NOVELTIES
REMO is a new algorithm for constructing protein atomic structures from C-alpha traces by optimizing the backbone hydrogen-bonding networks. References: Yunqi Li and Yang Zhang. REMO: A new protocol to refine full atomic protein models from C-alpha traces by optimizing hydrogen-bonding networks. Proteins, 2009, 76: 665-676. Registration not required.
Click here for more informationsPublished on 2011-06-05 13:54:28
FG-MD is a molecular dynamics (MD) based algorithm for high-resolution protein structure refinement. Given an initial protein or protein complex 3D model (either in C-alpha or full-atom), FG-MD first identifies analogous fragments from the PDB by the structural alignment program TM-align. Spatial restraints extracted from the fragments are then used to guide the molecular dynamics simulations. In general, FG-MD aims to refine the initial models closer to the native structure. It also improves the local geometry of the structures by removing the steric clashes and improving the torsion angle and the hydrogen-binding networks. Registration not required.
Click here for more informationsPublished on 2011-06-05 13:53:30
SEGMER is a segmental threading algorithm designed to recoginzing substructure motifs from the Protein Data Bank (PDB) library. It first splits target sequences into segments which consists of 2-4 consecutive or non-consecutive secondary structure elements (alpha-helix, beta-strand). The sequence segments are then threaded through the PDB to identify conserved substructures. It often identifies better conserved structure motifs than the whole-chain threading methods, especially when there is no similar global fold existing in the PDB. References: S. Wu, Y. Zhang. SEGMER:identifying protein sub-structural similarity by segmental threading. Structure, vol 18, 858-867 (2010). Registration not required.
Click here for more informationsPublished on 2011-06-05 13:41:46
MUSTER (MUlti-Sources ThreadER) is a new protein threading algorithm to identify the template structures from the PDB library. It generate sequence-template alignments by combining sequence profile-profile alignment with multiple structural information. References: S. Wu, Y. Zhang. MUSTER: Improving protein sequence profile-profile alignments by using multiple sources of structure information. Proteins: Structure, Function, and Bioinformatics 2008; 72: 547-556. Registration not required.
Click here for more informationsPublished on 2011-06-05 13:40:21
LOMETS (Local Meta-Threading-Server) is a locally installed meta-server for protein structure prediction. It generates 3D models by collecting consensus target-to-template alignments from 9 locally-installed threading programs (FUGUE, HHsearch, PAINT, PPA-I, PPA-II, PROSPECT2, SAM-T02, SPARKS, SP3). References: S. Wu, Y. Zhang. LOMETS: A local meta-threading-server for protein structure prediction. Nucleic Acids Research 2007; 35: 3375-3382 Registration not required.
Click here for more informationsPublished on 2011-06-05 13:39:18
QUARK is a computer algorithm for ab initio protein folding and protein structure prediction, which aims to construct the correct protein 3D model from amino acid sequence only. QUARK models are built from a small fragments (1-20 residues long) by replica-exchange Monte Carlo simulation under the guide of an atomic-level knowledge-based force field. QUARK was ranked as the No 1 server in Free-modeling (FM) in CASP9. Since no global template information is used in QUARK simulation, the server is suitable for proteins which are considered without homologous templates. References: D. Xu, Y. Zhang, QUARK Ab Intio Protein Structure Prediction I: Methodology developments (in preparation) Registration not required.
Click here for more informationsPublished on 2011-06-05 13:38:10
sTRAP (Transcription factor Affinity Prediction) is a web application to calculate how the binding of different TFs is affected by the sequence differences (e.g. by single-nucleotide polymorphism) Registration not required.
Click here for more informationsPublished on 2011-05-24 10:13:54
PASTAA is a web app to evaluate if there is a regulatory association between transcription factors and groups of genes. Input: List of gene IDs. Registration not required.
Click here for more informationsPublished on 2011-05-20 13:20:47
TRAP (multiple sequences) is a web tool to evaluate which TFs are over represented in a data set (Chip-seq or Chip-chip data). Registration not required.
Click here for more informationsPublished on 2011-05-20 12:10:06
TRAP (from Max Planck Isntitute of Molecular genetics) is a web tool to predict which transcription factors are susceptible to bind a DNA sequence (e.g. promotor of a gene of interest) Registration not required.
Click here for more informationsPublished on 2011-05-20 12:00:40
Which sequence is more susceptible to be bound to your transcription factor represented by your matrix? Input data: Multiple DNA sequences, personal matrix. Registration not required.
Click here for more informationsPublished on 2011-05-20 11:52:13
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Category: Proteomics data analysis, Gene expression
GenPattern Proteomics allows: Broad
GenePatern allowr various data analyses for proteomics: MRM-MS; peptide signature prediction; PEPPeR algorhitms; detection and alignment features across runs in LC-MS; support for SELDI/MALDI data. Registration not required.
Click here for more informationsPublished on 2011-05-16 12:46:39
The TRIP Database is a clinical search engine designed to allow clinicians to quickly find answers to their clinical questions using the best available evidence. The creation of the TRIP Database allowed the simultaneous searching of multiple sites, hence speeding up the question answering process. The evolution of the TRIP Database has been guided by the desire to answer real clinical questions using the principles of evidence based medicine. TRIP Database Ltd’s involvement in clinical question answering has shown the type of material that is useful in answering genuine questions health professionals have. Registration not required.
Click here for more informationsPublished on 2011-05-16 12:44:04
Upload a file containing Fasta-formatted DNA sequences or alternatively a *.aln file, select the control one wants over the primer design from an extensive list Registration not required.
Click here for more informationsPublished on 2011-05-12 08:01:07
Proteome Commons is a public proteomics database for annotations and other information linked to the Tranche data repository and to other resources. The site is a project management tool that functions like some social networking websites. Users register, sign into the system, create a new project, and then invite colleagues and collaborators to the project. Invitees are given permissions and responsibilities by the project’s creator. Registration required.
Click here for more informationsPublished on 2011-05-11 06:11:06
Oligo Analysis Tool calculates molecular weight (MW), extinction coefficient (E260), pmoles/µg, pmoles/OD and µg/OD. Also displayed for your convenience are the % GC Content, melting temp (TM),the reverse complement of the oligo sequence you enter, and show primer-dimer sets Registration not required.
Click here for more informationsPublished on 2011-05-06 11:59:01
OpenMS is an open-source software C++ library for LC/MS data management and analyses, developed by researchers at three German Universities in Tübingen, Berlin and Saarbrücken. It offers an infrastructure for the development of mass spectrometry related software. OpenMS is free software available under the LGPL. Registration not required.
Click here for more informationsPublished on 2011-05-04 11:05:28
The Trans-Proteomic Pipeline (TPP) is a collection of integrated tools for MS/MS proteomics, developed at the Seattle Proteomics Center. Registration not required.
Click here for more informationsPublished on 2011-05-04 10:55:34
GenePattern is a powerful genomic analysis platform that provides access to more than 150 tools for gene expression analysis, proteomics, SNP analysis, flow cytometry, RNA-seq analysis, and common data processing tasks. A web-based interface provides easy access to these tools and allows the creation of multi-step analysis pipelines that enable reproducible in silico research. Registration not required.
Click here for more informationsPublished on 2011-05-04 09:47:29
Mascot is a powerful and widely used search engine that uses mass spectrometry data to identify proteins from primary sequence databases.
Click here for more informationsPublished on 2011-05-04 08:46:20
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