Ecosyste.ms: Papers

An open API service providing mapping between scientific papers and software projects that are mentioned in them.
All mentions data is based on the CZI Software Mentions dataset.

Projects: pypi: rmsd

https://packages.ecosyste.ms/registries/pypi.org/packages/rmsd

Calculate root-mean-square deviation (RMSD) between two sets of cartesian coordinates (XYZ or PDB format), using rotation (fx. Kabsch algorithm), atom reordering (fx. Hungarian algorithm), and axis reflections, resulting in the minimal RMSD.
9 versions
Latest release: almost 2 years ago
8 dependent packages
25,253 downloads last month

Papers Mentioning rmsd 12

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

10.1038/s41598-020-61132-w

Long-range replica exchange molecular dynamics guided drug repurposing against tyrosine kinase PtkA of Mycobacterium tuberculosis
Cited by: 10
Author(s): Priya Nagpal, Salma Jamal, Hina Singh, Waseem Ali, Sana Tanweer, Rahul Sharma, Abhinav Grover, Sonam Grover
Software Mentions: 3
Published: almost 5 years ago

10.1038/s41598-020-70202-y

Identification and characterization of cytosolic malate dehydrogenase from the liver fluke Fasciola gigantica
Cited by: 6
Author(s): Purna B Chetri, Rohit Shukla, Timir Tripathi
Software Mentions: 3
Published: over 4 years ago

10.6026/97320630013339

A QSAR model of Olanzapine derivatives as potential inhibitors for 5-HT2A Receptor
Cited by: 3
Author(s): Pooja Mitra, Aishwarya Rastogi, Mayank Rajpoot, Ajay Kumar, Vivek Srivastava
Software Mentions: 2
Published: about 7 years ago

10.1038/s41598-021-93266-w

An immunoinformatics approach to design a multi-epitope vaccine against Mycobacterium tuberculosis exploiting secreted exosome proteins
Cited by: 14
Author(s): Rahul Sharma, Vikrant Singh Rajput, Salma Jamal, Abhinav Grover, Sonam Grover
Software Mentions: 2
Published: over 3 years ago

10.1371/journal.pone.0061908

p.Arg82Leu von Hippel-Lindau (VHL) Gene Mutation among Three Members of a Family with Familial Bilateral Pheochromocytoma in India: Molecular Analysis and In Silico Characterization
Cited by: 9
Author(s): Anulekha Mary John, George Priya Doss C, Andrew Ebenazer, M. S. Seshadri, Aravindan Nair, Simon Rajaratnam, Rekha Pai
Software Mentions: 2
Published: over 11 years ago

10.3390/ijms18030482

L1198F Mutation Resensitizes Crizotinib to ALK by Altering the Conformation of Inhibitor and ATP Binding Sites
Cited by: 17
Author(s): Jian Li, Rong Sun, Yuehong Wu, Mingxin Song, Jia Li, Qianye Yang, Xiaoyi Chen, Ji Bao, Qi Zhao
Software Mentions: 1
Published: almost 8 years ago

10.6026/97320630013256

Marine sponge derived natural products as inhibitors of mycothiol-S-conjugate amidase
Cited by: 1
Author(s): Akansha Saxena, S. K. Mishra
Software Mentions: 1
Published: over 7 years ago

10.1371/journal.pntd.0002188

Sulfated Polysaccharide, Curdlan Sulfate, Efficiently Prevents Entry/Fusion and Restricts Antibody-Dependent Enhancement of Dengue Virus Infection In Vitro: A Possible Candidate for Clinical Application
Cited by: 60
Author(s): Koji Ichiyama, Sindhoora Bhargavi Gopala Reddy, Li Feng Zhang, Wei-Xin Chin, Tegshi Muschin, Lars Heinig, Youichi Suzuki, Nanjundappa Haraprasad, Yoshiyuki Yoshinaka, Akihide Ryo, Nobuo Nomura, Eng Eong Ooi, Subhash G. Vasudevan, Takashi Yoshida, Naoki Yamamoto
Software Mentions: 1
Published: over 11 years ago

10.1186/s13321-017-0227-x

Efficient conformational sampling and weak scoring in docking programs? Strategy of the wisdom of crowds
Cited by: 41
Author(s): Ludovic Chaput, Liliane Mouawad
Software Mentions: 1
Published: over 7 years ago

10.1371/journal.ppat.1006553

Destabilizing polymorphism in cervid prion protein hydrophobic core determines prion conformation and conversion efficiency
Cited by: 28
Author(s): Samia Hannaoui, Sara Amidian, Yo Ching Cheng, Camilo Duque Velásquez, Lyudmyla Dorosh, Sampson Law, Glenn C. Telling, Maria Stepanova, Debbie McKenzie, Holger Wille, Sabine Gilch
Software Mentions: 1
Published: over 7 years ago

10.1186/s12868-018-0472-6

Biaryl scaffold-focused virtual screening for anti-aggregatory and neuroprotective effects in Alzheimer’s disease
Cited by: 19
Author(s): Sidra Khalid, Maryam Zahid, Hussain Ali, Yeong S. Kim, Salman Khan
Software Mentions: 1
Published: about 6 years ago