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UCSF Chimera (or simply Chimera) is an extensible program for interactive visualization and analysis of molecular structures and related data, including density maps, supramolecular assemblies, sequence alignments, docking results, trajectories, and conformational ensembles. [1]
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 ...
Software to identify cross-linked peptides from mass spectrometric data written in Java that can be used for a wide variety of cross linkers and proteases used in the cross linking MS experiment; it compares theoretical peptide-peptide cross link combinations for the analyzed proteins to MS/MS data.
SpliceR An R package for classification of alternative splicing and prediction of coding potential from RNA-seq data. SpliceSEQ SpliceViewer is a Java application that allows researchers to investigate alternative mRNA splicing patterns in data from high-throughput mRNA sequencing studies. Sequence reads are mapped to splice graphs that ...
Protein structure prediction for disease research Tn-grid 8 papers [51] 2013-12-19 3,201 volunteers [52] Windows, Linux, macOS [53] No University of Trento: Genetics: Currently deploying gene@home work to expand gene networks World Community Grid: 77 papers [54] 2004-11-16 85,119 volunteers [55] Windows, Linux, ARM, macOS, Android [56] GPU CPU
Linear representation of protein sequence above shows the relative positions of the conserved amino acid motifs in the structure (colors match with 3D structure) The ABC domain consists of two domains, the catalytic core domain similar to RecA -like motor ATPases and a smaller, structurally diverse α-helical subdomain that is unique to ABC ...
Apache Tomcat (called "Tomcat" for short) is a free and open-source implementation of the Jakarta Servlet, Jakarta Expression Language, and WebSocket technologies. It provides a "pure Java" HTTP web server environment in which Java code can also run. Thus it is a Java web application server, although not a full JEE application server.
Quantitative structure–activity relationship models (QSAR models) are regression or classification models used in the chemical and biological sciences and engineering. Like other regression models, QSAR regression models relate a set of "predictor" variables (X) to the potency of the response variable (Y), while classification QSAR models ...