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A Fast 3 × N Matrix Multiply Routine for Calculation of Protein RMSD

https://doi.org/10.1101/008631
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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

inferredcites →https://doi.org/10.1002/jcc.21439openalex-snapshot
Fast determination of the optimal rotational matrix for macromolecular superpositions
inferredcites →https://doi.org/10.1002/pro.5560011217openalex-snapshot
A database of protein structure families with common folding motifs
inferredcites →https://doi.org/10.1016/0304-3975(85)90224-5openalex-snapshot
Clustering to minimize the maximum intercluster distance
inferredcites →https://doi.org/10.1016/j.jcss.2004.10.006openalex-snapshot
Performance guarantees for hierarchical clustering
inferredcites →https://doi.org/10.1016/j.ymeth.2009.04.013openalex-snapshot
Using generalized ensemble simulations and Markov state models to identify conformational states
inferredcites →https://doi.org/10.1016/j.ymeth.2010.06.002openalex-snapshot
Everything you wanted to know about Markov State Models but were afraid to ask
inferredcites →https://doi.org/10.1021/ct700301qopenalex-snapshot
GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation
inferredcites →https://doi.org/10.1038/nrd2220openalex-snapshot
A decade of fragment-based drug design: strategic advances and lessons learned
inferredcites →https://doi.org/10.1063/1.3216567openalex-snapshot
Progress and challenges in the automated construction of Markov state models for full protein systems
inferredcites →https://doi.org/10.1073/pnas.0509355103openalex-snapshot
Physically realistic homology models built with rosetta can be more accurate than their templates
inferredcites →https://doi.org/10.1073/pnas.0905466106openalex-snapshot
Constructing the equilibrium ensemble of folding pathways from short off-equilibrium simulations
inferredcites →https://doi.org/10.1093/nar/28.1.235openalex-snapshot
The Protein Data Bank
inferredcites →https://doi.org/10.1107/s0108767305015266openalex-snapshot
Rapid calculation of RMSDs using a quaternion-based characteristic polynomial
inferredcites →https://doi.org/10.1126/science.289.5481.905openalex-snapshot
The Complete Atomic Structure of the Large Ribosomal Subunit at 2.4 Å Resolution
inferredcites →https://doi.org/10.1126/science.289.5481.920openalex-snapshot
The Structural Basis of Ribosome Activity in Peptide Bond Synthesis
inferredcites →https://doi.org/10.1145/1377603.1377607openalex-snapshot
High-performance implementation of the level-3 BLAS

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.1007/978-1-4939-6753-7_3openalex-snapshot
Application of Hidden Markov Models in Biomolecular Simulations
inferred← citeshttps://doi.org/10.1016/j.bpj.2015.08.015openalex-snapshot
MDTraj: A Modern Open Library for the Analysis of Molecular Dynamics Trajectories
inferred← citeshttps://doi.org/10.1038/srep24065openalex-snapshot
Unfolding mechanism of thrombin-binding aptamer revealed by molecular dynamics simulation and Markov State Model
inferred← citeshttps://doi.org/10.1039/d3cp02042hopenalex-snapshot
Probing conformational landscapes of binding and allostery in the SARS-CoV-2 omicron variant complexes using microsecond atomistic simulations and perturbation-based profiling approaches: hidden role of omicron mutations as modulators of allosteric signaling and epistatic relationships
inferred← citeshttps://doi.org/10.1101/2023.09.11.557205openalex-snapshot
Examining Functional Linkages Between Conformational Dynamics, Protein Stability and Evolution of Cryptic Binding Pockets in the SARS-CoV-2 Omicron Spike Complexes with the ACE2 Host Receptor: Recombinant Omicron Variants Mediate Variability of Conserved Allosteric Sites and Binding Epitopes
inferred← citeshttps://doi.org/10.1101/2025.10.31.685956openalex-snapshot
Neutral Frustration Landscape Architecture of SARS-CoV-2 Spike-Antibody Interfaces Shapes Immune Evasion Mechanisms for Ultrapotent Neutralizing Antibodies and Determines Pathways of Viral Adaptation: Insights from Integrative Computational Approach
inferred← citeshttps://doi.org/10.3389/fphar.2022.844293openalex-snapshot
From Data to Knowledge: Systematic Review of Tools for Automatic Analysis of Molecular Dynamics Output
inferred← citeshttps://doi.org/10.3390/v15102073openalex-snapshot
Comparative Analysis of Conformational Dynamics and Systematic Characterization of Cryptic Pockets in the SARS-CoV-2 Omicron BA.2, BA.2.75 and XBB.1 Spike Complexes with the ACE2 Host Receptor: Confluence of Binding and Structural Plasticity in Mediating Networks of Conserved Allosteric Sites
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