A stable, rapidly converging conjugate gradient method for energy minimization

Watowich, Stanley J.; Meyer, Eric S.; Hagstrom, Ray; Josephs, Robert

doi:10.1002/jcc.540090611

Cited by 66 publications

(37 citation statements)

References 19 publications

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“…Shifted limited‐memory variable metric method of Vlček and Lukšan3 in the recommended variant 2 with the ratio of shift parameters as correction parameter c Shanno derived methodd proposed in Watowitch et al23. …”

Section: Resultsmentioning

confidence: 99%

Connections of functional areas in the mustached bat's auditory cortex with the auditory thalamus

Pearson

Crocker

Fitzpatrick

2006

J of Comparative Neurology

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The auditory thalamus is the major target of the inferior colliculus and connects in turn with the auditory cortex. In the mustached bat, biosonar information is represented according to frequency in the central nucleus of the inferior colliculus (ICc) but according to response type in the cortex. In addition, the cortex has multiple areas with neurons of similar response type compared to the single tonotopic representation in the ICc. To investigate whether these transformations occur at the level of the thalamus, we injected anatomical tracers into physiologically defined locations in the mustached bat's auditory cortex. Injections in areas used for target ranging labeled contiguous regions of the auditory thalamus rather than separate patches corresponding to regions that respond to the different harmonic frequencies used for ranging. Injections in the two largest ranging areas produced labeling in separate locations. These results indicate that the thalamus is organized according to response type rather than frequency and that multiple mappings of response types exist. Injections in areas used for target detection labeled thalamic regions that were largely separate from those that interconnect with ranging areas. However, injections in an area used for determining target velocity overlapped with the areas connected to ranging areas and areas involved in target detection. Thus, separation by functional type and multiplication of areas with similar response type occurs by the thalamic level, but connections with the cortex segregate the functional types more completely than occurs in the thalamus.

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Section: Resultsmentioning

confidence: 99%

Connections of functional areas in the mustached bat's auditory cortex with the auditory thalamus

Pearson

Crocker

Fitzpatrick

2006

J of Comparative Neurology

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“…23 Conjugate Gradient algorithm was used for optimization with a total of 200 steps. 24 During minimization, the structure was updated every 1 step and minimization was terminated when the energy difference is less than 0.1. Energy minimized structures were saved in *.pdbqt format.…”

Section: Ligand Preparationmentioning

confidence: 99%

Ilimaquinone (marine sponge metabolite) as a novel inhibitor of SARS-CoV-2 key target proteins in comparison with suggested COVID-19 drugs: designing, docking and molecular dynamics simulation study

et al. 2020

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“…After completion, the best map was selected out of these preliminary results, based on minimal sum-of-adjacent-recombination-frequencies and maximal sum-of-adjacent-LOD-scores (Buntjer 2002;Buntjer et al 2002;Mank and Van Haaren 2003). Finally, the genetic distances in this map were optimized using methods described by Watowich et al (1988).…”

Section: Map Constructionmentioning

confidence: 99%

High resolution map of eggplant (Solanum melongena) reveals extensive chromosome rearrangement in domesticated members of the Solanaceae

et al. 2014

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A linkage map of eggplant was constructed for an interspecific F 2 population derived from a cross between Solanum linnaeanum MM195 and S. melongena MM738. The map contains 400 AFLP Ò (amplified fragment length polymorphism), 348 RFLP (restriction fragment length polymorphism) and 116 COSII (conserved ortholog set) markers. The 864 mapped markers encompass 12 linkage groups, span 1,518 cM and are spaced at an average interval of 1.8 cM. Use of orthologous markers allowed confirmation of the established syntenic relationships between eggplant and tomato chromosomes and helped delineate the nature of the 33 chromosomal rearrangements and 11 transpositions distinguishing the two species. This genetic map provides a 2-to 3-fold improvement in marker density compared to previously published interspecific maps. Because the interspecific mapping population is rich in morphological variation, this greater genome saturation will be useful for QTL (quantitative trait locus) analyses. The recent release of the tomato genome sequence will provide additional opportunities for exploiting this map for comparative genomics and crop improvement.

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A stable, rapidly converging conjugate gradient method for energy minimization

Cited by 66 publications

References 19 publications

Connections of functional areas in the mustached bat's auditory cortex with the auditory thalamus

Connections of functional areas in the mustached bat's auditory cortex with the auditory thalamus

Ilimaquinone (marine sponge metabolite) as a novel inhibitor of SARS-CoV-2 key target proteins in comparison with suggested COVID-19 drugs: designing, docking and molecular dynamics simulation study

High resolution map of eggplant (Solanum melongena) reveals extensive chromosome rearrangement in domesticated members of the Solanaceae

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