Toolkit Items

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.

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.

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.

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.

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.

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.

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 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.

Artificial Intelligence (AI)-have emerged as transformative tools to accelerate nanocarrier design and optimise their properties... AI-driven models accelerate the discovery of lipid-based nanoparticle formulations by analysing vast chemical datasets and predicting optimal structures for gene delivery and vaccine development

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 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.

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.

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.

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.

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.

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.

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.

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.

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.

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 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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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 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.

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.

We present ORFannotate, a lightweight, GTF-native Python command-line tool that predicts ORFs from transcript annotations and reinserts precise, exon-aware CDS and UTR features into the original GTF/GFF file.