pypi: acpype | Projects | Ecosyste.ms: Papers

10.1371/journal.ppat.1009729

Definition of the immune evasion-replication interface of rabies virus P protein
Cited by: 10
Author(s): Jingyu Zhan, Angela R. Harrison, Stephanie Portelli, Thanh Bình Nguyễn, Isshu Kojima, Siqiong Zheng, Fei Yan, Tsutomu Matsui, Stephen M. Rawlinson, Ashish Sethi, Naoto Ito, David B. Ascher, Gregory W. Moseley, Paul R. Gooley
Software Mentions: 5
Published: almost 3 years ago

10.1186/s13321-020-00451-6

Intuitive, reproducible high-throughput molecular dynamics in Galaxy: a tutorial
Cited by: 9
Author(s): Simon Bray, Tharindu Senapathi, Christopher B. Barnett, Björn Grüning
Software Mentions: 4
Published: over 3 years ago

10.3389/fphar.2017.00393

Molecular Simulations of Carbohydrates with a Fucose-Binding Burkholderia ambifaria Lectin Suggest Modulation by Surface Residues Outside the Fucose-Binding Pocket
Cited by: 6
Author(s): Tamir Dingjan, Anne Imberty, Serge Pérez, Elizabeth Yuriev, Paul A. Ramsland
Software Mentions: 3
Published: almost 7 years ago

10.3389/fmolb.2021.643728

Structural Design and Analysis of the RHOA-ARHGEF1 Binding Mode: Challenges and Applications for Protein-Protein Interface Prediction
Cited by: 1
Author(s): Ennys Gheyouche, Matthias Bagueneau, Gervaise Loirand, Bernard Offmann, Stéphane Téletchéa
Software Mentions: 3
Published: about 3 years ago

10.1371/journal.pone.0172743

Waterdock 2.0: Water placement prediction for Holo-structures with a pymol plugin
Cited by: 35
Author(s): Akshay Sridhar, Gregory A. Ross, Philip C. Biggin
Software Mentions: 3
Published: over 7 years ago

10.1038/s41598-019-48155-8

Solution structure of the autophagy-related protein LC3C reveals a polyproline II motif on a mobile tether with phosphorylation site
Cited by: 11
Author(s): Carsten Krichel, Christina Möckel, Oliver Schillinger, Pitter F. Huesgen, Heinrich Sticht, Birgit Strodel, Oliver H. Weiergräber, Dieter Willbold, Philipp Neudecker
Software Mentions: 3
Published: over 4 years ago

10.1186/1756-0500-5-367

ACPYPE - AnteChamber PYthon Parser interfacE
Cited by: 1,683
Author(s): Alan Wilter Sousa da Silva, Wim Vranken
Software Mentions: 2
Published: almost 12 years ago

10.1093/bioinformatics/btx037

Ligandbook: an online repository for small and drug-like molecule force field parameters
Cited by: 15
Author(s): Jan Domański, Oliver Beckstein, Bogdan I. Iorga
Software Mentions: 2
Published: over 7 years ago

10.3390/biom9100633

Disclosing the Impact of Carcinogenic SF3b Mutations on Pre-mRNA Recognition Via All-Atom Simulations
Cited by: 20
Author(s): Jure Borišek, Andrea Saltalamacchia, Anna Gallì, Giulia Palermo, Elisabetta Molteni, Luca Malcovati, Alessandra Magistrato
Software Mentions: 2
Published: over 4 years ago

10.1371/journal.pone.0071380

Structural Dynamics of Human Telomeric G-Quadruplex Loops Studied by Molecular Dynamics Simulations
Cited by: 28
Author(s): Hong Zhu, Shiyan Xiao, Haojun Liang
Software Mentions: 2
Published: almost 11 years ago

10.1371/journal.pone.0043253

Modeling of Arylamide Helix Mimetics in the p53 Peptide Binding Site of hDM2 Suggests Parallel and Anti-Parallel Conformations Are Both Stable
Cited by: 16
Author(s): Jonathan C. Fuller, Richard M. Jackson, Thomas A. Edwards, Andrew J. Wilson, Michael R. Shirts
Software Mentions: 2
Published: almost 12 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: almost 3 years ago

10.1039/c5sc02678d

Accurate calculation of the absolute free energy of binding for drug molecules
Cited by: 229
Author(s): Matteo Aldeghi, Alexander Heifetz, Michael J. Bodkin, S. Knapp, Philip C. Biggin
Software Mentions: 2
Published: over 8 years ago

10.1038/s41598-020-58877-9

Improvement in predicting drug sensitivity changes associated with protein mutations using a molecular dynamics based alchemical mutation method
Cited by: 5
Author(s): Fumie Ono, Shuntaro Chiba, Yuta Isaka, Shigeyuki Matsumoto, Biao Ma, Ryohei Katayama, Mitsugu Araki, Yasushi Okuno
Software Mentions: 2
Published: over 4 years ago

10.3390/jfb6020171

Carbohydrate-Derived Amphiphilic Macromolecules: A Biophysical Structural Characterization and Analysis of Binding Behaviors to Model Membranes
Cited by: 1
Author(s): Adriana A. T. Martin, Michael D. Tomasini, Vladyslav Kholodovych, Li Gu, Sven D. Sommerfeld, Kathryn E. Uhrich, N. Sanjeeva Murthy, William J. Welsh, Prabhas V. Moghe
Software Mentions: 2
Published: about 9 years ago

10.3390/ijms150915994

In Silico Discovery of Potential VEGFR-2 Inhibitors from Natural Derivatives for Anti-Angiogenesis Therapy
Cited by: 44
Author(s): Jing Li, Nan Zhou, Kun Luo, Wei Zhang, Xinru Li, Chuanfang Wu, Ji Bao
Software Mentions: 2
Published: over 9 years ago

10.1007/s00249-019-01407-x

Effect of lipid saturation on amyloid-beta peptide partitioning and aggregation in neuronal membranes: molecular dynamics simulations
Cited by: 20
Author(s): Nikolaos Ntarakas, Inna Ermilova, Alexander P. Lyubartsev
Software Mentions: 1
Published: over 4 years ago

10.3389/fchem.2020.582861

Virtual Screening and Bioactivity Evaluation of Novel Androgen Receptor Antagonists From Anti-PCa Traditional Chinese Medicine Prescriptions
Cited by: 9
Author(s): Han Wei, Yong Shi, Jie Su, Zhennan Zhao, Xin Wang, Jiazhong Li, Huanxiang Liu
Software Mentions: 1
Published: over 3 years ago

10.3389/fchem.2020.00164

In silico Design of Novel HIV-1 NNRTIs Based on Combined Modeling Studies of Dihydrofuro[3,4-d]pyrimidines
Cited by: 24
Author(s): Yanming Chen, Yafeng Tian, Ya Gao, Fengshou Wu, Xiaogang Luo, Xin Ju, Genyan Liu
Software Mentions: 1
Published: about 4 years ago

10.1371/journal.pone.0104778

On Calculation of the Electrostatic Potential of a Phosphatidylinositol Phosphate-Containing Phosphatidylcholine Lipid Membrane Accounting for Membrane Dynamics
Cited by: 4
Author(s): Jonathan C. Fuller, Michael D. Martinez, Rebecca C. Wade
Software Mentions: 1
Published: almost 10 years ago

10.1371/journal.pcbi.1003114

Molecular Mechanisms in the Activation of Abscisic Acid Receptor PYR1
Cited by: 18
Author(s): Lyudmyla Dorosh, Olesya A. Kharenko, Nandhakishore Rajagopalan, Michèle C. Loewen, Maria Stepanova
Software Mentions: 1
Published: almost 11 years ago

10.3390/pharmaceutics10030101

Relative Contributions of Solubility and Mobility to the Stability of Amorphous Solid Dispersions of Poorly Soluble Drugs: A Molecular Dynamics Simulation Study
Cited by: 17
Author(s): Michael Brunsteiner, Johannes G. Khinast, Amrit Paudel
Software Mentions: 1
Published: almost 6 years ago

10.1007/s10822-017-0074-x

Prediction of binding poses to FXR using multi-targeted docking combined with molecular dynamics and enhanced sampling
Cited by: 5
Author(s): Soumendranath Bhakat, Emil Åberg, Pär Söderhjelm
Software Mentions: 1
Published: over 6 years ago

10.1371/journal.ppat.1007951

Molecular basis for functional diversity among microbial Nep1-like proteins
Cited by: 19
Author(s): Tea Lenarčič, Katja Pirc, Vesna Hodnik, Isabell Albert, Jure Borišek, Alessandra Magistrato, Thorsten Nürnberger, Marjetka Podobnik, Gregor Anderluh
Software Mentions: 1
Published: over 4 years ago

10.3390/molecules25143171

Discovery of Novel Tankyrase Inhibitors through Molecular Docking-Based Virtual Screening and Molecular Dynamics Simulation Studies
Cited by: 18
Author(s): Vladimir Berishvili, А. Н. Куимов, A. E. Voronkov, Eugene V. Radchenko, Pradeep Kumar, Yahya E. Choonara, Viness Pillay, Ähmed Kamal, Vladimir A. Palyulin
Software Mentions: 1
Published: almost 4 years ago

10.1371/journal.pone.0118796

Inhibiting EGFR Dimerization Using Triazolyl-Bridged Dimerization Arm Mimics
Cited by: 30
Author(s): Laura E. Hanold, Krishnadev Oruganty, Norman T. Ton, Aaron M. Beedle, Natarajan Kannan, Eileen J. Kennedy
Software Mentions: 1
Published: about 9 years ago

10.1042/BJ20141223

Identification of key binding site residues of MCT1 for AR-C155858 reveals the molecular basis of its isoform selectivity
Cited by: 35
Author(s): Bethany Nancolas, Richard B. Sessions, Andrew P. Halestrap
Software Mentions: 1
Published: over 9 years ago

10.1371/journal.pone.0041070

The Impact of Small Molecule Binding on the Energy Landscape of the Intrinsically Disordered Protein C-Myc
Cited by: 61
Author(s): Julien Michel, Rémi Cuchillo
Software Mentions: 1
Published: almost 12 years ago

10.7554/eLife.64518

Development of antibacterial compounds that constrain evolutionary pathways to resistance
Cited by: 7
Author(s): Yanmin Zhang, Sourav Chowdhury, João V. Rodrigues, E. I. Shakhnovich
Software Mentions: 1
Published: almost 3 years ago

10.1038/s41598-020-59403-7

Conversion of chemical to mechanical energy by the nucleotide binding domains of ABCB1
Cited by: 5
Author(s): Dániel Szöllősi, Peter Chiba, Gergely Szakács, Thomas Stockner
Software Mentions: 1
Published: over 4 years ago

10.1038/s41598-021-83069-4

Imidazopyridine hydrazone derivatives exert antiproliferative effect on lung and pancreatic cancer cells and potentially inhibit receptor tyrosine kinases including c-Met
Cited by: 19
Author(s): Tahereh Damghani, Fatemeh Moosavi, Mahsima Khoshneviszadeh, Mojtaba Mortazavi, Somayeh Pirhadi, Zahra Kayani, Luciano Saso, Najmeh Edraki, Omidreza Firuzi
Software Mentions: 1
Published: over 3 years ago

10.1016/j.csbj.2014.12.002

What can we learn from molecular dynamics simulations for GPCR drug design?
Cited by: 55
Author(s): Christofer S. Tautermann, Daniel Seeliger, Jan M. Kriegl
Software Mentions: 1
Published: over 9 years ago

Ecosyste.ms: Papers

Projects: pypi: acpype

Papers Mentioning acpype 32