Ecosyste.ms: Papers

10.3390/ijms22031164

Comparative Study of Interactions between Human cGAS and Inhibitors: Insights from Molecular Dynamics and MM/PBSA Studies
Cited by: 2
Author(s): Xiaowen Wang, Wenjin Li
Software Mentions: 1
Published: almost 4 years ago

10.3390/ijms22083895

Proliferation to Apoptosis Tumor Cell Ratio as a Biomarker to Improve Clinical Management of Pre-Malignant and Symptomatic Plasma Cell Neoplasms
Cited by: 3
Author(s): María A Vasco-Mogorrón, José A. Campillo, Adela Periago, Valentín Cabañas, M Berenguer, María C García-Garay, Lourdes Gimeno, María F Soto-Ramírez, María D Martínez-Hernández, Manuel Muro, Alfredo Minguela
Software Mentions: 1
Published: over 3 years ago

10.3390/ijms22147455

In Vitro and In Silico Characterization of an Antimalarial Compound with Antitumor Activity Targeting Human DNA Topoisomerase IB
Cited by: 4
Author(s): Bini Chhetri Soren, Jagadish Babu Dasari, Alessio Ottaviani, Beatrice Messina, Giada Andreotti, Alice Romeo, Federico Iacovelli, Mattia Falconi, Alessandro Desideri, Paola Fiorani
Software Mentions: 1
Published: over 3 years ago

10.3390/ijms22168714

Molecular Dynamics Studies on the Structural Characteristics for the Stability Prediction of SARS-CoV-2
Cited by: 5
Author(s): Kwang-Eun Choi, Jeong‐Min Kim, JeeEun Rhee, Ae Kyung Park, Eun Jin Kim, Nam Sook Kang
Software Mentions: 1
Published: over 3 years ago

10.3390/ijms221910220

In Silico Identification and Evaluation of Natural Products as Potential Tumor Necrosis Factor Function Inhibitors Using Advanced Enalos Asclepios KNIME Nodes
Cited by: 6
Author(s): Dimitra Papadopoulou, Antonios Drakopoulos, Panagiotis Lagarias, Georgia Melagraki, George Kollias, Antreas Afantitis
Software Mentions: 1
Published: about 3 years ago

10.1063/5.0037793

Recent advancements in enzyme-mediated crosslinkable hydrogels: <i>In vivo</i>-mimicking strategies
Cited by: 31
Author(s): Wonmoon Song, Junghyeon Ko, Young Hwan Choi, Nathaniel S. Hwang
Software Mentions: 1
Published: over 3 years ago

10.1021/acs.jnatprod.9b01024

Antibacterial and ATP Synthesis Modulating Compounds from <i>Salvia tingitana</i>
Cited by: 13
Author(s): Angela Bisio, Anna Maria Schito, Francesca Pedrelli, Ombeline Danton, Jakob K. Reinhardt, Giulio Poli, Tiziano Tuccinardi, Thomas Bürgi, Francesco De Riccardis, Mauro Giacomini, Daniela Calzia, Isabella Panfoli, Gian Carlo Schito, Matthias Hamburger, Nunziatina De Tommasi
Software Mentions: 1
Published: over 4 years ago

10.1186/s40478-020-00990-x

Towards an improved early diagnosis of neurodegenerative diseases: the emerging role of in vitro conversion assays for protein amyloids
Cited by: 38
Author(s): Niccolò Candelise, Simone Baiardi, Alessia Franceschini, Marcello Rossi, Piero Parchi
Software Mentions: 1
Published: over 4 years ago

10.1155/2014/850628

Binding Energy Calculation of Patchouli Alcohol Isomer Cyclooxygenase Complexes Suggested as COX-1/COX-2 Selective Inhibitor
Cited by: 13
Author(s): Sentot Joko Raharjo, Chanif Mahdi, Nurdiana Nurdiana, Takheshi Kikuchi, Fatchiyah Fatchiyah
Software Mentions: 1
Published: about 10 years ago

10.1002/advs.202100249

Exploiting Generative Design for 3D Printing of Bacterial Biofilm Resistant Composite Devices
Cited by: 7
Author(s): Yinfeng He, Meisam Abdi, Gustavo F. Trindade, Belén Begines, Jean‐Frédéric Dubern, Elisabetta Prina, Andrew L. Hook, Gabriel Y. H. Choong, Javier Ledesma, Christopher Tuck, Felicity R. A. J. Rose, Richard Hague, Clive J. Roberts, Davide S.A. De Focatiis, Ian Ashcroft, Paul Williams, Derek J. Irvine, Morgan R. Alexander, Ricky Wildman
Software Mentions: 1
Published: over 3 years ago

10.3390/antibiotics9120917

A Simple Protocol for the Determination of Lysostaphin Enzymatic Activity
Cited by: 7
Author(s): A. V. Grishin, Svetlana V. Konstantinova, I.V. Vasina, Nikita V. Shestak, A. S. Karyagina, В. Г. Лунин
Software Mentions: 1
Published: almost 4 years ago

10.3390/antibiotics9090559

Anti-Tubercular Properties of 4-Amino-5-(4-Fluoro-3- Phenoxyphenyl)-4H-1,2,4-Triazole-3-Thiol and Its Schiff Bases: Computational Input and Molecular Dynamics
Cited by: 22
Author(s): Katharigatta N. Venugopala, Mahmoud Kandeel, Melendhran Pillay, Pran Kishore Deb, Hassan H. Abdallah, Mohamad Fawzi Mahomoodally, Deepak Chopra
Software Mentions: 1
Published: about 4 years ago

10.3390/antibiotics9120846

Proposal of Potent Inhibitors for a Bacterial Cell Division Protein FtsZ: Molecular Simulations Based on Molecular Docking and ab Initio Molecular Orbital Calculations
Cited by: 1
Author(s): Shohei Yamamoto, Ryosuke Saito, Shunya Nakamura, Haruki Sogawa, П. А. Карпов, Sergiy Shulga, Yaroslav B. Blume, Noriyuki Kurita
Software Mentions: 1
Published: almost 4 years ago

10.1186/ar4343

Lack of change in urate deposition by dual-energy computed tomography among clinically stable patients with long-standing tophaceous gout: a prospective longitudinal study
Cited by: 34
Author(s): Aravind Rajan, Opetaia Aati, Ramanamma Kalluru, Gregory D. Gamble, Anne Horne, Anthony Doyle, Fiona McQueen, Nicola Dalbeth
Software Mentions: 1
Published: almost 12 years ago

10.1186/s13065-019-0525-7

Antitumor effect of proanthocyanidin induced apoptosis in human colorectal cancer (HT-29) cells and its molecular docking studies
Cited by: 12
Author(s): Mani Suganya, Balasubramanian Mythili Gnanamangai, Balasubramani Ravindran, Soon Woong Chang, Selvaraj Arokiyaraj, Chandramohan Govindasamy, Mohamed Farouk Elsadek, P. Ponmurugan
Software Mentions: 1
Published: almost 6 years ago

10.1186/s12864-019-6291-z

Improving CRISPR guide design with consensus approaches
Cited by: 5
Author(s): Jacob Bradford, Dimitri Perrin
Software Mentions: 1
Published: almost 5 years ago

10.1186/s12911-017-0453-1

Modeling long-term human activeness using recurrent neural networks for biometric data
Cited by: 6
Author(s): Zae Myung Kim, Hyungrai Oh, Han‐Gyu Kim, Chae-Gyun Lim, Kyo-Joong Oh, Ho-Jin Choi
Software Mentions: 1
Published: over 7 years ago

10.1186/s12911-017-0421-9

Mobile Technology for Community Health in Ghana: what happens when technical functionality threatens the effectiveness of digital health programs?
Cited by: 55
Author(s): Amnesty LeFevre, Diwakar Mohan, David Hutchful, Larissa Jennings, Garrett Mehl, Alain Labrique, Karen Romano, Anitha Moorthy
Software Mentions: 1
Published: over 7 years ago

10.1186/1753-6561-6-S2-S2

Comparison of the analyses of the XVth QTLMAS common dataset II: QTL analysis
Cited by: 1
Author(s): Olivier Demeure, Olivier Filangi, Jean-Michel Elsen, Pascale Le Roy
Software Mentions: 1
Published: over 12 years ago

10.1186/1472-6807-12-8

Are different stoichiometries feasible for complexes between lymphotoxin-alpha and tumor necrosis factor receptor 1?
Cited by: 2
Author(s): Nahren Manuel Mascarenhas, Johannes Kästner
Software Mentions: 1
Published: almost 13 years ago

10.3390/bs11090125

A Multilevel Approach to Explore the Wandering Mind and Its Connections with Mindfulness and Personality
Cited by: 2
Author(s): Damiano Cantone, Susanna Feruglio, Cristiano Crescentini, Sabrina Cinot, Alessio Matiz
Software Mentions: 1
Published: about 3 years ago

10.1042/BST20170218

Structure and function of the cytochrome P450 peroxygenase enzymes
Cited by: 123
Author(s): Andrew W. Munro, Kirsty J. McLean, Job L. Grant, Thomas M. Makris
Software Mentions: 1
Published: almost 7 years ago

10.1002/btm2.10105

In silico analytico-mathematical interpretation of biopolymeric assemblies: Quantification of energy surfaces and molecular attributes via atomistic simulations
Cited by: 16
Author(s): Pradeep Kumar, Yahya E. Choonara, Viness Pillay
Software Mentions: 1
Published: about 6 years ago

10.3390/biology10080789

Phytochemicals from Leucas zeylanica Targeting Main Protease of SARS-CoV-2: Chemical Profiles, Molecular Docking, and Molecular Dynamics Simulations
Cited by: 30
Author(s): Mycal Dutta, Abu Montakim Tareq, Ahmed Rakib, Shafi Mahmud, Saad Ahmed Sami, Jewel Mallick, Mohammad Nazmul Islam, Mohuya Majumder, Zia Uddin, Abdullah Alsubaie, Abdulraheem S. A. Almalki, Mayeen Uddin Khandaker, D.A. Bradley, Md. Sohel Rana, Talha Bin Emran
Software Mentions: 1
Published: over 3 years ago

10.1155/2017/2105610

Sulfonanilide Derivatives in Identifying Novel Aromatase Inhibitors by Applying Docking, Virtual Screening, and MD Simulations Studies
Cited by: 19
Author(s): Shailima Rampogu, Maeng-Hyun Son, Chanin Park, Hyong-Ha Kim, Jung Keun Suh, Keun Woo Lee
Software Mentions: 1
Published: almost 8 years ago

10.1155/2013/569470

A Novel Multilayered Multidisk Oral Tablet for Chronotherapeutic Drug Delivery
Cited by: 6
Author(s): Zafar Ahmed Khan, Yahya E. Choonara, Pradeep Kumar, Lisa C. du Toit, Valence M. K. Ndesendo, Viness Pillay
Software Mentions: 1
Published: almost 12 years ago

10.1155/2019/8207056

Dihydroartemisinin Sensitizes Mutant p53 (R248Q)-Expressing Hepatocellular Carcinoma Cells to Doxorubicin by Inhibiting P-gp Expression
Cited by: 49
Author(s): Yue Yang, Jianxin He, Jing Chen, Li Lin, Yongqi Liu, Cunmin Zhou, Yun Su, Hulai Wei
Software Mentions: 1
Published: almost 5 years ago

10.1155/2013/460936

Prolonged Delivery of Ciprofloxacin and Diclofenac Sodium from a Polymeric Fibre Device for the Treatment of Peridontal Disease
Cited by: 17
Author(s): Deanne Johnston, Yahya E. Choonara, Pradeep Kumar, Lisa C. du Toit, Sandy van Vuuren, Viness Pillay
Software Mentions: 1
Published: almost 12 years ago

10.3390/biomedicines9081063

Novel Biomimetic Human TLR2-Derived Peptides for Potential Targeting of Lipoteichoic Acid: An In Silico Assessment
Cited by: 1
Author(s): Nikita Devnarain, Ayman Y. Waddad, Beatriz G. de la Torre, Fernando Alberício, Thirumala Govender
Software Mentions: 1
Published: over 3 years ago

10.3390/biom10091205

Multivalent and Bidirectional Binding of Transcriptional Transactivation Domains to the MED25 Coactivator
Cited by: 1
Author(s): Heather Jeffery, Robert O. J. Weinzierl
Software Mentions: 1
Published: over 4 years ago

10.3390/biom9100545

Enhanced Solubility and Anticancer Potential of Mansonone G By β-Cyclodextrin-Based Host-Guest Complexation: A Computational and Experimental Study
Cited by: 40
Author(s): Panupong Mahalapbutr, Piyanuch Wonganan, Thanapon Charoenwongpaiboon, Manchumas Hengsakul Prousoontorn, Warinthorn Chavasiri, Thanyada Rungrotmongkol
Software Mentions: 1
Published: about 5 years ago

10.3390/biom11091349

Advanced Molecular Dynamics Approaches to Model a Tertiary Complex APRIL/TACI with Long Glycosaminoglycans
Cited by: 5
Author(s): Mateusz Marcisz, Martyna Maszota‐Zieleniak, Bertrand Huard, Sergey A. Samsonov
Software Mentions: 1
Published: about 3 years ago

10.1177/1073274819856885

Overall Results for a National Program of Photodynamic Therapy for Basal Cell Carcinoma: A Multicenter Clinical Study to Bring New Techniques to Social Health Care
Cited by: 19
Author(s): Hilde Harb Buzzá, Lílian Tan Moriyama, José Dirceu Vollet‐Filho, Natália Mayumi Inada, Ana Paula da Silva, Mirian Denise Stringasci, Michelle Barreto Requena, Cintia Teles de Andrade, Kate Cristina Blanco, Dora Patrícia Ramirez, Cristina Kurachi, Ana Gabriela Sálvio, Vanderlei Salvador Bagnato
Software Mentions: 1
Published: almost 6 years ago

10.1186/1475-2875-11-10

Novel strategies lead to pre-elimination of malaria in previously high-risk areas in Suriname, South America
Cited by: 42
Author(s): Hélène Hiwat, L. Hardjopawiro, Willem Takken, Leopoldo Villegas
Software Mentions: 1
Published: almost 13 years ago

10.3390/md19070367

Potency- and Selectivity-Enhancing Mutations of Conotoxins for Nicotinic Acetylcholine Receptors Can Be Predicted Using Accurate Free-Energy Calculations
Cited by: 8
Author(s): Dana Katz, Michael A. DiMattia, Daniel J. Sindhikara, Hubert Li, Nikita Abraham, Abba E. Leffler
Software Mentions: 1
Published: over 3 years ago

10.3390/ma9060482

Spark Plasma Co-Sintering of Mechanically Milled Tool Steel and High Speed Steel Powders.
Cited by: 8
Author(s): M. Pellizzari, A. Fedrizzi, M. Zadra
Software Mentions: 1
Published: over 8 years ago

10.1007/s00044-016-1591-1

Identification of novel natural compound inhibitors for human complement component 5a receptor by homology modeling and virtual screening
Cited by: 14
Author(s): Faraz Shaikh, Yain-Whar Si
Software Mentions: 1
Published: over 8 years ago

10.3390/molecules26020493

Achiral Molecular Recognition of Substituted Aniline Position Isomers by Crown Ether Type Chiral Stationary Phase
Cited by: 9
Author(s): Akira Ohnishi, Tsugumichi Shibata, Tatsuya Imase, Satoshi Shinkura, Kanji Nagai
Software Mentions: 1
Published: almost 4 years ago

10.3390/molecules25143178

Alkyl and Aryl Derivatives Based on p-Coumaric Acid Modification and Inhibitory Action against Leishmania braziliensis and Plasmodium falciparum
Cited by: 22
Author(s): Susiany P. Lopes, Lina M. Yepes, Yunierkis Pérez-Castillo, Sara M. Robledo, Damião Pergentino de Sousa
Software Mentions: 1
Published: over 4 years ago

10.3390/molecules24061021

Molecular Simulation of the Separation of Isoleucine Enantiomers by β-Cyclodextrin
Cited by: 12
Author(s): E. Alvira
Software Mentions: 1
Published: over 5 years ago

10.3390/molecules22010079

Computer-Aided Drug Design Using Sesquiterpene Lactones as Sources of New Structures with Potential Activity against Infectious Neglected Diseases
Cited by: 31
Author(s): Chonny Herrera‐Acevedo, Luciana Scotti, Mateus Feitosa Alves, Margareth de Fátima Formiga Melo Diniz
Software Mentions: 1
Published: almost 8 years ago

10.3390/molecules201219865

Unfolded Protein Response and Macroautophagy in Alzheimer’s, Parkinson’s and Prion Diseases
Cited by: 29
Author(s): Irina Milisav, Dušan Šuput, Samo Ribarič
Software Mentions: 1
Published: almost 9 years ago

10.3390/molecules191119152

Spectral and Kinetic Properties of Radicals Derived from Oxidation of Quinoxalin-2-One and Its Methyl Derivative
Cited by: 7
Author(s): Konrad Skotnicki, Julio R. De la Fuente, Álvaro Cañete, Krzysztof Bobrowski
Software Mentions: 1
Published: about 10 years ago

10.3390/molecules23113018

Prediction of GluN2B-CT1290-1310/DAPK1 Interaction by Protein–Peptide Docking and Molecular Dynamics Simulation
Cited by: 15
Author(s): Gao Tu, Tingting Fu, Fengyuan Yang, Lixia Yao, Weiwei Xue, Feng Zhu
Software Mentions: 1
Published: about 6 years ago

10.3390/molecules26092605

Predicting Accurate Lead Structures for Screening Molecular Libraries: A Quantum Crystallographic Approach
Cited by: 0
Author(s): Suman Kumar Mandal, Parthapratim Munshi
Software Mentions: 1
Published: over 3 years ago

10.3390/molecules26113264

Development of Halogenated Pyrazolines as Selective Monoamine Oxidase-B Inhibitors: Deciphering via Molecular Dynamics Approach
Cited by: 8
Author(s): Aathira Sujathan Nair, Jong‐Min Oh, Vishal Payyalot Koyiparambath, Sunil Kumar, Sachithra Thazhathuveedu Sudevan, Opeyemi Soremekun, Mahmoud E. S. Soliman, Ahmed Khames, Mohamed A. Abdelgawad, Leena K. Pappachen, Bijo Mathew, Hoon Kim
Software Mentions: 1
Published: over 3 years ago

10.3390/molecules22071143

Review of Ligand Specificity Factors for CYP1A Subfamily Enzymes from Molecular Modeling Studies Reported to-Date
Cited by: 41
Author(s): Jayalakshmi Sridhar, Navneet Goyal, Jiawang Liu, Maryam Foroozesh
Software Mentions: 1
Published: over 7 years ago

10.3390/molecules26082383

An Effective MM/GBSA Protocol for Absolute Binding Free Energy Calculations: A Case Study on SARS-CoV-2 Spike Protein and the Human ACE2 Receptor
Cited by: 39
Author(s): Negin Forouzesh, Nikita Mishra
Software Mentions: 1
Published: over 3 years ago

10.3390/molecules26051302

Interactions of Sea Anemone Toxins with Insect Sodium Channel—Insights from Electrophysiology and Molecular Docking Studies
Cited by: 4
Author(s): Beata Niklas, Milena Jankowska, Dalia Gordon, L. Béress, Maria Stankiewicz, Wiesław Nowak
Software Mentions: 1
Published: over 3 years ago

10.3390/molecules24224116

Identification of The Fipronil Resistance Associated Mutations in Nilaparvata lugens GABA Receptors by Molecular Modeling
Cited by: 13
Author(s): Yafeng Tian, Ya Gao, Yanming Chen, Genyan Liu, Xin Ju
Software Mentions: 1
Published: about 5 years ago

10.3390/molecules24040750

Chlamyphilone, a Novel Pochonia chlamydosporia Metabolite with Insecticidal Activity
Cited by: 11
Author(s): Federica Lacatena, Roberta Marra, Pierluigi Mazzei, Alessandro Piccolo, M. Cristina Digilio, Massimo Giorgini, Sheridan Lois Woo, Pierpaolo Cavallo, Matteo Lorito, Francesco Vinale
Software Mentions: 1
Published: almost 6 years ago

10.3390/molecules26195780

The Design, Synthesis, and Biological Activities of Pyrrole-Based Carboxamides: The Novel Tubulin Inhibitors Targeting the Colchicine-Binding Site
Cited by: 11
Author(s): Sergei Boichuk, Aigul Galembikova, Kirill Syuzov, Pavel Dunaev, Firuza Bikinieva, Aida Aukhadieva, С. С. Зыкова, Н. М. Игидов, Ksenia Gankova, М. В. Новикова, Pavel Kopnin
Software Mentions: 1
Published: about 3 years ago

10.3390/molecules25133084

Iron’s Wake: The Performance of Quantum Mechanical-Derived Versus General-Purpose Force Fields Tested on a Luminescent Iron Complex
Cited by: 7
Author(s): Valentin Diez‐Cabanes, Giacomo Prampolini, Antonio Francés‐Monerris, Antonio Monari, Mariachiara Pastore
Software Mentions: 1
Published: over 4 years ago

10.3390/molecules25051165

Interaction of Coumarin Phytoestrogens with ERα and ERβ: A Molecular Dynamics Simulation Study
Cited by: 10
Author(s): Ting Wang, Yunfei Wang, Xuming Zhuang, Feng Luan, Chunyan Zhao, M. Natália D. S. Cordeiro
Software Mentions: 1
Published: over 4 years ago

10.3390/molecules25204683

Kaempferol Facilitated Extinction Learning in Contextual Fear Conditioned Rats via Inhibition of Fatty-Acid Amide Hydrolase
Cited by: 11
Author(s): Hammad Ahmad, Khalid Rauf, Wahid Zada, Margaret M. McCarthy, Ghulam Abbas, Fareeha Anwar, Abdul Jabbar Shah
Software Mentions: 1
Published: about 4 years ago

10.3390/molecules26082211

Identification of Vinyl Sulfone Derivatives as EGFR Tyrosine Kinase Inhibitor: In Vitro and In Silico Studies
Cited by: 19
Author(s): Thitinan Aiebchun, Panupong Mahalapbutr, Atima Auepattanapong, Onnicha Khaikate, Supaphorn Seetaha, Lueacha Tabtimmai, Chutima Kuhakarn, Kiattawee Choowongkomon, Thanyada Rungrotmongkol
Software Mentions: 1
Published: over 3 years ago

10.3390/molecules26123730

Further Validation of Quantum Crystallography Approaches
Cited by: 6
Author(s): Monika Wanat, Maura Malińska, Anna A. Hoser, Krzysztof Woźniak
Software Mentions: 1
Published: over 3 years ago

10.3390/molecules17067415

Application of 4D-QSAR Studies to a Series of Raloxifene Analogs and Design of Potential Selective Estrogen Receptor Modulators
Cited by: 10
Author(s): Sodero Ac, Romeiro Nc, da Cunha Ef, de Oliveira Magalhaães U, de Alencastro Rb, Rodrígues Cr, Cabral Lm, Helena C. Castro, Magaly Girão Albuquerque
Software Mentions: 1
Published: over 12 years ago

10.7717/peerj.7832

Exploration of the selective binding mechanism of protein kinase Aurora A selectivity via a comprehensive molecular modeling study
Cited by: 5
Author(s): Zhe Zhang, Yafei Xu, Jian Wu, Ying Shen, Hao Cheng, Yi Xiang
Software Mentions: 1
Published: about 5 years ago

10.3390/ph11010022

A Novel Interaction Between the TLR7 and a Colchicine Derivative Revealed Through a Computational and Experimental Study
Cited by: 3
Author(s): Francesco Gentile, Marco Agostino Deriu, Khaled Barakat, Andrea Danani, Jack A. Tuszyński
Software Mentions: 1
Published: almost 7 years ago

10.3390/ph5060591

a-Anilinoketones, Esters and Amides: A Chemical Study
Cited by: 8
Author(s): Amjad M. Qandil, Lara Fakhouri
Software Mentions: 1
Published: over 12 years ago

10.3390/pharmaceutics10040233

In Vitro and In Silico Analyses of Nicotine Release from a Gelisphere-Loaded Compressed Polymeric Matrix for Potential Parkinson’s Disease Interventions
Cited by: 6
Author(s): Pradeep Kumar, Yahya E. Choonara, Lisa C. du Toit, Neha Atulkumar Singh, Viness Pillay
Software Mentions: 1
Published: about 6 years ago

10.1371/journal.pcbi.1003874

Predicting the Functions and Specificity of Triterpenoid Synthases: A Mechanism-Based Multi-intermediate Docking Approach
Cited by: 22
Author(s): Bo Xue Tian, Frank Wallrapp, Gemma L. Holiday, Jeng Yeong Chow, Patricia C. Babbitt, C. Dale Poulter, Matthew P. Jacobson
Software Mentions: 1
Published: about 10 years ago

10.1371/journal.pcbi.1003742

Membrane Interaction of Bound Ligands Contributes to the Negative Binding Cooperativity of the EGF Receptor
Cited by: 39
Author(s): Anton Arkhipov, Yibing Shan, Eric T. Kim, David E. Shaw
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pcbi.1002083

Predicting Binding to P-Glycoprotein by Flexible Receptor Docking
Cited by: 90
Author(s): Elena Dolghih, Clifford Bryant, Adam R. Renslo, Matthew P. Jacobson
Software Mentions: 1
Published: over 13 years ago

10.1371/journal.pcbi.1002034

Accessing a Hidden Conformation of the Maltose Binding Protein Using Accelerated Molecular Dynamics
Cited by: 105
Author(s): Denis Bucher, Barry J. Grant, Phineus R. L. Markwick, J. Andrew McCammon
Software Mentions: 1
Published: over 13 years ago

10.1371/journal.pcbi.1006504

The Cultural Brain Hypothesis: How culture drives brain expansion, sociality, and life history
Cited by: 74
Author(s): Michael Muthukrishna, Michael Doebeli, Maciej Chudek, Joseph Henrich
Software Mentions: 1
Published: about 6 years ago

10.1371/journal.pcbi.1003686

ODE Constrained Mixture Modelling: A Method for Unraveling Subpopulation Structures and Dynamics
Cited by: 46
Author(s): Jan Hasenauer, Christine Hasenauer, Tim Hucho, Fabian J. Theis
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pcbi.1000546

Investigation of the Interaction between the Large and Small Subunits of Potato ADP-Glucose Pyrophosphorylase
Cited by: 23
Author(s): İbrahim Barış, Aytuğ Tuncel, Natali Özber, Özlem Keskin, İbrahim Halil Kavaklı
Software Mentions: 1
Published: about 15 years ago

10.1371/journal.pcbi.1008767

Deep6mA: A deep learning framework for exploring similar patterns in DNA N6-methyladenine sites across different species
Cited by: 26
Author(s): Zutan Li, Hangjin Jiang, Lingpeng Kong, Yuanyuan Chen, Kun Lang, Xiaodan Fan, Liangyun Zhang, Cong Pian
Software Mentions: 1
Published: almost 4 years ago

10.1371/journal.pone.0143065

Investigating DNA Binding and Conformational Variation in Temperature Sensitive p53 Cancer Mutants Using QM-MM Simulations
Cited by: 8
Author(s): Shruti Koulgi, Archana Achalere, Uddhavesh Sonavane, Rajendra Joshi
Software Mentions: 1
Published: about 9 years ago

10.1371/journal.pone.0064675

Coarse-Grained/Molecular Mechanics of the TAS2R38 Bitter Taste Receptor: Experimentally-Validated Detailed Structural Prediction of Agonist Binding
Cited by: 63
Author(s): Alessandro Marchiori, Luciana Capece, Alejandro Giorgetti, Paolo Gasparini, Maik Behrens, Paolo Carloni, Wolfgang Meyerhof
Software Mentions: 1
Published: over 11 years ago

10.1371/journal.pone.0071340

An In Silico Analysis of the Binding Modes and Binding Affinities of Small Molecule Modulators of PDZ-Peptide Interactions
Cited by: 19
Author(s): Garima Tiwari, Debasisa Mohanty
Software Mentions: 1
Published: over 11 years ago

10.1371/journal.pone.0137897

Glycosylation Effects on FSH-FSHR Interaction Dynamics: A Case Study of Different FSH Glycoforms by Molecular Dynamics Simulations
Cited by: 28
Author(s): Biswa Ranjan Meher, Anshuman Dixit, George R. Bousfield, Gerald H. Lushington
Software Mentions: 1
Published: about 9 years ago

10.1371/journal.pone.0070521

Conformational Stability of Fibrillar Amyloid-Beta Oligomers via Protofilament Pair Formation – A Systematic Computational Study
Cited by: 63
Author(s): Anna K. Kähler, Heinrich Sticht, Anselm H. C. Horn
Software Mentions: 1
Published: over 11 years ago

10.1371/journal.pone.0228153

Novel MscL agonists that allow multiple antibiotics cytoplasmic access activate the channel through a common binding site
Cited by: 13
Author(s): Robin Wray, Junmei Wang, Irene Iscla, Paul Blount
Software Mentions: 1
Published: almost 5 years ago

10.1371/journal.pone.0120675

Assessment of In Vivo and In Vitro Genotoxicity of Glibenclamide in Eukaryotic Cells
Cited by: 16
Author(s): Juliane Rocha de Sant’Anna, Claudinéia Conationi da Silva Franco, Paulo Cézar de Freitas Mathias, Marialba Avezum Alves de Castro-Prado
Software Mentions: 1
Published: over 9 years ago

10.1371/journal.pone.0077081

Discovery of Mycobacterium tuberculosis Protein Tyrosine Phosphatase B (PtpB) Inhibitors from Natural Products
Cited by: 45
Author(s): Alessandra Mascarello, Mattia Mori, Louise Domeneghini Chiaradia-Delatorre, Angela Camila Orbem Menegatti, Franco Delle Monachè, Franco Ferrari, Rosendo A. Yunes, Ricardo José Nunes, Hernán Terenzi, Bruno Botta, Maurizio Botta
Software Mentions: 1
Published: about 11 years ago

10.1371/journal.pone.0161868

Computational Investigation of the Interplay of Substrate Positioning and Reactivity in Catechol O-Methyltransferase
Cited by: 34
Author(s): Niladri Patra, Efthymios Ioannis Ioannidis, Heather J. Kulik
Software Mentions: 1
Published: about 8 years ago

10.1371/journal.pone.0073344

Locking the 150-Cavity Open: In Silico Design and Verification of Influenza Neuraminidase Inhibitors
Cited by: 2
Author(s): Nanyu Han, Yuguang Mu
Software Mentions: 1
Published: about 11 years ago

10.1371/journal.pone.0090799

Molecular Modeling Study on the Allosteric Inhibition Mechanism of HIV-1 Integrase by LEDGF/p75 Binding Site Inhibitors
Cited by: 18
Author(s): Weiwei Xue, Huanxiang Liu, Xiaojun Yao
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pone.0227637

Hesperidin improves insulin resistance via down-regulation of inflammatory responses: Biochemical analysis and in silico validation
Cited by: 17
Author(s): Kanwal Rehman, Syeda Mehak Munawar, Muhammad Sajid Hamid Akash, Manal Buabeid, Tahir Ali Chohan, Muhammad Tariq, Komal Jabeen, El‐Shaimaa A. Arafa
Software Mentions: 1
Published: almost 5 years ago

10.1371/journal.pone.0221032

Computational and experimental elucidation of Plasmodium falciparum phosphoethanolamine methyltransferase inhibitors: Pivotal drug target
Cited by: 5
Author(s): Jagbir Singh, Sonam Vijay, Rani Mansuri, Ritu Rawal, Kavita Kadian, Ganesh Chandra Sahoo, Mahesh Kumar, Arun Dev Sharma
Software Mentions: 1
Published: over 5 years ago

10.1371/journal.pone.0210869

Thioguanine-based DENV-2 NS2B/NS3 protease inhibitors: Virtual screening, synthesis, biological evaluation and molecular modelling
Cited by: 30
Author(s): Maywan Hariono, Sy Bing Choi, Ros Fatihah Roslim, Mohamed Sufian Mohd. Nawi, Mei Lan Tan, Ezatul Ezleen Kamarulzaman, Norita Mohamed, Rohana Yusof, Shatrah Othman, Noorsaadah Abd. Rahman, Rozana Othman, Habibah A. Wahab
Software Mentions: 1
Published: almost 6 years ago

10.1371/journal.pone.0024949

Identification of a Negative Allosteric Site on Human α4β2 and α3β4 Neuronal Nicotinic Acetylcholine Receptors
Cited by: 16
Author(s): Ryan E. Pavlovicz, Brandon J. Henderson, Andrew B. Bonnell, Ryan L. Boyd, Dennis B. McKay, Chenglong Li
Software Mentions: 1
Published: about 13 years ago

10.1371/journal.pone.0077141

Reaction Trajectory Revealed by a Joint Analysis of Protein Data Bank
Cited by: 16
Author(s): Zhong Ren
Software Mentions: 1
Published: about 11 years ago

10.1371/journal.pone.0194934

Interaction of microtubule depolymerizing agent indanocine with different human αβ tubulin isotypes
Cited by: 15
Author(s): Bajarang Vasant Kumbhar, Dulal Panda, Ambarish Kunwar
Software Mentions: 1
Published: over 6 years ago

10.1371/journal.pone.0152403

Determinants of Cofactor Specificity for the Glucose-6-Phosphate Dehydrogenase from Escherichia coli: Simulation, Kinetics and Evolutionary Studies
Cited by: 14
Author(s): Matías Fuentealba, Rodrigo A.A. Muñoz, Pablo Maturana, Adriana R. Krapp, Ricardo Cabrera
Software Mentions: 1
Published: over 8 years ago

10.1371/journal.pone.0109639

Study of the Affinity between the Protein Kinase PKA and Peptide Substrates Derived from Kemptide Using Molecular Dynamics Simulations and MM/GBSA
Cited by: 17
Author(s): Karel Mena-Ulecia, Ariela Vergara-Jaque, Horacio Poblete, William Tiznado, Julio Caballero
Software Mentions: 1
Published: about 10 years ago

10.1371/journal.pone.0078479

Differential Effects of Genistein on Prostate Cancer Cells Depend on Mutational Status of the Androgen Receptor
Cited by: 49
Author(s): Abeer M. Mahmoud, Tian Ran Zhu, Aijaz Parray, Hifzur R. Siddique, Wancai Yang, Mohammad Saleem, Maarten C. Bosland
Software Mentions: 1
Published: about 11 years ago

10.1371/journal.pone.0058173

T3_MM: A Markov Model Effectively Classifies Bacterial Type III Secretion Signals
Cited by: 35
Author(s): Yejun Wang, Miao‐Kun Sun, Hongchu Bao, Aaron P. White
Software Mentions: 1
Published: over 11 years ago

10.1371/journal.pone.0041479

Structure and Dynamics of Amyloid-β Segmental Polymorphisms
Cited by: 71
Author(s): Workalemahu M. Berhanu, Ulrich H. E. Hansmann
Software Mentions: 1
Published: over 12 years ago

10.1371/journal.pone.0147190

Exploration of Novel Inhibitors for Bruton’s Tyrosine Kinase by 3D QSAR Modeling and Molecular Dynamics Simulation
Cited by: 23
Author(s): Rohit Bavi, Raj Kumar, Light Choi, Keun Woo Lee
Software Mentions: 1
Published: almost 9 years ago

10.1371/journal.pone.0130203

Molecular Determinants Underlying Binding Specificities of the ABL Kinase Inhibitors: Combining Alanine Scanning of Binding Hot Spots with Network Analysis of Residue Interactions and Coevolution
Cited by: 31
Author(s): Amanda Tse, Gennady M. Verkhivker
Software Mentions: 1
Published: over 9 years ago

10.1371/journal.pone.0149014

Hydrophobic Interactions Are a Key to MDM2 Inhibition by Polyphenols as Revealed by Molecular Dynamics Simulations and MM/PBSA Free Energy Calculations
Cited by: 61
Author(s): Subhash Verma, Sonam Grover, Chetna Tyagi, Sumit Goyal, Salma Jamal, Aditi Singh, Abhinav Grover
Software Mentions: 1
Published: almost 9 years ago

10.1371/journal.pone.0030904

Enhanced Functional Recovery in MRL/MpJ Mice after Spinal Cord Dorsal Hemisection
Cited by: 33
Author(s): Sandrine Thuret, Michaela Thallmair, Laura L. Horky, Fred H. Gage
Software Mentions: 1
Published: almost 13 years ago

10.1371/journal.pone.0143752

Dancing through Life: Molecular Dynamics Simulations and Network-Centric Modeling of Allosteric Mechanisms in Hsp70 and Hsp110 Chaperone Proteins
Cited by: 45
Author(s): Gabrielle Stetz, Gennady M. Verkhivker
Software Mentions: 1
Published: almost 9 years ago

10.1371/journal.pone.0190267

Atomistic simulations and network-based modeling of the Hsp90-Cdc37 chaperone binding with Cdk4 client protein: A mechanism of chaperoning kinase clients by exploiting weak spots of intrinsically dynamic kinase domains
Cited by: 32
Author(s): Josh Czemeres, Kurt Buse, Gennady M. Verkhivker
Software Mentions: 1
Published: almost 7 years ago

10.1371/journal.pone.0096031

Resolving Hot Spots in the C-Terminal Dimerization Domain that Determine the Stability of the Molecular Chaperone Hsp90
Cited by: 25
Author(s): Emanuele Ciglia, Janina Vergin, Sven Reimann, Sander H. J. Smits, Lutz Schmitt, Georg Groth, Holger Gohlke
Software Mentions: 1
Published: over 10 years ago

10.3390/cancers13174332

Minimal Residual Disease in Multiple Myeloma: Something Old, Something New
Cited by: 6
Author(s): Carlos Bravo-Pérez, M. A. Sola, Raúl Teruel‐Montoya, María-Dolores García-Malo, Francisco José Ortuño, Vicente Vicente, Felipe de Arriba, Andrés Jerez
Software Mentions: 1
Published: about 3 years ago