett Hinsenkamp, Zoltán Gáspári
Software Mentions: 1
Published: about 4 years ago

10.3390/antiox9020162

Transcriptomic Analysis Reveals Cu/Zn SODs Acting as Hub Genes of SODs in Hylocereus undatus Induced by Trypsin during Storage
Cited by: 8
Author(s): Xinyue Pang, Xinling Li, Xueru Liu, Luning Cai, Bairu Li
Software Mentions: 1
Published: almost 5 years ago

10.1038/s41598-017-05659-5

Characterization of HIV-1 integrase interaction with human Ku70 protein and initial implications for drug targeting
Cited by: 16
Author(s): Andrey Anisenko, Ekaterina Knyazhanskaya, Arthur O. Zalevsky, Julia Agapkina, Aleksander I. Sizov, Timofei S. Zatsepin, Marina Gottikh
Software Mentions: 1
Published: over 7 years ago

10.1038/s41598-017-06586-1

An in-silico glimpse into the pH dependent structural changes of T7 RNA polymerase: a protein with simplicity
Cited by: 10
Author(s): Subhomoi Borkotoky, Chetan Kumar Meena, G. M. Bhalerao, Ayaluru Murali
Software Mentions: 1
Published: over 7 years ago

10.1038/s41598-017-09482-w

Nanomechanics of multidomain neuronal cell adhesion protein contactin revealed by single molecule AFM and SMD
Cited by: 16
Author(s): Karolina Mikulska-Ruminska, A. Kulik, Carine Benadiba, İvet Bahar, Giovanni Dietler, Wiesław Nowak
Software Mentions: 1
Published: over 7 years ago

10.1038/s41598-017-15452-z

Structure-function relationships in ABCG2: insights from molecular dynamics simulations and molecular docking studies
Cited by: 47
Author(s): Ricardo B. Ferreira, Cátia A. Bonito, M. Natália D. S. Cordeiro, Maria‐José U. Ferreira, Daniel J. V. A. dos Santos
Software Mentions: 1
Published: about 7 years ago

10.3390/ijms22105253

NO● Represses the Oxygenation of Arachidonoyl PE by 15LOX/PEBP1: Mechanism and Role in Ferroptosis
Cited by: 16
Author(s): Karolina Mikulska-Ruminska, Tamil S. Anthonymuthu, Anastasia Levkina, Indira H. Shrivastava, Alexandr A. Kapralov, Hülya Bayır, Valerian E. Kagan, İvet Bahar
Software Mentions: 1
Published: over 3 years ago

10.1038/s41598-018-35902-6

Rotational direction of flagellar motor from the conformation of FliG middle domain in marine Vibrio
Cited by: 22
Author(s): Tatsuro Nishikino, Atsushi Hijikata, Yohei Miyanoiri, Yasuhiro Onoue, Seiji Kojima, Tomoyuki Shirai, Michio Homma
Software Mentions: 1
Published: almost 6 years ago

10.1007/s12551-015-0163-9

Global low-frequency motions in protein allostery: CAP as a model system
Cited by: 20
Author(s): Philip D. Townsend, Thomas L. Rodgers, Ehmke Pohl, Mark R. Wilson, Tom McLeish, Martin J. Cann
Software Mentions: 1
Published: almost 10 years ago

10.1038/s41598-019-48878-8

Biosynthesis of Hyaluronic acid polymer: Dissecting the role of sub structural elements of hyaluronan synthase
Cited by: 22
Author(s): Garima Agarwal, Kathiresan Krishnan, Shashi Bala Prasad, Anirban Bhaduri, Guhan Jayaraman
Software Mentions: 1
Published: about 5 years ago

10.1038/s41598-020-63957-x

Orthosteric muscarinic receptor activation by the insect repellent IR3535 opens new prospects in insecticide-based vector control
Cited by: 12
Author(s): Eléonore Moreau, Karolina Mikulska-Ruminska, Mathilde Goulu, Stéphane Perrier, Caroline Deshayes, Maria Stankiewicz, Véronique Apaire-Marchais, Wiesław Nowak, Bruno Lapied
Software Mentions: 1
Published: over 4 years ago

10.1038/s41598-020-66310-4

Probing the Structural Dynamics of the Catalytic Domain of Human Soluble Guanylate Cyclase
Cited by: 4
Author(s): Rana Rehan Khalid, Arooma Maryam, Uğur Sezerman, Efstratios Mylonas, Abdul Rauf Siddiqi, Michael Kokkinidis
Software Mentions: 1
Published: over 4 years ago

10.1371/journal.pcbi.1006008

Same but not alike: Structure, flexibility and energetics of domains in multi-domain proteins are influenced by the presence of other domains
Cited by: 37
Author(s): Sneha Vishwanath, Alexandre G. de Brevern, Narayanaswamy Srinivasan
Software Mentions: 1
Published: almost 7 years ago

10.1371/journal.pcbi.1003879

Complete Mapping of Substrate Translocation Highlights the Role of LeuT N-terminal Segment in Regulating Transport Cycle
Cited by: 59
Author(s): Mary Hongying Cheng, İvet Bahar
Software Mentions: 1
Published: about 10 years ago

10.1098/rstb.2017.0177

Shared dynamics of LeuT superfamily members and allosteric differentiation by structural irregularities and multimerization
Cited by: 22
Author(s): Luca Ponzoni, She Zhang, Mary Hongying Cheng, İvet Bahar
Software Mentions: 1
Published: over 6 years ago

10.1038/s41598-020-72243-9

Thyroxine binding to type III iodothyronine deiodinase
Cited by: 12
Author(s): Craig A. Bayse, Eric S. Marsan, Jenna R. Garcia, Alexis T. Tran-Thompson
Software Mentions: 1
Published: about 4 years ago

10.1038/s41598-020-77700-z

Targeting the coronavirus SARS-CoV-2: computational insights into the mechanism of action of the protease inhibitors lopinavir, ritonavir and nelfinavir
Cited by: 40
Author(s): Giovanni Bolcato, Maicol Bissaro, Matteo Pavan, Mattia Sturlese, Stefano Moro
Software Mentions: 1
Published: almost 4 years ago

10.1371/journal.pone.0115856

On the Modularity of the Intrinsic Flexibility of the µ Opioid Receptor: A Computational Study
Cited by: 14
Author(s): Mathieu Fossépré, Laurence Leherte, Aatto Laaksonen, Daniel P. Vercauteren
Software Mentions: 1
Published: almost 10 years ago

10.1371/journal.pone.0101552

Characterization of a Novel BCHE “Silent” Allele: Point Mutation (p.Val204Asp) Causes Loss of Activity and Prolonged Apnea with Suxamethonium
Cited by: 35
Author(s): Hervé Delacour, Sofya V. Lushchekina, Isabelle Mabboux, Aurore Bousquet, F. Ceppa, Lawrence M. Schopfer, Oksana Lockridge, Patrick Masson
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pone.0097528

Inherent Dynamics of Head Domain Correlates with ATP-Recognition of P2X4 Receptors: Insights Gained from Molecular Simulations
Cited by: 28
Author(s): Li‐Dong Huang, Ying-Zhe Fan, Yun Tian, Yang Yang, Yan Liu, Jin Wang, Wenshan Zhao, Wenchao Zhou, Xiaoyang Cheng, Peng Cao, Xiangyang Lu, Ye Yu
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pone.0216142

Different modes of barrel opening suggest a complex pathway of ligand binding in human gastrotropin
Cited by: 2
Author(s): Zita Harmat, András László Szabó, Orsolya Tőke, Zoltán Gáspári
Software Mentions: 1
Published: over 5 years ago

10.1371/journal.pone.0194425

Dynamics of Scabin toxin. A proposal for the binding mode of the DNA substrate
Cited by: 10
Author(s): Miguel R. Lugo, Bronwyn Lyons, Cristina Lento, Derek J. Wilson, A. Rod Merrill
Software Mentions: 1
Published: over 6 years ago

10.3390/molecules23092141

Comparative Studies of the Dynamics Effects of BAY60-2770 and BAY58-2667 Binding with Human and Bacterial H-NOX Domains
Cited by: 18
Author(s): Rana Rehan Khalid, Muhammad Tahir ul Qamar, Arooma Maryam, Ayesha Ashique, Farooq Anwar, Mohammed H. Geesi, Abdul Rauf Siddiqi
Software Mentions: 1
Published: about 6 years ago

10.1038/s41598-021-86471-0

Molecular dynamics and in silico mutagenesis on the reversible inhibitor-bound SARS-CoV-2 main protease complexes reveal the role of lateral pocket in enhancing the ligand affinity
Cited by: 27
Author(s): Ying Li Weng, Shiv Rakesh Naik, Nadia Dingelstad, Miguel R. Lugo, Subha Kalyaanamoorthy, Aravindhan Ganesan
Software Mentions: 1
Published: over 3 years ago

10.3390/biom10121664

Impact of Sucrose as Osmolyte on Molecular Dynamics of Mouse Acetylcholinesterase
Cited by: 7
Author(s): Sofya V. Lushchekina, Gaetan Inidjel, Nicolás Martínez, Patrick Masson, M. Trovaslet-Leroy, Florian Nachon, Michael Marek Koza, Tilo Seydel, Judith Peters
Software Mentions: 1
Published: almost 4 years ago

10.3390/molecules190914961

A Multi-Scale–Multi-Stable Model for the Rhodopsin Photocycle
Cited by: 11
Author(s): Francesco Tavanti, Valentina Tozzini
Software Mentions: 1
Published: about 10 years ago

Projects: pypi: ProDy

Papers Mentioning ProDy 97