pypi: gromacs | Projects | Ecosyste.ms: Papers

10.1016/j.csbj.2021.05.005

Comparison of the pH- and thermally-induced fluctuations of a therapeutic antibody Fab fragment by molecular dynamics simulation
Cited by: 6
Author(s): Cheng Zhang, Nuria Codina, Jiazhi Tang, Haoran Yu, Nesrine Chakroun, Frank Kozielski, Paul A. Dalby
Software Mentions: 6
Published: over 3 years ago

10.1111/acel.12296

Proteins in aggregates functionally impact multiple neurodegenerative disease models by forming proteasome‐blocking complexes
Cited by: 51
Author(s): Srinivas Ayyadevara, Meenakshisundaram Balasubramaniam, Yuan Gao, Li‐Rong Yu, Ramani Alla, Robert Shmookler Reis
Software Mentions: 5
Published: almost 10 years ago

10.1002/2211-5463.12491

Crystal structure of the retroviral protease‐like domain of a protozoal <scp>DNA</scp> damage‐inducible 1 protein
Cited by: 9
Author(s): Sushant Kumar, K. Suguna
Software Mentions: 5
Published: about 6 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

10.7554/eLife.66662

Homo-oligomerization of the human adenosine A2A receptor is driven by the intrinsically disordered C-terminus
Cited by: 9
Author(s): Khanh D. Nguyen, Michael Vigers, Eric Sefah, Susanna Seppälä, Jennifer Paige Hoover, Nicole S. Schonenbach, Blake Mertz, Michelle O’Malley, Songi Han
Software Mentions: 4
Published: about 3 years ago

10.1371/journal.pone.0200607

In Silico evaluation and identification of fungi capable of producing endo-inulinase enzyme
Cited by: 9
Author(s): Jayaram Chikkerur, A.K. Samanta, A. Dhali, Atul P. Kolte, Sohini Roy, M. Pratheepa
Software Mentions: 4
Published: about 6 years ago

10.12688/f1000research.6831.1

Molecular Dynamics Simulations of the Temperature Induced Unfolding of Crambin Follow the Arrhenius Equation.
Cited by: 3
Author(s): Andrew R. Dalby, Mohd Shahir Shamsir
Software Mentions: 4
Published: about 9 years ago

10.1111/j.1747-0285.2011.01101.x

Applying Molecular Dynamics Simulations to Identify Rarely Sampled Ligand‐bound Conformational States of Undecaprenyl Pyrophosphate Synthase, an Antibacterial Target
Cited by: 37
Author(s): William Sinko, César de Oliveira, S. Williams, Adam Van Wynsberghe, Jacob D. Durrant, Rong Cao, Eric Oldfield, J. Andrew McCammon
Software Mentions: 4
Published: over 13 years ago

10.1038/s41598-019-47249-7

Differential binding affinity of tau repeat region R2 with neuronal-specific β-tubulin isotypes
Cited by: 13
Author(s): Vishwambhar Vishnu Bhandare, Bajarang Vasant Kumbhar, Ambarish Kunwar
Software Mentions: 3
Published: about 5 years ago

10.1038/s41598-020-58138-9

Structural characterization and in-silico analysis of Momordica charantia 7S globulin for stability and ACE inhibition
Cited by: 26
Author(s): Pooja Kesari, Shivendra Pratap, Poonam Dhankhar, Vikram Dalal, Manisha Mishra, Pradyumna Kumar Singh, Harsh Chauhan, Pravindra Kumar
Software Mentions: 3
Published: over 4 years ago

10.1002/2211-5463.12225

Analyzing the role of CagV, a VirB8 homolog of the type <scp>IV</scp> secretion system of Helicobacter pylori
Cited by: 10
Author(s): Navin Kumar, Mohd Shariq, Amarjeet Kumar, Rajesh Kumari, Naidu Subbarao, Rakesh K. Tyagi, Gauranga Mukhopadhyay
Software Mentions: 3
Published: over 7 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: over 5 years ago

10.1002/2211-5463.12053

A disulfide bridge in the calcium binding site of a polyester hydrolase increases its thermal stability and activity against polyethylene terephthalate
Cited by: 80
Author(s): Johannes Then, Ren Wei, Thorsten Oeser, André Gerdts, Juliane Schmidt, Markus Barth, Wolfgang Zimmermann
Software Mentions: 3
Published: over 8 years ago

10.1083/jcb.202011078

Cysteine cross-linking in native membranes establishes the transmembrane architecture of Ire1
Cited by: 6
Author(s): Kristina Väth, Carsten Mattes, John F. Reinhard, Roberto Covino, Heike Stumpf, Gerhard Hummer, Robert Ernst
Software Mentions: 3
Published: about 3 years ago

10.3389/fpls.2017.00609

In Silico Identification of Mimicking Molecules as Defense Inducers Triggering Jasmonic Acid Mediated Immunity against Alternaria Blight Disease in Brassica Species
Cited by: 41
Author(s): Rajesh Kumar Pathak, Mamta Baunthiyal, Rohit Shukla, Dinesh Pandey, Gohar Taj, Anil Kumar
Software Mentions: 3
Published: over 7 years ago

10.1155/2013/697051

In SilicoScreening and Molecular Dynamics Simulation of Disease-Associated nsSNP in TYRP1 Gene and Its Structural Consequences in OCA3
Cited by: 63
Author(s): Balu Kamaraj, Rituraj Purohit
Software Mentions: 3
Published: over 11 years ago

10.1371/journal.pcbi.1007777

Molecular mechanism for bidirectional regulation of CD44 for lipid raft affiliation by palmitoylations and PIP2
Cited by: 18
Author(s): Fude Sun, Carsten Schroer, Carlos R Palacios, Libin Xu, Shi-Zhong Luo, Siewert J. Marrink
Software Mentions: 3
Published: over 4 years ago

10.3389/fphar.2015.00248

Molecular features of interaction between VEGFA and anti-angiogenic drugs used in retinal diseases: a computational approach
Cited by: 69
Author(s): Chiara Bianca Maria Platania, Luisa Di Paola, Gian Marco Leggio, Giovanni Luca Romano, Filippo Drago, Salvatore Salomone, Claudio Bucolo
Software Mentions: 3
Published: almost 9 years ago

10.1116/1.4971381

Predicting the orientation of protein G B1 on hydrophobic surfaces using Monte Carlo simulations
Cited by: 25
Author(s): Elisa T. Harrison, Tobias Weidner, David G. Castner, Gianluca Interlandi
Software Mentions: 3
Published: almost 8 years ago

10.1111/febs.13208

‘Dopamine‐first’ mechanism enables the rational engineering of the norcoclaurine synthase aldehyde activity profile
Cited by: 60
Author(s): Benjamin R. Lichman, Markus Gershater, Eleanor D. Lamming, Thomas Pesnot, Altin Sula, Nicholas H. Keep, Helen C. Hailes, John M. Ward
Software Mentions: 3
Published: over 9 years ago

10.1371/journal.pone.0234836

Comparative MD simulations and advanced analytics based studies on wild-type and hot-spot mutant A59G HRas
Cited by: 2
Author(s): Nitin Sharma, Uddhavesh Sonavane, Rajendra Joshi
Software Mentions: 2
Published: almost 4 years ago

10.1186/s13065-021-00777-8

Carcinogen-induced DNA structural distortion differences in the RAS gene isoforms; the importance of local sequence
Cited by: 2
Author(s): Georgina E. Menzies, Ian A. Prior, Andrea Brancale, Simon H. Reed, Paul D. Lewis
Software Mentions: 2
Published: about 3 years ago

10.6026/97320630016611

Molecular docking analysis of α2-containing GABAA receptors with benzimidazoles derivatives
Cited by: 3
Author(s): Abdellatif Bouayyadi, Aissam El Aliani, Yassine Kasmi, Ahmed Moussaïf, Najia El Abbadi, Abdelhalem Mesfioui, El Mokhtar Essassi, Mohammed El Mzibri
Software Mentions: 2
Published: about 4 years ago

10.1155/2016/7562368

Identification of Deleterious Mutations inMyostatinGene of Rohu Carp (Labeo rohita) Using Modeling and Molecular Dynamic Simulation Approaches
Cited by: 8
Author(s): Kiran D. Rasal, Vemulawada Chakrapani, Swagat Kumar Patra, SD Mohapatra, S.K. Nayak, Sasmita Jena, Jitendra Kumar Sundaray, P. Jayasankar, Hirak Kumar Barman
Software Mentions: 2
Published: over 8 years ago

10.3390/md18110579

Endolysins from Antarctic Pseudomonas Display Lysozyme Activity at Low Temperature
Cited by: 8
Author(s): Marco Orlando, Sandra Pucciarelli, Marina Lotti
Software Mentions: 2
Published: almost 4 years ago

10.1186/s43556-021-00050-3

Computationally repurposed drugs and natural products against RNA dependent RNA polymerase as potential COVID-19 therapies
Cited by: 9
Author(s): Sakshi Piplani, Puneet Kumar Singh, David A. Winkler, Nikolai Petrovsky
Software Mentions: 2
Published: almost 3 years ago

10.1111/j.1365-2958.2008.06508.x

Analysis of structure and function of the giant protein Pf332 inPlasmodium falciparum
Cited by: 38
Author(s): Anthony N. Hodder, Alexander G. Maier, Melanie Rug, Monica Brown, Mirja Hommel, Ivan Pantic, Marina Puig-de-Morales-Marinkovic, Brian J. Smith, Tony Triglia, James G. Beeson, Alan F. Cowman
Software Mentions: 2
Published: over 15 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: almost 7 years ago

10.1371/journal.pone.0076211

Sulfamethoxazole Induces a Switch Mechanism in T Cell Receptors Containing TCRVβ20-1, Altering pHLA Recognition
Cited by: 52
Author(s): Stephan Watkins, Werner J. Pichler
Software Mentions: 2
Published: almost 11 years ago

10.1371/journal.pone.0064364

Cancer Associated E17K Mutation Causes Rapid Conformational Drift in AKT1 Pleckstrin Homology (PH) Domain
Cited by: 48
Author(s): Ambuj Kumar, Rituraj Purohit
Software Mentions: 2
Published: over 11 years ago

10.1371/journal.pone.0077453

Molecular Dynamic Simulation Reveals Damaging Impact of RAC1 F28L Mutation in the Switch I Region
Cited by: 40
Author(s): Ambuj Kumar, Vidya Rajendran, Rao Sethumadhavan, Rituraj Purohit
Software Mentions: 2
Published: almost 11 years ago

10.1186/s12964-018-0239-9

The design of high affinity human PD-1 mutants by using molecular dynamics simulations (MD)
Cited by: 23
Author(s): Jiangfeng Du, Yijing Qin, Yahong Wu, Wenshan Zhao, Wenjie Zhai, Yuanming Qi, Chuchu Wang, Jiangfeng Du
Software Mentions: 2
Published: over 6 years ago

10.1039/d1sc00933h

Targeting structural features of viral genomes with a nano-sized supramolecular drug
Cited by: 5
Author(s): Lazaros Melidis, Iain B. Styles, Michael J. Hannon
Software Mentions: 2
Published: over 3 years ago

10.15252/embr.202052289

Role of FAM134 paralogues in endoplasmic reticulum remodeling, ER‐phagy, and Collagen quality control
Cited by: 42
Author(s): Alessio Reggio, Viviana Buonomo, Rayene Berkane, Ramachandra M Bhaskara, Mariana Edith Tellechea, Ilaria Peluso, Elena Polishchuk, Giorgia Di Lorenzo, Carmine Cirillo, Marianna Esposito, Adeela Hussain, Antje K. Huebner, Christian A. Hübner, Carmine Settembre, Gerhard Hummer, Paolo Grumati, Alexandra Stolz
Software Mentions: 2
Published: about 3 years ago

10.1111/febs.14175

An engineered photoswitchable mammalian pyruvate kinase
Cited by: 26
Author(s): Stefanie Gehrig, Jamie A. Macpherson, Paul C. Driscoll, Alastair Symon, Stephen R. Martin, James I. MacRae, Jens Kleinjung, Franca Fraternali, Dimitrios Anastasiou
Software Mentions: 2
Published: about 7 years ago

10.1002/2211-5463.12316

Evaluation of Sox2 binding affinities for distinct DNA patterns using steered molecular dynamics simulation
Cited by: 16
Author(s): Dhanusha Yesudhas, Muhammad Ayaz Anwar, Paladugu Suresh, Han-Kyul Kim, Sangdun Choi
Software Mentions: 2
Published: almost 7 years ago

10.1002/2211-5463.12069

Understanding the dynamics of monomeric, dimeric, and tetrameric α‐synuclein structures in water
Cited by: 14
Author(s): Jonathan Y. Mane, Maria Stepanova
Software Mentions: 2
Published: over 8 years ago

10.3389/fbioe.2019.00240

Structural Analysis of PfSec62-Autophagy Interacting Motifs (AIM) and PfAtg8 Interactions for Its Implications in RecovER-phagy in Plasmodium falciparum
Cited by: 2
Author(s): Ashalatha Sreshty Mamidi, Ananya Ray, Namita Surolia
Software Mentions: 2
Published: almost 5 years ago

10.3389/fnins.2016.00606

Mechanistic Insights into the Binding of Class IIa HDAC Inhibitors toward Spinocerebellar Ataxia Type-2: A 3D-QSAR and Pharmacophore Modeling Approach
Cited by: 7
Author(s): Siddharth Sinha, Sumit Goyal, Pallavi Somvanshi, Abhinav Grover
Software Mentions: 2
Published: over 7 years ago

10.1038/s41598-018-22883-9

Analysis of mutations in pncA reveals non-overlapping patterns among various lineages of Mycobacterium tuberculosis
Cited by: 3
Author(s): Ramani Baddam, Narender Kumar, Lothar H. Wieler, Aditya Kumar Lankapalli, Niyaz Ahmed, Sharon J. Peacock, Torsten Semmler
Software Mentions: 2
Published: over 6 years ago

10.1038/s41598-020-65288-3

Molecular Basis of Differential Stability and Temperature Sensitivity of ZIKA versus Dengue Virus Protein Shells
Cited by: 7
Author(s): Chinmai Pindi, Venkat R. Chirasani, Mohammad Homaidur Rahman, Mohd Ahsan, Prasanna D. Revanasiddappa, Sanjib Senapati
Software Mentions: 2
Published: over 4 years ago

10.1016/j.str.2018.05.001

Structural Basis of Phosphatidic Acid Sensing by APH in Apicomplexan Parasites
Cited by: 22
Author(s): Nick Darvill, David Jean Dubois, Sarah L. Rouse, Pierre‐Mehdi Hammoudi, Thomas C. A. Blake, Stefi Benjamin, Bing Liu, Dominique Soldati‐Favre, Steve Matthews
Software Mentions: 2
Published: about 6 years ago

10.1016/j.str.2018.12.007

Dynamic Role of the G Protein in Stabilizing the Active State of the Adenosine A2A Receptor
Cited by: 28
Author(s): Sangbae Lee, Anita K. Nivedha, Christopher G. Tate, Nagarajan Vaidehi
Software Mentions: 2
Published: over 5 years ago

10.3390/ijms19071933

p19-Targeting ILP Protein Blockers of IL-23/Th-17 Pro-Inflammatory Axis Displayed on Engineered Bacteria of Food Origin
Cited by: 15
Author(s): Katja Škrlec, Petra Zadravec, Marie Hlavničková, Milan Kuchař, Lucie Vaňková, Hana Petroková, Lucie Křížová, Jiří Černý, Aleš Berlec, Petr Mály
Software Mentions: 2
Published: about 6 years ago

10.1371/journal.pone.0175796

Interactions between mitoNEET and NAF-1 in cells
Cited by: 42
Author(s): Ola Karmi, Sarah H. Holt, Liang Song, Sagi Tamir, Yuting Luo, Fang Bai, Ammar Adenwalla, Merav Darash-Yahana, Yang-Sung Sohn, Patricia A. Jennings, Rajeev K. Azad, José N. Onuchic, Faruck Morcos, Rachel Nechushtai, Ron Mittler
Software Mentions: 1
Published: over 7 years ago

10.1002/2211-5463.12321

Cholera toxin B subunit induces local curvature on lipid bilayers
Cited by: 34
Author(s): Weria Pezeshkian, Lina J. Nåbo, John Hjort Ipsen
Software Mentions: 1
Published: almost 7 years ago

10.1371/journal.pone.0195792

Role of the keratin 1 and keratin 10 tails in the pathogenesis of ichthyosis hystrix of Curth Macklin
Cited by: 8
Author(s): Alessandro Terrinoni, Biagio Didona, Sabrina Caporali, Giovanni Chillemi, Alessandro Lo Surdo, Mauro Paradisi, Margherita Annichiarico-Petruzzelli, Eleonora Candi, Sergio Bernardini, Gerry Melino
Software Mentions: 1
Published: over 6 years ago

10.18502/jri.v21i4.4329

Estrogenic Effect of Scoparia dulcis (Linn) Extract in Mice Uterus and In Silico Molecular Docking Studies of Certain Compounds with Human Estrogen Receptors
Cited by: 2
Author(s): Khamhee Wangsa, Indira Sarma, Purbajyoti Saikia, Dhanabalan Ananthakrishnan, Hari Prasad Sarma, D. Velmurugan
Software Mentions: 1
Published: almost 4 years ago

10.1371/journal.pone.0214964

Identification of GCC-box and TCC-box motifs in the promoters of differentially expressed genes in rice (Oryza sativa L.): Experimental and computational approaches
Cited by: 2
Author(s): Gopal Kumar Prajapati, Bharati Pandey, Awdhesh Kumar Mishra, Kwang-Hyun Baek, Dev Mani Pandey
Software Mentions: 1
Published: over 5 years ago

10.3389/fmolb.2017.00085

Chlorophyll-Derivative Modulation of Rhodopsin Signaling Properties through Evolutionarily Conserved Interaction Pathways
Cited by: 9
Author(s): K. N. Woods, Jürgen Pfeffer, Judith Klein‐Seetharaman
Software Mentions: 1
Published: almost 7 years ago

10.3390/ijms19103089

ABD-Derived Protein Blockers of Human IL-17 Receptor A as Non-IgG Alternatives for Modulation of IL-17-Dependent Pro-Inflammatory Axis
Cited by: 9
Author(s): Marie Hlavničková, Milan Kuchař, Radim Osička, Lucie Vaňková, Hana Petroková, Michal Malý, Jiří Černý, Petr Arenberger, Petr Mály
Software Mentions: 1
Published: almost 6 years ago

10.1371/journal.pcbi.1003058

Probing the Energy Landscape of Activation Gating of the Bacterial Potassium Channel KcsA
Cited by: 35
Author(s): Tobias Linder, Bert L. de Groot, Anna Stary-Weinzinger
Software Mentions: 1
Published: over 11 years ago

10.3389/fpls.2016.00217

Improved Shoot Regeneration, Salinity Tolerance and Reduced Fungal Susceptibility in Transgenic Tobacco Constitutively Expressing PR-10a Gene
Cited by: 14
Author(s): Parinita Agarwal, Mitali Dabi, Prashant More, Khantika Patel, Kalyanashis Jana, Pradeep K. Agarwal
Software Mentions: 1
Published: over 8 years ago

10.1371/journal.pcbi.1003911

Lipid Clustering Correlates with Membrane Curvature as Revealed by Molecular Simulations of Complex Lipid Bilayers
Cited by: 184
Author(s): Heidi Koldsø, David Shorthouse, Jean Hélie, Mark S.P. Sansom
Software Mentions: 1
Published: almost 10 years ago

10.1016/j.jbc.2021.100282

The allosteric inhibition of glycine transporter 2 by bioactive lipid analgesics is controlled by penetration into a deep lipid cavity
Cited by: 6
Author(s): Katie A. Wilson, Shannon N. Mostyn, Zachary J. Frangos, Susan Shimmon, Tristan Rawling, Robert J. Vandenberg, Megan L. O’Mara
Software Mentions: 1
Published: over 3 years ago

10.1186/1423-0127-20-67

Whiskers-less HIV-protease: a possible way for HIV-1 deactivation
Cited by: 8
Author(s): Mohammad Reza Dayer, Mohammad Saaid Dayer
Software Mentions: 1
Published: over 11 years ago

10.3390/pharmaceutics13010041

Antimicrobial Contribution of Chitosan Surface-Modified Nanoliposomes Combined with Colistin against Sensitive and Colistin-Resistant Clinical Pseudomonas aeruginosa
Cited by: 6
Author(s): Valentina Laverde-Rojas, Yamil Liscano, Sandra Patricia Rivera Sánchez, Iván Darío Ocampo-Ibáñez, Yeiston Betancourt, Maria J. Alhajj, Cristhian J. Yarce, Constaín H. Salamanca, José Oñate-Garzón
Software Mentions: 1
Published: over 3 years ago

10.1111/jcmm.14329

Glibenclamide and HMR1098 normalize Cantú syndrome‐associated gain‐of‐function currents
Cited by: 10
Author(s): Marien J C Houtman, Xingyu Chen, Muge Qile, Karen Duran, Gijs van Haaften, Anna Stary-Weinzinger, Marcel A.G. van der Heyden
Software Mentions: 1
Published: over 5 years ago

10.1038/srep17038

Shearing of the CENP-A dimerization interface mediates plasticity in the octameric centromeric nucleosome
Cited by: 37
Author(s): David Winogradoff, Haiqing Zhao, Yamini Dalal, Garegin A. Papoian
Software Mentions: 1
Published: almost 9 years ago

10.1038/srep45829

Nucleotide Dependent Switching in Rho GTPase: Conformational Heterogeneity and Competing Molecular Interactions
Cited by: 18
Author(s): Amit Kumawat, Suman Chakrabarty, Kiran Kulkarni
Software Mentions: 1
Published: over 7 years ago

10.1038/s41598-017-07250-4

Spatial structure of TLR4 transmembrane domain in bicelles provides the insight into the receptor activation mechanism
Cited by: 21
Author(s): Konstantin S. Mineev, Sergey A. Goncharuk, Marina V. Goncharuk, Pavel E. Volynsky, Ekaterina V. Novikova, Alexander S. Aresinev
Software Mentions: 1
Published: about 7 years ago

10.3390/ijms21020436

Preferential Coupling of Dopamine D2S and D2L Receptor Isoforms with Gi1 and Gi2 Proteins—In Silico Study
Cited by: 13
Author(s): Justyna Żuk, Damian Bartuzi, Dariusz Matosiuk, Agnieszka A. Kaczor
Software Mentions: 1
Published: over 4 years ago

10.1038/s41598-018-31480-9

E-hooks provide guidance and a soft landing for the microtubule binding domain of dynein
Cited by: 16
Author(s): Nayere Tajielyato, Lin Li, Yunhui Peng, Joshua Alper, Emil Alexov
Software Mentions: 1
Published: about 6 years ago

10.7717/peerj.6568

Evaluation of potential molecular interaction between quorum sensing receptor, LuxP and grouper fatty acids: in-silico screening and simulation
Cited by: 8
Author(s): Chen Fei Low, Mohd Shahir Shamsir, Zeti‐Azura Mohamed‐Hussein, Syarul Nataqain Baharum
Software Mentions: 1
Published: over 5 years ago

10.3390/membranes7010005

Effect of Sodium and Chloride Binding on a Lecithin Bilayer. A Molecular Dynamics Study
Cited by: 7
Author(s): Maria M. Reif, Christopher Kallies, Volker Knecht
Software Mentions: 1
Published: over 7 years ago

10.1186/s12864-017-3912-2

Investigating Ebola virus pathogenicity using molecular dynamics
Cited by: 10
Author(s): Morena Pappalardo, Francesca Collu, James Macpherson, Martin Michaelis, Franca Fraternali, Mark N. Wass
Software Mentions: 1
Published: about 7 years ago

10.3390/ijms22168466

Cytosine-Rich DNA Fragments Covalently Bound to Carbon Nanotube as Factors Triggering Doxorubicin Release at Acidic pH. A Molecular Dynamics Study
Cited by: 7
Author(s): Pawel Wolski, Krzysztof Nieszporek, Tomasz Pańczyk
Software Mentions: 1
Published: about 3 years ago

10.1038/s41598-021-86121-5

Structure based analysis of KATP channel with a DEND syndrome mutation in murine skeletal muscle
Cited by: 4
Author(s): Shoichiro Horita, Tomoyuki Ono, Saul González-Resines, Yuko Ono, Megumi Yamachi, Shen Zhao, Carmen Domene, Yuko Maejima, Kenju Shimomura
Software Mentions: 1
Published: over 3 years ago

10.1038/s41598-021-92388-5

In silico comparison of SARS-CoV-2 spike protein-ACE2 binding affinities across species and implications for virus origin
Cited by: 69
Author(s): Sakshi Piplani, Puneet Kumar Singh, David A. Winkler, Nikolai Petrovsky
Software Mentions: 1
Published: about 3 years ago

10.1371/journal.pone.0049527

Structural Insight into Inhibitor of Apoptosis Proteins Recognition by a Potent Divalent Smac-Mimetic
Cited by: 13
Author(s): Federica Cossu, Mario Milani, Patrice Vachette, Francesca Malvezzi, Serena Grassi, Daniele Lecis, Domenico Delia, Carmelo Drago, Pierfausto Seneci, Martino Bolognesi, Eloise Mastrangelo
Software Mentions: 1
Published: almost 12 years ago

10.1371/journal.pone.0127741

Atomic Insight into the Altered O6-Methylguanine-DNA Methyltransferase Protein Architecture in Gastric Cancer
Cited by: 9
Author(s): Naveed Anjum Chikan, Shoiab Bukhari, Nadeem Shabir, Asif Amin, Sheikh Muzamil Shafi, Raies A. Qadri, Trupti Patel
Software Mentions: 1
Published: over 9 years ago

10.1021/acs.jpca.1c02869

Multiscale Reweighted Stochastic Embedding: Deep Learning of Collective Variables for Enhanced Sampling
Cited by: 20
Author(s): Jakub Rydzewski, Ómar Valsson
Software Mentions: 1
Published: about 3 years ago

10.1111/febs.14111

The pathological Trento variant of alpha-1-antitrypsin (E75V) shows nonclassical behaviour during polymerization
Cited by: 21
Author(s): Elena Miranda, Ilaria Ferrarotti, Romina Berardelli, Mattia Laffranchi, Marta Cerea, Fabrizio Gangemi, Imran Ul Haq, Stefania Ottaviani, David A. Lomas, James A. Irving, Annamaria Fra
Software Mentions: 1
Published: over 7 years ago

10.1002/2211-5463.12731

Evaluating the strengths of salt bridges in the CutA1 protein using molecular dynamic simulations: a comparison of different force fields
Cited by: 1
Author(s): Yoshinori Matsuura, Yasumasa Joti, B. Bagautdinov, Katsuhide Yutani
Software Mentions: 1
Published: almost 5 years ago

10.1021/acs.jpcb.0c09742

Machine Learning of Allosteric Effects: The Analysis of Ligand-Induced Dynamics to Predict Functional Effects in TRAP1
Cited by: 19
Author(s): Mariarosaria Ferraro, Elisabetta Moroni, Emiliano Ippoliti, Silvia Rinaldi, Carlos Sánchez-Martín, Andrea Rasola, Luca F. Pavarino, Giorgio Colombo
Software Mentions: 1
Published: over 3 years ago

10.1002/2211-5463.12352

Mutual influence of secondary and key drug-resistance mutations on catalytic properties and thermal stability of TEM-type β-lactamases
Cited by: 9
Author(s): G.M. Grigorenko, I. V. Uporov, M. Yu. Rubtsova, И. П. Андреева, Dmitrii S. Shcherbinin, A. V. Veselovsky, О. В. Серова, M.M. Ulyashova, I. V. Ishtubaev, A. M. Egorov
Software Mentions: 1
Published: almost 7 years ago

10.3390/antiox9020117

Identification of New Peptides from Fermented Milk Showing Antioxidant Properties: Mechanism of Action
Cited by: 57
Author(s): Federica Tonolo, Federico Fiorese, Laura Moretto, Alessandra Folda, Valeria Scalcon, Alessandro Grinzato, Stefania Ferro, Giorgio Arrigoni, Alberto Bindoli, Emiliano Feller, Marco Bellamio, Oriano Marin, Maria Pia Rigobello
Software Mentions: 1
Published: over 4 years ago

10.1371/journal.pone.0033931

Exploring Protein Dynamics Space: The Dynasome as the Missing Link between Protein Structure and Function
Cited by: 85
Author(s): Ulf Hensen, Tim Meyer, Jürgen Haas, René Rex, Gert Vriend, Helmut Grubmüller
Software Mentions: 1
Published: over 12 years ago

10.1002/2211-5463.13171

A Plasmodium falciparum protein tyrosine phosphatase inhibitor identified from the ChEMBL‐NTD database blocks parasite growth
Cited by: 1
Author(s): Rajan Kumar Pandey, Priya Gupta, Asif Mohmmed, Pawan Malhotra, Dinesh Gupta
Software Mentions: 1
Published: over 3 years ago

Projects: pypi: gromacs

Papers Mentioning gromacs 79