:: DESCRIPTION
TOPS & Tops editor are source code of TPOS dadabase (an enhanced database of protein structural topology).
::DEVELOPER
University of Leeds Bioinformatics Group
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Ioannis Michalopoulos, Gilleain M. Torrance1, David R. Gilbert1 and David R. Westhead
TOPS: an enhanced database of protein structural topology
Nucl. Acids Res. (2004) 32 (suppl 1): D251-D254.
:: DESCRIPTION
PROTEUS is an universal protein structure prediction server that will take any query protein sequence and predict the secondary structure, membrane spanning helices, membrane spanning beta strands, signal peptides, and 3D structures.For water-soluble protein Proteus is able to achieve a very high level of accuracy (Q3=88%, SOV=90%). In the rare situation (20-30%) where a query protein shows no similarity whatsoever to any known structure, PROTEUS is still able to achieve a Q3 score of 79%. Proteus is not restricted to generating accurate secondary structures for water-soluble proteins, as it appears to perform well for integral membrane proteins (both helix-containing proteins and beta-sheet containing porins) that have remote homologues or a portion of a homologue in the PDB.
::DEVELOPER
Wishart Pharmaceutical Research Group
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Scott Montgomerie, Shan Sundararaj, Warren J Gallin and David S Wishar
Improving the accuracy of protein secondary structure prediction using structural alignment
BMC Bioinformatics 2006, 7:301
:: DESCRIPTION
ProSMoS searches for 3D patterns in protein structures, e.g. find all proteins with a fold defined by a user.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
S-Y.Shi, B.Chitturi, and N.V.Grishin (2009)
“ProSMoS server: a pattern-based search using interaction matrix representation of protein structures.”
Nucl. Acids Res. (2009) doi: 10.1093/nar/gkp316 First published online: May 6, 2009
:: DESCRIPTION
PROTARCH package uses a united-residue representation of the polypeptide chain and the Conformational Space Annealing search method to predict a protein structure. The key stage of the method is global optimization of the energy of a polypeptide chain at the simplified united-residue level. PROTARCH also includes computational tools to carry out cluster analysis and construction of all-atom backbone from the united-residue chain using the dipole-path method.
::DEVELOPER
Computational Biology Service Unit
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
Jackal is a collection of programs designed for the modeling and analysis of protein structures. Its core program is a versatile homology modeling package nest. JACKAL has the following capabilities: 1) comparative modeling based on single, composite or multiple templates; 2) side-chain prediction; 3) modeling residue mutation, insertion or deletion; 4) loop prediction; 5) structure refinement; 6) reconstruction of protein missing atoms;7) reconstruction of protein missing residues; 8) prediction of hydrogen atoms; 9) fast calculation of solvent accessible surface area; 10) structure superimposition.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
PROCHECK checks the stereochemical quality of a protein structure, producing a number of PostScript plots analysing its overall and residue-by-residue geometry. It includes PROCHECK-NMR for checking the quality of structures solved by NMR.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
AQUA and PROCHECK-NMR: programs for checking the quality of protein structures solved by NMR.
Laskowski RA, Rullmannn JA, MacArthur MW, Kaptein R, Thornton JM.
J Biomol NMR. 1996 Dec;8(4):477-86.
:: DESCRIPTION
BnP is the Buffalo’s Pittsburgh Interface for complete protein phasing suite includes SnB and Phases.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Weeks, C. M., Blessing, R. H., Miller, R., Mungee, R., Potter, S. A., Rappleye, J., Smith, G. D., Xu, H. & Furey, W.
Towards automated protein structure determination: BnP, the SnB-PHASES interface,
Z. Kristallogr. 217, 686-693 (2002).
:: DESCRIPTION
PROSPECT (PROtein Structure Prediction and Evaluation Computer Toolkit) is a threading-based protein structure prediction system. PROSPECT is designed particularly for the recognization of the fold template whose sequence has insignificant homology to the target sequence.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
D. Kim, D. Xu, J. Guo, K. Ellrott, Ying Xu,
“PROSPECT II: protein structure prediction program for genome-scale application“,
Protein Engineering, 16 (9), 641 – 650, 2003
:: DESCRIPTION
DomainParser uses a new algorithm for the decomposition of a multi-domain protein into individual structural domains. The underlying principle used is that residue-residue contacts are denser within a domain than between domains. We have formulated the domain decomposition problem as a network flow problem, in which each residue is represented as a node of a network and each residue-residue contact is represented as an edge with a particular capacity, depending on the type of the contact.
::DEVELOPER
Dr. Ying Xu @ CSBL
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Ying Xu, Dong Xu, and Harold N. Gabow.
Protein Domain Decomposition using a Graph-Theoretic Approach.
Bioinformatics. 16:1091-1104. 2000.
:: DESCRIPTION
Graphlet kernelis a supervised learning framework for annotating functional residues in protein structures. Each residue is represented as a vector of counts of labeled non‐isomorphic subgraphs (called graphlets) in the protein contact graph, and a similarity measure between two vertices is expressed as the inner product of their respective count vectors
::DEVELOPER
the Algorithms and Computational Biology Lab
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Vladimir Vacic, Lilia Iakoucheva, Stefano Lonardi, and Predrag Radivojac
“Graphlet kernels for prediction of functional residues in protein structures”
Journal of Computational Biology. 17(1):55-72. (2010)
