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relaxed random walk (rrw) diffusion model implemented in the software package beast x  (Eleva GmbH)

 
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    Eleva GmbH relaxed random walk (rrw) diffusion model implemented in the software package beast x
    Relaxed Random Walk (Rrw) Diffusion Model Implemented In The Software Package Beast X, supplied by Eleva GmbH, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/software+modeling+package/relaxed+random+walk++rrw++diffusion+model+implemented+in+the+software+package+beast+x/pm40569388-173-31-8
    Average 90 stars, based on 1 article reviews
    relaxed random walk (rrw) diffusion model implemented in the software package beast x - by Bioz Stars, 2026-11
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    Diffusion-based Assay:

    Article Title: Comparative performance of viral landscape phylogeography approaches.
    Article Snippet: Prior-informed landscape phylogeographic analyses 10 9 8 7 6 5 4 3 2 1975 1980 1985 1990 1995 2000 Scenario 1: only the impact of spa al distance Scenario 3: only the impact of the eleva on layer (+) Scenario 2: an intermediate scenario with an impact inbetween scenarios 1 and 3 (branch lengths propor onal to a value between spa al and environmental distances)19951985 Actual sampling coordinates Simula on of RNA sequences along the tree topologies obtained from the con nuous phylogeographic simula ons (using the program πBUSS) 0 40 80 0 20 40 60 R2null = 0.004 0 0 20 40 60 R2env = 0.056 0 0 40 80 R2null = 0.005 0 3000 6000 0 40 80 R2env = 0.041 0 10 20 30 40 0 R2null = 0.006 0 0 40 80 R2env = 0.059 0 0 R2null = 0.011 0 5 10 15 0 40 80 R2env = 0.053 0.0 0.1 0.2 0 Bayes factor (BF) = 99 for Qrandomisations > Qposterior -0.05 0 0.05 0.10 0.15 0 10 20 30 0 0.05 0.10 0.15 0.20 0 4 8 12 -0.10 -0.05 0 0.05 0.10 0 10 20 20 40 100 200 1000 2000 40 80 10 20 30 40 80 200000 400000Br an ch d ur at io n x 4 Pa tri st ic d is ta nc e Br an ch d ur at io n x 4 Br an ch d ur at io n x 4 Environmental distance (log) between tips (null raster) (elevation raster) Branch environmental distance squared (null raster) (elevation raster) Branch Euclidean distance squared (null raster) (elevation raster) Branch Euclidean distance squared (null raster) (elevation raster) D en si ty D en si ty D en si ty D en si ty Q2 statistic (= R 2 env - R 2 null) Q1 statistic (= R 2 env - R 2 null) Q3 statistic (= R 2 env - R 2 null) Q4 statistic (= R 2 env - R 2 null) BF = 24 for Qrandomisations > Qposterior BF = 134 for 0 < Qposterior BF = 6.3 for 0 < Qposterior 2.2. .. Cartogram transforma on 10 8 6 4 2 Eleva on (rescaled) y x Con nuous phylogeographic reconstruc ons conducted with the relaxed random walk (RRW) diffusion model implemented in the so ware package BEAST X. ..



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    Image Search Results


    AlphaFold3 models of TNFR1-ICM11 complexes (A) Native TNFR1–TNF reference structure for epitope orientation (adapted from PDB: 1TNR ). The following contact residues defines TNF binding site: Lys18, Ser49, His52, Trp93, Glu95, Arg132, Lys143, Lys144, Glu42, Ser43, His55, Cys56, Cys59, Ser60, Lys61, Arg63, Lys64, Glu65, and Met66. (B–D) AF3 models for 1:1, 2×, and 3× TNFR1-ICM11 assemblies. The AF3 confidences are indicated in the figure: ipTM provides confidence in the interface quality, and pTM summarizes the overall complex topology. The resulting contact residues of the 1:1 complex are: Arg63, Glu65, His91, Tyr92, Trp93, Glu95, Asn96, Gln99, Phe101, Lys118, Arg132, Glu133, Glu135, Glu147, and Lys150. Shared TNFR1 hotspot residues shared by both TNF and ICM11: Arg63, Glu65, Trp93, Glu95, Arg132. Interface/contact residues were computed via Molecular Operating Environment (MOE) software.

    Journal: iScience

    Article Title: Antigen-directed single domain antibody-based TNFR1 agonists elicit preferential killing of HER2-overexpressing cancer cells

    doi: 10.1016/j.isci.2026.115327

    Figure Lengend Snippet: AlphaFold3 models of TNFR1-ICM11 complexes (A) Native TNFR1–TNF reference structure for epitope orientation (adapted from PDB: 1TNR ). The following contact residues defines TNF binding site: Lys18, Ser49, His52, Trp93, Glu95, Arg132, Lys143, Lys144, Glu42, Ser43, His55, Cys56, Cys59, Ser60, Lys61, Arg63, Lys64, Glu65, and Met66. (B–D) AF3 models for 1:1, 2×, and 3× TNFR1-ICM11 assemblies. The AF3 confidences are indicated in the figure: ipTM provides confidence in the interface quality, and pTM summarizes the overall complex topology. The resulting contact residues of the 1:1 complex are: Arg63, Glu65, His91, Tyr92, Trp93, Glu95, Asn96, Gln99, Phe101, Lys118, Arg132, Glu133, Glu135, Glu147, and Lys150. Shared TNFR1 hotspot residues shared by both TNF and ICM11: Arg63, Glu65, Trp93, Glu95, Arg132. Interface/contact residues were computed via Molecular Operating Environment (MOE) software.

    Article Snippet: molecular modeling software package MOE (Molecular Operating Environment) , Chemical Computing Group Inc. , RRID: SCR_014882.

    Techniques: Binding Assay, Software