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Constituent amino-acids can be analyzed to predict secondary, tertiary and quaternary protein structure. This list of protein structure prediction software summarizes notable used software tools in protein structure prediction, including homology modeling, protein threading, ab initio methods, secondary structure prediction, and transmembrane helix and signal peptide prediction.
Spectrolyzer is a Microsoft Windows-based software package developed by Binary Detect (previously named Medicwave) that provides bioinformatics data analysis tools for different mass spectrometers. It focuses on finding protein biomarkers and detecting protein deviations.
High performance GPU-accelerated ab initio molecular dynamics and TD/DFT software package for very large molecular or even nanoscale systems. Runs on NVIDIA GPUs and 64-bit Linux, has heavily optimized CUDA code. Proprietary, trial licenses available PetaChem LLC: TINKER: I Yes Yes Yes Yes I I Yes Yes Software tools for molecular design-Tinker ...
List of software for Monte Carlo molecular modeling; Comparison of software for molecular mechanics modeling; Molecular design software; Molecule editor; Molecular modeling on GPUs; List of software for nanostructures modeling; Semi-empirical quantum chemistry method; Computational chemical methods in solid-state physics, with periodic boundary ...
[7] EasyGene: The gene finder is based on a hidden Markov model (HMM) that is automatically estimated for a new genome. Prokaryotes [8] [9] EuGene: Integrative gene finding: Prokaryotes, Eukaryotes [10] [11] FGENESH: HMM-based gene structure prediction: multiple genes, both chains: Eukaryotes [12] FrameD: Find genes and frameshift in G+C rich ...
Octopus is a software package for performing Kohn–Sham density functional theory (DFT) and time-dependent density functional theory (TDDFT) calculations. [ 1 ] Octopus employs pseudopotentials and real-space numerical grids to propagate the Kohn–Sham orbitals in real time under the influence of time-varying electromagnetic fields.
The global predictor is a single-level, 4096-entry branch history table. Each entry is a 2-bit saturating counter; the value of this counter determines whether the current branch is taken or not taken. The choice predictor records the history of the local and global predictors to determine which predictor is the best for a particular branch.
Structure prediction can be constrained using experimental data, including SHAPE, enzymatic cleavage, and chemical modification accessibility. Graphical user interfaces are available for Windows, Mac OS X, Linux. Programs are also available for use with Unix-style text interfaces. Also, a C++ class library is available. Yes: source & binaries ...