Search Results for "proteins"
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45 programs for "proteins" with 1 filter applied:
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relax
Molecular dynamics by NMR data analysis
The software package 'relax' is designed for the study of molecular dynamics through the analysis of experimental NMR data. Organic molecules, proteins, RNA, DNA, sugars, and other biomolecules are all supported. It supports exponential curve fitting for the calculation of the R1 and R2 relaxation rates, calculation of the NOE, reduced spectral density mapping, the Lipari and Szabo model-free analysis, study of domain motions via the N-state model and frame order dynamics theories using... -
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Phaistos is a framework for all-atom Monte Carlo simulations of proteins. It incorporates several advanced probabilistic models of protein structure for conformational sampling, efficient move-algorithms and the OPLS and PROFASI forcefields.
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MSqBAT
Label-free protein quantification for LC-MS
MSqBAT is a freely-available all-platform software application for label-free quantification of proteins from LS-MS data. It was developed in the lab of Dr. Christoph Rösli at the Heidelberg Institude for Stem Cells and Experimental Medicine (HI-STEM) and the German Cancer Research Center (DKFZ). It’s main features are 1) Label-free, MS1-based quantification 2) Support both LC-MALDI-MS- as well as LC-ESI-MS data 3) Supports both GeLC-MALDI-MS- and GeLC-ESI-MS data 4) Convenient, graphical user... -
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eSBMTools
python tools for enhanced native structure-based modeling
eSBMTools: python tools that assist the setup and evaluation of native structure-based simulations of proteins and nucleic acids, both at the Cα and all-atom level. The tools interface with GROMACS and support its standard output formats. Information from other sources like bioinformatics or experimental data can be added to the standard native structure-based model (SBM). Publication to be cited: Benjamin Lutz, Claude Sinner, Geertje Heuermann, Abhinav Verma, and Alexander Schug. eSBMTools... -
From improving customer experience through seamless sign-on to making MFA as easy as a click of a button – your login box must find the right balance between user convenience, privacy and security.
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DiSir
In-silico digestion of proteins.
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pipasic
pipasic: Protein Abundance Correction in Metaproteomic Data
Metaproteomic analysis allows studying the interplay of organisms or functional groups and has become increasingly popular also for diagnostic purposes. However, difficulties arise due to the high sequence similarity between related organisms. Further, the state of conservation of proteins between species can be correlated with their expression level which can lead to significant bias in results and interpretation. These challenges are similar but not identical to the challenges arising... -
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Toolkit to examine the topology of a phylogenetic tree, place amino acid substitutions on specific branches, polarize them and compare amino acid sequences of homologous proteins to answer a wide range of questions about protein evolution.
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Just_Annotate_My_Genome
Comprehensively annotate your non-model species genome.
Uses an existing exonerate output or just predicted proteins (e.g. from Transdecoder or just a FASTA file) to prepare gene prediction inputs for Augustus, SNAP and geneid. Exonerate is run (enabled via AAT) if it is not provided. GTF file is produced to judge quality of annotation. Sorts out high quality alignments from those that don't meet the criteria. -
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DNATweezer
A suite of BioPerl wrappers for manipulating DNA and protein sequences
DNATweezer is a suite of Perl scripts for manipulating DNA and proteins sequences. These scripts provide command-line access to the most frequently used BioPerl DNA object methods e.g. reverse-complement and translation of DNA sequences, slicing a sequence alignment, rerooting a phylogenetic tree, and calculating diversity of a population of DNA sequences. -
ChangeGear provides IT staff with the functions required to manage everything from ticketing to incident, change and asset management and more. ChangeGear includes a virtual agent, self-service portals and AI-based features to support analyst and end user productivity.
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xPyder PyMOL Plugin
Analyze and visualize coupled residues and their networks in proteins
xPyder is a PyMOL plugin to analyze and visualize on the 3D structure dynamical cross-correlation matrices (DCCM), linear mutual information (LMI), communication propensities (CP), intra- and inter-molecular interactions (e.g. PSN), and more, to produce highly customizable publication-quality images. xPyder identifies networks (using concepts from graph theory, such as hubs and shortest path searching), compares matrices and focuses the analysis on relevant information by filtering the data... -
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FIAP
Fully Integrated Annotation Pipeline
FIAP (Fully Integrated Annotation Pipeline) is a fast bacterial genome multithreading annotation pipeline written in Perl that detects genes coding for proteins, tRNAs, and rRNAs (5S, 16S and 23S). FIAP also allows users to include an infinite number of custom databases. This feature is extremely valuable because it allows users to add a personal “flavor” to the annotation and optimize the process for a specific bacterial genome. FIAP can annotate single and multiple sequences, which allows... -
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SABLE is a public domain package for structural bioinformatics that can be used to predict from amino acid sequence secondary structure and solvent accessibility profiles in proteins (see Adamczak, Porollo and Meller, Proteins 56, 2004).
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RASPnmr
Protein NMR backbone resonance assignment
RASP uses structure-based chemical shift predictions to solve the backbone resonance assignment problem in protein NMR spectroscopy. This enables rapid determination of highly accurate assignments on the basis of minimal experimental datasets, even for spectroscopically challenging proteins. RASP takes as input spin systems assembled on the basis of an arbitrary set of conventional triple-resonance NMR experiments. Uniquely, RASP is capable of extensive assignments even in the abscence... -
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Smart Virus
Play the role of a virus in a quest to replicate.
A smart virus is born, but it lacks the DNA needed to successfully replicate and create new viruses with smart capabilities. That DNA is found in a master cell, but to find it, you must first go through and infect a series of other cells to obtain the proteins needed to locate the elusive master cell which releases a signaling chemical through diffusion. Track down the origin of this chemical and you track down the master cell and achieve replicative success. -
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PIVOT
PIVOT is a simple yet flexible visualization data tool
PIVOT is a simple yet flexible visualization tool based on Circos (Krzywinski et al., 2009), which offers a fast and aesthetical visualization of data and information. The Protein Interaction Visualization and Observation Tool (PIVOT) was developed specifically for the visualization of protein interaction. It is difficult to spot the proteins that have an interaction when given a large list of proteins but with PIVOT, it is easy to identify the them at a glance. PIVOT displays an image showing... -
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TreeLiker
TreeLiker is a collection of fast algorithms for working with complex
TreeLiker is a collection of fast algorithms for working with complex structured data in relational form. The data can, for example, describe large organic molecules such as proteins or groups of individuals such as social networks or predator-prey networks etc. The algorithms included in TreeLiker are unique in that, in principle, they are able to search given sets of relational patterns exhaustively, thus guaranteeing that if some good pattern capturing an important feature of the problem... -
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AlignMe
Alignment of membrane proteins
AlignMe is a C++ program to align distantly related membrane proteins by including several input parameters. Alignments based on substitution matrices, Position Specific Matrices (PSSMs), hydrophobicity scales and any kind of profiles (membrane predictions, secondary structure predictions etc.). -
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PhpLabware is a web-based groupware application suite tailored to research laboratories. Initial services include databases for reagents (strains, antibodies, plasmids, proteins), pdf files (a 'reprint' repository), and protocols.
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ProteinTracker
Protein Reagent Tracking and Request
A web based application to track protein related reagents including DNA constructs, cell lines, supes, and purified proteins. Supports creating, tracking, and prioritizing requests for transfections and DNA. Includes search and PDF reports. -
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A rule-based modelling framework for allosteric proteins and biochemical networks.
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Software to identify cavities and crevices in proteins. The goal is to be able to take a protein structure, and to differentiate between five different types of environments for each residue: buried, surface, interfacial, cavity, or crevice.
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BLOSpectrum tools provide programs to automatically classify proteins according to SCOP database. In order to achieve such a goal, they implements all the required information theory widgets on BLOSpectrum fingerprints.
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FAUNUS is an object oriented class library for molecular simulation, written in C++. It contains routines and utility programs for, Metropolis Monte Carlo sampling (NVT, NPT, NmuT ensembles), Macromolecules, Proton Titration, Widom Analysis etc.
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TransposonPSI is an analysis tool to identify protein or nucleic acid sequence homology to proteins encoded by diverse families of transposable elements.
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D-finder is a bioinformatic search algorithm for the identification of D-sites in JNK interacting proteins. The algorithm is a combination of pattern matching and a hidden markov model (HMM) based on a training set of known JNK D-sites.