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predict both 3-state and 8-state secondary structure using conditional neural fields from PSI-BLAST profiles: Webserver/downloadable: server download: 2011 GOR: Information theory/Bayesian inference: Many implementations: Basic GOR GOR V: 2002 (GOR V) Jpred: Multiple Neural network assignment from PSI-BLAST and HMMER profiles. Predicts ...
Valence shell electron pair repulsion (VSEPR) theory (/ ˈ v ɛ s p ər, v ə ˈ s ɛ p ər / VESP-ər, [1]: 410 və-SEP-ər [2]) is a model used in chemistry to predict the geometry of individual molecules from the number of electron pairs surrounding their central atoms. [3]
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.
10.1: 2016-11-14: Proprietary commercial software: Paid: Windows, Linux: deal.II: Comprehensive set of tools for finite element codes, scaling from laptops to clusters with 100,000+ cores. Written in C++, it supports all widely used finite element types, serial and parallel meshes, and h and hp adaptivity.
The nitrogen in ammonia has 5 valence electrons and bonds with three hydrogen atoms to complete the octet.This would result in the geometry of a regular tetrahedron with each bond angle equal to arccos(− 1 / 3 ) ≈ 109.5°.
Name Description Knots [Note 1]Links References trRosettaRNA: trRosettaRNA is an algorithm for automated prediction of RNA 3D structure. It builds the RNA structure by Rosetta energy minimization, with deep learning restraints from a transformer network (RNAformer). trRosettaRNA has been validated in blind tests, including CASP15 and RNA-Puzzles, which suggests that the automated predictions ...
The QUAO analysis allows users to study bonding patterns in molecules or small to medium size with a high degree of accuracy. While the program does not directly perform molecular mechanics , it can do mixed quantum mechanics and molecular mechanics calculations through effective fragment potentials or through an interface with the Tinker code.
A computer-assisted design (CAD) tool for synthetic biology, used to design genetic constructs based on grammar rules. Linux, macOS, Windows: Apache License 2.0 GenoCAD Team (Virginia Bioinformatics Institute) Genomespace: Centralized web application that provides data format transformations and facilitates connections with other bioinformatics ...
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