Search Results for "proteins" - Page 5
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Showing 175 open source projects for "proteins"
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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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Autmated Peptide Screening
Screening peptides for MHC and/or MHC-T cell receptor affinity
Modified version of AutoGrow, autogrow.ucsd.edu/ , with a mutation script added in the class files, and a global change of the defined mutation point from Hydrogen atoms to Calphas, to allow placement of Amino Acids. Deposited are 3 versions, used for my PhD Thesis. These allow for mutation of short 2-15 amino acid peptides, and associated screening of these using AutoDock or AutoDock Vina, allowing for 8 CPU systems to screen 10K peptides a day or 1-2K with flexible residues added in. A... -
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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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Mirroring co-evolving trees
Mirroring co-evolving trees in the light of their topologies
Determining the interaction partners among protein/domain families poses hard computational problems, in particular in the presence of paralogous proteins. Available approaches aim to identify interaction partners among protein/domain families through maximizing the similarity between trimmed versions of their phylogenetic trees. Since maximization of any natural similarity score is computationally difficult, many approaches employ heuristics to evaluate the distance matrices... -
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EnzML
Prediction of enzyme commission numbers of proteins.
Code now superseded by ml2db. You can download ml2db at https://sourceforge.net/projects/ml2db/ If using this code, please quote: BMC Bioinformatics, EnzML: multi-label prediction of enzyme classes using InterPro signatures, Luna De Ferrari, Stuart Aitken, Jano van Hemert and Igor Goryanin http://www.biomedcentral.com/1471-2105/13/61 -
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ChEMBLspace
ChEMBLSpace explores the target-ligand network based on ChEMBL data.
ChEMBLSpace is a Java application for the visual exploration and analysis of the chemogenomic space extracted from the ChEMBL database. The space is defined as a network whereby the nodes correspond to proteins that have at least one ligand in common with other protein targets. The user can interactively select proteins and list their ligands and then iteratively design an activity profile by adding more targets or anti-targets to the selection and adjusting protein-specific activity thresholds... -
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SeqHunter2
a stand-alone bioinformatics software for querying genome sequences
SeqHunter2 is a stand-alone software with graphical user interface, running on Microsoft windows system. It is programmed with the following functions: 1) collect and manage local sequence databases; 2) run blast search by using a batch of sequences and with abundant output formats; 3) extract sequences by a set of IDs or coordinates; 4) generate sequences alignment; 5) edit sequence and translate nucleotide to proteins; 6) browse genome and search genes; 7) collect resource items and link... -
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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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inhibitomev1
A systems-level host-factor survey of viral proteins that modulate inn
Viral gene products that modulate the cellular antiviral immune response targets of such viral proteins are often not known. We performed a functional proteomic approach to identify cellular binding partners of viral innate immune modulators. We used a Tet-on system to express such viral proteins in HEK293 cells and isolated protein complexes by tandem affinity purification. Altogether, we used 70 viral proteins (from 30 viruses) resulting in identification of 579 unique host proteins... -
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cascade_scan
cascade_scan
Signal transduction plays an essential role in response to environment changes. This biological process is usually characterized by phosphorylation/dephosphorylation of some key proteins (e.g. kinases) and generally involves in a signal cascade. The signal transduction process often starts from a membrane protein (usually a membrane surface receptor), comes by a series of intercellular signaling proteins and then transfers to transcription factors in nucleolus, and subsequently raises... -
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ProtDB
A protein database management framework
This repository is outdated, the project has been renamed to SysBioTK and can be found at: https://sysbiotk.sourceforge.io/ ProtDB is a framework which aims to aid in the management of information on proteins from several databases, storing the information in a library. Several search functions are also included in order to filter the proteins in the library. Support for different screenings, such as control groups, is also included. -
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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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SMMP (Simple Molecular Mechanics for Proteins) is a program library for protein simulations with an emphasis on advanced Monte Carlo algorithms. It includes various force fields to calculate the energy of a protein and protein-protein interactions.
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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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GuiTope
Identifies significant regions in proteins from peptide selections.
Random-sequence peptide libraries are a commonly used tool to identify novel ligands for binding antibodies, other proteins, and small molecules. It is often of interest to compare the selected peptide sequences to the natural protein binding partners to infer the exact binding site or the importance of particular residues. GuiTope provides a convenient method for comparing selected peptide sequences to protein sequences, including flexible alignment parameters, novel alignment features... -
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PDBpaint mirror: http://cbdm.mdc-berlin.de/~pdbpaint/ PDBpaint is a server for developers doing prediction structure from raw sequences of proteins.
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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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PDBtag is a webtool devoted to display the structure of proteins within a small java applet and tag it using a extra webservice such as Pfam or Uniprot. It can also display specific annotations you want.
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BioSpring is a molecular simulation software based on a spring network model, including non-bonded interactions, especially designed for Interactive Molecular Dynamics. It incorporates MyPal for locating ion binding sites and IMPALA for interactive placement of membrane proteins in a membrane environment.
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This is a research-level program used to track protein translocation in live cell imaging experiments when the nucleus is not specifically marked by either stain or transfected fluorescent proteins.
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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.