Computational Design

Accelerated MD simulation is an in silico computational method reported for elucidating the photoactivation mechanism of the AsLOV2 light-responsive domain. The available evidence supports its use as a mechanistic analysis approach for a protein photosensor rather than as a deployable biological reagent.

All-atom replica exchange discrete molecular dynamics is a computational docking method used to generate structural models of calcium and integrin binding protein 1 (CIB1) bound to α-integrin cytoplasmic tails. In the cited CIB1 study, it predicted that multiple α-integrin tails engage the same hydrophobic binding pocket on CIB1.

AlphaFold3 is a computational structure-prediction method used in the cited study to model the MagMboI–DNA complex. In that work, it was applied to infer interactions with the 5'-GATC-3' recognition sequence and to guide optimization of the photoactivatable endonuclease variant MagMboI-plus for top-down genome engineering.

The Anderson-Darling test is a nonparametric computational method applied in genome-wide association studies of complex quantitative traits. In an enlarged maize association panel, it identified loci across 17 agronomic traits, including both previously known loci and additional candidate loci detected only by this test.

This Bayesian computational approach is a data-analysis method developed to improve prediction of split protein behavior by contextualizing errors inherent to experimental procedures. In the cited study, it was applied to pooled, sequencing-based screening data from split Cre recombinase constructs generated with optogenetic dimers, enabling comprehensive analysis of split sites across the protein.

The Bayesian optimization framework is a computational method built from high-throughput Lustro measurements to guide control of blue light-sensitive optogenetic systems. It uses data-driven learning, uncertainty quantification, and experimental design to identify light induction conditions for multiplexed regulation in Saccharomyces cerevisiae.

The binding equilibrium model is a computational modeling approach used to quantitatively describe how proteins partition into engineered synthetic condensates. In the reported synthetic membraneless organelle framework, it supports prediction of condensate composition based on affinity-dependent recruitment.

This computation method is a bioinformatic analysis applied to protein components of the Saccharomyces cerevisiae ribosome assembly pathway. In the cited study, it compared ribosome biogenesis factors with ribosomal proteins and found that biogenesis factors contain significantly more predicted trans interacting regions.

BROAD is a computational protein design method that combines Rosetta-based structure modeling, machine learning, and integer linear programming to improve design search beyond Rosetta sampling alone. It was demonstrated in antibody design to increase the predicted HIV neutralization breadth of VRC23 across a panel of 180 divergent viral strains.

Chemogenetically driven repositioning of lysosomes is an experimental perturbation used to causally alter lysosome localization and test how lysosome positioning regulates endoplasmic reticulum remodeling. In the cited 2020 Science Advances study, chemo- and optogenetically driven lysosome repositioning was used to validate a causal link between lysosome movement and ER network organization.

Clathrin endocytosis is a host-cell internalization pathway described in a review as one route used by Kaposi’s sarcoma-associated herpesvirus (KSHV) to enter fibroblast infection models. In this context, it serves as a cellular uptake mechanism associated with viral entry and subsequent trafficking events linked to host signaling pathways.

This computational design strategy combines in silico design with biophysical experiments to improve the response kinetics of protein conformational switches. In the cited 2018 Nature Communications study, it was applied to an engineered protein-based Ca2+ sensor and rationally accelerated its response into the range of fast physiological Ca2+ fluctuations.

Computational methods for LOV-based optogenetic tool development are design-enabling approaches used in the ongoing development of Light-Oxygen-Voltage domain-based optogenetic systems. The cited evidence supports a role for computational methods as one of several factors advancing LOV-based tools for light-controlled biological regulation.

Computational modeling was used to analyze how promoters decode light-driven transcription factor nuclear translocation dynamics. In the cited work, the modeling identified promoter kinetic regimes that enable efficient expression under short light pulses and proposed a multi-stage, thresholded activation scheme to explain opposite promoter-response phenotypes.

Computational protein design is an engineering methodology described in a 2018 review as a next-generation tool for expanding synthetic biology applications. The supplied evidence frames it as a design approach used alongside phage display and high-throughput binding assays rather than as a single molecular reagent.

Conditional gene mutation is a genetic engineering method for creating gene alterations that are activated in spatially restricted and/or temporally restricted ways. In mice, these conditional mutations enable controlled genetic perturbation for experimental studies and disease modeling.

Conventional replica exchange molecular dynamics (REMD) is a molecular simulation method used for statistical sampling of biomolecular conformational ensembles. In the cited evidence, it functions as the benchmark comparator against two coarse kMC-based replica exchange methods.

CRISPR/Cas9 is a genome editing technique used in the cited study to generate Cib1 and Cib2 knockout mice. In this evidence set, its demonstrated function is targeted gene disruption for mouse model production.

Duplex CRISPR/Cas9 technology is a genome-editing method that uses two guide RNAs to target intronic sequences flanking an exon, enabling excision of the intervening exon by Cas9-mediated cleavage. In human U-2 OS osteosarcoma cells, it was applied to generate CRY1 knockout, CRY2 knockout, and CRY1/CRY2 double knockout cell models.

Dynamic multiplexing is a computational design principle for synthetic gene networks that encodes and decodes time-varying inputs into distinct gene expression states. In the cited 2021 study, it increased information transmission from signal to gene expression and enabled dynamic signal decoding using engineered regulators with different response kinetics.

The elastic network model (ENM) is a computational method for analyzing protein structural dynamics from an elastic network representation. In the cited PAS domain superfamily study, ENM was used to quantify residue fluctuations and vibrational patterns and to relate these dynamic features to sequence conservation, structural features, and biological function.

Electron-electron double resonance (ELDOR) spectroscopy is a structural assay method that, when combined with site-directed spin labelling, was used to chart light-induced structural transitions in the engineered LOV histidine kinase YF1. In the cited study, it provided pairwise distance information used to model blue-light-driven quaternary rearrangements in a signaling photoreceptor.

Fernando's model is a computational model of a synthetic molecular circuit designed to mimic Hebbian learning in a neural network architecture. It is described as one of the earliest models in this area to use Hill equation-based regulatory modeling, and computational analysis indicated that a reinforcement effect can be obtained with appropriate parameter choices.

FRASE, also described as FRASE-bot, is a computational fragment-based ligand discovery method that mines 3D ligand–protein complex structures to build a database of fragments in structural environments. It screens this database against a target protein, seeds the target structure with relevant ligand fragments, and uses a neural network to prioritize fragments with the highest likelihood of being native binders.

FRASE-bot is an in silico fragment-based hit-finding method for drug discovery against unconventional therapeutic targets. It mines thousands of 3D protein-ligand complex structures to build a fragment-in-structural-environment database, matches target protein environments to that database, and uses machine learning to prioritize seeded fragments as candidate binders.

Free-energy calculations are an in silico prediction method used in the rational design of human Caspase-2 mutants. In the cited study, they were applied alongside sequence and structural comparisons of Caspase-2 and Caspase-3 to predict effects of active-site mutations on substrate recognition and to support engineering of broader amino-acid acceptance.

Gene editing technology is an engineering method used for animal model construction. The supplied evidence specifically states that it has been widely applied to nonhuman primate model generation in recent years.

This tool is a generalised computational modeling technique for simulating optogenetic mechanisms in the NEURON environment. It was presented using channelrhodopsin-2 and halorhodopsin to model optical activation and optical silencing in neurons.

High-resolution live imaging is cited as a methodological approach that provides new opportunities to study branching morphogenesis in living systems. The supplied evidence identifies it only at the level of a general live-imaging assay and does not specify the imaging modality, reporter strategy, or biological model.

In silico feedback control strategies are computationally implemented control schemes coupled to optogenetic measurement and light stimulation platforms. They are used to create computer-controlled living systems through automated measurement and stimulation workflows.

Inducible RNAi depletion of CIB1 is a conditional gene-silencing method used in vitro and in vivo to reduce expression of calcium- and integrin-binding protein 1 (CIB1). In triple-negative breast cancer models, CIB1 knockdown impaired cell survival, altered transcriptional programs linked to reduced proliferation and increased cell death, and caused marked shrinkage of MDA-MB-468 xenograft tumors.

The input reconstruction algorithm is a computational method used to infer prior light pulse inputs from cellular signaling outputs. In the cited MAPK/ERK communication study, it detected light pulses with 1-minute accuracy 5 minutes after their occurrence.

Integrated Classification Pipeline (ICP) is a computational method developed to decompose and categorize CRISPR/Cas9-generated mutations at genomic target sites in complex multicellular insects. It classifies mixed DNA double-strand break repair outcomes, including non-homologous end joining and homology-directed repair events within the same samples.

Likelihood maximization analysis is a computational method for selecting reaction coordinate models for individual substeps of a conformational transition and inferring tentative transition states. In the cited application, it was applied to transition path sampling data from explicit-solvent molecular dynamics of the millisecond partial unfolding transition in the photoactive yellow protein photocycle.

Linkage disequilibrium mapping is a computational genetic association method used here in Arabidopsis thaliana to connect natural CRY2 sequence variation with flowering-time phenotypes. In the cited study, it identified strong haplotype-phenotype associations under short-day photoperiod and implicated a candidate serine substitution linked to early flowering.

Macropinocytosis is a host-cell endocytic uptake route described in Kaposi’s sarcoma-associated herpesvirus (KSHV) infection models. In the cited review, KSHV enters adherent endothelial cells through membrane bleb- and actin-mediated macropinocytosis as part of broader hijacking of host signaling and membrane dynamics.

Markov State Modeling (MSM) is a computational method applied with molecular dynamics simulations to resolve conformational dynamics in the AsLOV2 photosensory domain. In the cited 2023 study, MSM was used to explain blue-light-induced stepwise unfolding of the C-terminal Jα-helix and to identify seven structurally distinguishable unfolding states spanning initiation and post-initiation phases.

Mathematical and statistical modelling is a computational design approach used in synthetic biology to improve the predictability of engineered biological systems. In the cited plant synthetic biology literature, it supports model-informed rational design for engineering plant gene regulation and metabolism.

This mathematical model is a computational method used to quantitatively analyze the kinetics of blue light-inducible and blue light-repressible gene expression in an EL222-based bidirectional promoter system in Escherichia coli. It describes expression dynamics under optical input in the context of a rapidly reversible bacterial optogenetic transcription system.

This tool is a mathematical modeling method used together with an optogenetically engineered cell line and custom hardware to optically re-create calcium oscillation patterns. It enables independent variation of a single calcium waveform component within reconstructed oscillatory inputs.

This computation method is a mathematical model that integrates tissue mechanics into morphogen dynamics to quantitatively explain tissue-scale responses to BMP4 signaling in human gastrula models. In the cited study context, it was linked to BMP4-driven SMAD1-5 phosphorylation and amnion differentiation.

This tool is a mathematical model used to quantitatively analyze light-induced gene expression kinetics in a red/far-red light-responsive mammalian gene switch. It supports interpretation of how illumination drives expression dynamics in that optogenetic expression system.

Mathematical modeling is a computational method used to guide the rational design of synthetic gene circuits. The cited literature also places it alongside live-cell imaging and within quantitative model systems used to study microbial drug resistance and spatial-temporal features of cancer in mammalian cells.

This computational method compares and meta-analyzes transcriptomic datasets generated after manipulation of ethylene levels or signaling under varying light conditions. It is used to identify ethylene-responsive transcriptional programs that are light-dependent versus light-independent.

The mixed linear model (MLM) is a computational genome-wide association study method applied in an enlarged maize association panel. In the cited 2014 study, MLM identified ten loci across five agronomic traits at a Bonferroni-corrected significance threshold of -log10(P) > 5.74.

ML Int&in is a machine learning–guided computational design method for identifying unnatural split sites in the fast split inteins gp41-1 and NrdJ-1. In the cited preprint, these designs yielded functional split intein variants with reduced fragment affinity and supported blue-light-activatable protein splicing systems that controlled Cre recombinase in mammalian cells.

Model bioinformatics analysis in this context is a computation-based analysis of Arabidopsis thaliana transcript expression responses to UV-B light, drought, and cold stress using the AtGenExpress global stress dataset. It interprets stress-responsive gene expression patterns across multiple abiotic conditions measured with the Affymetrix ATH1 microarray under standardized parallel protocols.

Model-informed rational design is an engineering method in synthetic biology that uses models to guide the design of biological systems. In the cited plant context, it has been successfully applied to engineering plant gene regulation and metabolism.

Molecular dynamics simulations combined with Markov state modeling were used to characterize blue-light-induced conformational switching in the Avena sativa LOV2 (AsLOV2) domain. This computation method resolved C-terminal Jα-helix unfolding into seven structurally distinguishable steps spanning initiation and post-initiation phases.

Molecular dynamics is a computational method used to study signaling mechanisms of LOV domains through simulation-based analysis. In the cited literature, it functions as an in silico approach for mechanistic investigation rather than as a biological reagent or genetically encoded tool.

Molecular dynamics simulation is a computational method for modeling atomistic conformational dynamics of proteins and analyzing residue fluctuations and vibrational behavior. In the cited studies, it was used as a noninvasive approach to validate dynamic behavior and to compare PAS-domain dynamics across functional groups.

Molecular dynamics simulations were used as a computational design method to guide construction of the PiL[D24] photoswitchable mPKM2-LOV2 fusion reported in the 2017 FEBS Journal study. In that context, the simulations supported engineering of a light-responsive pyruvate kinase chimera that preserved LOV2 photoreactivity and showed illumination-dependent changes in enzyme activity.

Monte Carlo Tree Search (MCTS) is a computational search method used to identify an optimal program within a discrete program space. In the cited approach, it operates over a domain-specific language and associated transformation rules to construct candidate programs.

NCBI sequence screening for 2A/2A-like occurrence is a computational survey method that updates the distribution of viral 2A and 2A-like sequences by screening sequences deposited in the National Center for Biotechnology Information database. In the cited 2021 review, this approach identified 69 newly reported 2A-like occurrences across multiple virus groups.

The one-dimensional active gel model is a theoretical computational framework for contractile cell migration that incorporates the tendency of myosin II to assemble into minifilaments. It predicts bistability between sessile and motile cell states and models how optogenetic activation or inhibition of contractility can switch between these states.

The optimization-based control algorithm is an engineering method for predictive cruise control that uses short-range radar and traffic signal information to schedule an optimum vehicle velocity trajectory. It is intended to guide vehicle motion relative to upcoming signal phases and nearby traffic.

Optogenetic control of contractility is a light-based engineering method proposed to spatially modulate cellular contractility and thereby influence cell migration behavior. In a one-dimensional active gel model, optogenetic activation or inhibition of contractility is predicted to switch cells between sessile and motile states at realistic parameter values.

This optogenetic multiplexing method is an engineering approach for programming two simultaneous and independent gene expression signals within the same cell using light. The reported method uses a photoconversion model to compensate for spectral cross-reactivity between two optogenetic sensors.

Optogenetically driven repositioning of lysosomes is a light-controlled perturbation method used to move lysosomes and test their causal role in endoplasmic reticulum remodeling. In the cited 2020 study, chemo- and optogenetically driven lysosome repositioning was used to validate a causal link between lysosome positioning and ER network organization.

Phage display is an assay and selection method used during engineering workflows for light-responsive protein tools. In the cited context, it is applied alongside computational protein design and high-throughput binding assays in development of LOV2-based optogenetic systems such as improved light-induced dimers.

This computation method is a predictive design framework for transcriptional programs reported in Performance Prediction of Fundamental Transcriptional Programs. It uses experimentally characterized single-input logical operations and associated metrology to model and predict the performance of more complex compressed transcriptional logic programs, including two-input AND, NOR, and mixed-phenotype NIMPLY operations.

Protein design is a computational engineering method discussed in reviews on protein structure prediction and on optogenetic tool development. It is presented as enabling the creation of protein-based tools, including light-responsive optogenetic systems, that can manipulate and monitor cellular activities.

Protein structure prediction is a computational method for inferring protein three-dimensional structure. In the supplied evidence, it is identified only as a topic covered in a 2019 review on advances in protein structure prediction and protein design.

QM calculations are a quantum-chemical computational method used to predict conformer energetics, rotational barriers, and infrared spectra of transient glutamine isomers in LOV photoreceptors. In EL222, AsLOV2, and RsLOV, these calculations were used to infer favored glutamine orientations along an assumed light-driven reaction path and to interpret transient infrared behavior.

The QM(B3LYP/cc-pVDZ)/MM(AMBER) approach is a hybrid quantum mechanics/molecular mechanics computational method used for geometry optimization and vibrational frequency calculations in flavin-binding photoreceptor proteins. In the cited BLUF photoreceptor study, it was used to model light-induced structural changes and associated spectral shifts.

The quantitative mathematical model is a computational design method used to guide the combination of synthetic biology-derived functional modules within a polymer framework. In the cited biohybrid materials system, this model-supported design enabled light pulse-counting behavior linked to distinct molecular outputs.

This quantitative model is a computational analysis component used in a 2013 study of multi-chromatic optogenetic control of mammalian gene expression and signaling. It was applied to determine critical system parameters for the reported light-responsive expression platform.

Quantum chemistry is used here as a computational method to analyze the primary light-driven reactions of the LOV2 domain of phototropin. In the cited 2009 Biophysical Journal study, it is paired with ultrafast mid-infrared spectroscopy to investigate LOV2 photochemistry.

The radiative transfer equation is a computational method used to model light propagation in cylindrical mammalian cell culture bioreactors for optogenetic applications. In the cited 2023 study, it was applied to estimate whether incident light can penetrate dense cultures at production-relevant scales.

This tool is a reinforcement learning-based computational method for multi-intersection traffic signal scheduling that incorporates visible light communication (VLC) queuing, request, and response behaviors. It is described as part of a traffic management system integrating VLC localization services with learning-driven signal control.

Rosetta is a molecular modeling program used for computational design of new protein structures and protein complexes. The cited evidence specifically attributes its design capability to rotamer-based sequence optimization protocols that support accurate design of protein tertiary and quaternary structure.

The simple self-assembly model is a computational method for active mixtures of microtubules and molecular motors. It captures the extensile-to-contractile transition by representing competition between nematic and polar aligning interactions that drive formation of bundles or asters.

Single cell-based analysis is a quantitative cellular assay framework developed to compare the activities of overexpressed full-length guanine nucleotide exchange factors in primary human endothelial cells. It was applied with single-cell FRET Rho GTPase biosensors to measure GEF-driven activation of Cdc42 and Rac1.

SOS-CIS(D) is a quantum-chemical excited-state calculation method used to compute vertical excitation energies. In the cited 2010 BLUF photoreceptor study, it was applied to model flavin-associated structural and spectral changes and to evaluate light-induced states.

SpCas9-NG is an engineered Streptococcus pyogenes Cas9 nuclease variant that recognizes NGN protospacer-adjacent motifs instead of the NGG PAM required by wild-type SpCas9. In the cited 2021 Communications Biology study, it was used for RNA-guided genome editing to target the boundary of expanded CAG repeats and induce precise repeat contraction in a Huntington’s disease mouse model context.

SwiftLib is a computational method for optimizing degenerate codon libraries using dynamic programming. It is designed to rapidly generate degenerate-codon-library designs and was reported to improve on an existing integer-linear programming formulation for this task.

Switched differential equations were developed as a computational framework to model oscillatory behavior of circadian clock cells in the Madeira cockroach. The model was used to interpret RNAi perturbation phenotypes and to support a hypothesis of coupled morning and evening oscillators linked by mutual inhibition.

The theoretical probability of neighbor density (PND) is a computational method introduced to discern protein oligomeric states in cellular environments. It is described as robust, precise, and adaptable for analyzing oligomerization scenarios spanning monomers to hexamers.

Time-resolved vibrational spectroscopy coupled with isotope labeling is an assay method used to resolve light-triggered structural dynamics in the Avena sativa LOV2 (AsLOV2) photosensory domain. In the cited study, it mapped structural evolution from 100 fs to 1 ms after optical excitation and supported a sequential allosteric model linking the flavin pocket to Jα-helix unfolding.

Transition path sampling is a computational method applied to explicit-solvent molecular dynamics trajectories to extract atomistic features of conformational reaction networks. In the cited study, it was used to analyze the millisecond partial unfolding transition in the light-driven photocycle of photoactive yellow protein and to predict reaction coordinate models and tentative transition states.