NOVELTIES
Postdoctoral Fellowships of Human Frontier Science Program HFSP are available for scientists who wish to work in foreign laboratories, with emphasis on individuals early in their careers who wish to obtain training in a different field of research. Fellows who return to their home countries are eligible to apply for a Career Development Award. Cross-disciplinary fellowships are intended for postdoctoral fellows with a Ph.D. degree in the physical sciences, chemistry, mathematics, engineering and computer sciences who wish to receive training in biology Registration not required.
Click here for more informationsPublished on 2011-07-14 13:07:04
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design siRNA sequences
Category: SiRNA design
Scitools RNAi design allows: Design siRNA sequences
Scitools RNAi design is a web application to design siRNA sequences. Registration not required.
Click here for more informationsPublished on 2011-07-14 02:07:52
SILVA is a comprehensive on-line resource for quality checked and aligned ribosomal RNA sequence data, free for academic use. SILVA provides comprehensive, quality checked and regularly updated datasets of aligned small (16S/18S, SSU) and large subunit (23S/28S, LSU) ribosomal RNA (rRNA) sequences for all three domains of life (Bacteria, Archaea and Eukarya). Registration not required.
Click here for more informationsPublished on 2011-07-14 02:05:05
"Time Estimation for Bacteria Growth" web application is important for the preparation of chemical- or electro-competent cells and protein expression. The program may be used also for other organisms in the logarithmic stage of growth. It is possible to evaluate the precision of prognosis Registration not required.
Click here for more informationsPublished on 2011-07-14 02:04:18
Primer3 is a very powerful PCR primer design online application permitting one considerable control over the nature of the primers, including size of product desired, primer size and Tm range, and presence/absence of a 3’-GC clamp. Registration not required.
Click here for more informationsPublished on 2011-07-14 02:02:22
Commercial Company. The Charles River Animal Model Evaluation Program allows you to assess the quality and compatibility of available animal models before making a commitment. Whether you have a new research protocol, are conducting or fine-tuning a pilot study, or simply exploring the opportunity to switch to a new animal model, this program can help you make the right choice. Registration not required.
Click here for more informationsPublished on 2011-07-07 12:16:16
ArrayOligoSelector (AOS) systematically designs gene specific long oligo probes for entire genomes. The program optimizes the oligo selections for several parameters, including uniqueness in the genome, internal repeats, self-binding, and GC content. Registration not required.
Click here for more informationsPublished on 2011-06-16 06:29:16
SPICKER is a clustering algorithm to identify the near-native models from a pool of protein structure decoys. The cluster is defined by the pair-wise RMSD metrics of the structural decoys. References: Y. Zhang, J. Skolnick, SPICKER: Approach to clustering protein structures for near-native model selection, Journal of Computational Chemistry, 2004 25: 865-871. Registration not required.
Click here for more informationsPublished on 2011-06-07 01:43:55
MVP (Macromolecular Visualization and Processing) is a convenient tool for visualizing macromolecular structures and their derived information. It supports PDB format and EM density maps and has many drawing styles and color modes. It contains lots of convenient features, including computations of triangulated surfaces, depth, principal axes and estimate the secondary structures for protein structures etc. References: Dong Xu, Yang Zhang (2009) Generating Triangulated Macromolecular Surfaces by Euclidean Distance Transform. PLoS ONE 4(12): e8140. Registration not required.
Click here for more informationsPublished on 2011-06-07 01:42:22
EDTSurf is a open source program to construct triangulated surfaces for macromolecules. It can generate three major macromolecular surfaces of van der Waals surface, solvent-accessible surface and molecular surface (solvent-excluded surface), and identify cavities which are inside of macromolecules. Registration not required.
Click here for more informationsPublished on 2011-06-06 04:06:27
NW-align is simple and robust alignment program for protein sequence-sequence alignments based on the standard Needleman-Wunsch dynamic programming algorithm. The mutation matrix is from BLOSUM62 with gap openning penaly=-11 and gap extension panalty=-1. The source code of this program can be downloaded at the bottom of the NW-align website, which can be easily modified for different purposes. Registration not required.
Click here for more informationsPublished on 2011-06-06 04:04:42
MM-align is designed to structurally align multimeric protein complexes using heuristic iteration of dynamic programming based on TM-score rotation matrix. The multple chains in each complex are first joined, in every possible order, and then simultaneously aligned with cross-chain alignment prevented. The alignment on interface structures can be enhenced by MM-align by an interface-specific weighting factor. A TM-score is reported for assessing the structural similarity of two complexes. References: S. Mukherjee, Y. Zhang, MM-align: a quick algorithm for aligning multiple-chain protein complex structures using iterative dynamic programming. Nucleic Acids Research 2009; 37: e83 Registration not required.
Click here for more informationsPublished on 2011-06-06 04:03:49
TM-align is a computer algorithm for quick and accurate protein structure alignment using dynamic programming and TM-score rotation matrix. An optimal alignment between two proteins, as well as the TM-score, will be reported for each comparison. References:Y. Zhang, J. Skolnick, TM-align: A protein structure alignment algorithm based on TM-score. Nucleic Acids Research, 2005 33: 2302-2309 Registration not required.
Click here for more informationsPublished on 2011-06-06 04:02:49
TM-score is an algorithm to calculate the topological similarity of two protein structures. It can be used to quantitatively access the quality of protein structure predictions relative to the native. Because TM-score weights the close matches stronger than the distant matches, TM-score is more sensitive to the global topology of structures than the often-used root-mean-square deviation (RMSD). References: Y. Zhang, J. Skolnick, Scoring function for automated assessment of protein structure template quality. Proteins, 2004 57: 702-710 Registration not required.
Click here for more informationsPublished on 2011-06-06 04:01:43
BSP-SLIM is a blind molecular docking method on low-resolution protein structures. The method first identifies putative ligand binding sites by structurally matching the target to the template holo-structures. The ligand-protein docking conformation is then constructed by local shape and chemical feature complementarities between ligand and the negative image of binding pockets. Registration not required.
Click here for more informationsPublished on 2011-06-05 14:00:31
BSpred is a neural network based algorithm for predicting binding site of proteins from amino acid sequences. The algorithm was extensively trained on the sequence-based features including protein sequence profile, secondary structure prediction, and hydrophobicity scales of amino acids. References: S Mukherjee, Y Zhang Protein-protein complex structure prediction by multimeric threading and template recombination. Structure, in press (2011). Registration not required.
Click here for more informationsPublished on 2011-06-05 13:59:19
COTH (CO-THreader) is a multiple-chain protein threading algorithm to identify and recombine the protein complex structures from both tertiary and complex structure libraries. It first generates complex query-template alignments by sequence profile-profile alignment assisted by the ab initio binding-site predictions from BSpred. The monomer structures from tertiary template library are then combined into the complex framework by structure superposition. Registration not required.
Click here for more informationsPublished on 2011-06-05 13:58:25
ANGLOR is a machine-learning based algorithm for ab initio prediction of protein backbone torsion angles. For a given amino acid sequence, the real-value backbone torsion angles (phi and psi) for each residue are predicted by the combination of the neural network training and the support vector machine. References: S. Wu, Y. Zhang. ANGLOR: A Composite Machine-Learning Algorithm for Protein Backbone Torsion Angle Prediction. PLoS ONE 2008; 3: e3400. Registration not required.
Click here for more informationsPublished on 2011-06-05 13:57:18
SVMSEQ is a new algorithm for protein residue-residue contact prediction using Support Vector Machines. References: S. Wu, Y. Zhang. A comprehensive assessment of sequence-based and template-based methods for protein contact prediction. Bioinformatics, vol 24, 924-931 (2008). Registration not required.
Click here for more informationsPublished on 2011-06-05 13:56:19
HAAD is a computer algorithm for constructing hydrogen atoms from protein heavy-atom structures. The hydrgen is added by minimizing atomic overlap and encouraging hydrogen bonding. References: Yunqi Li, Roy Ambrish and Yang Zhang, HAAD: A Quick Algorithm for Accurate Prediction of Hydrogen Atoms in Protein Structures, PLoS One, 2009 4: e6701 Registration not required.
Click here for more informationsPublished on 2011-06-05 13:55:19
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