KYG – RNA Interface Residue Prediction from Protein 3D Structure

KYG

:: DESCRIPTION

KYG predicts RNA interfaces out of 3D structures of RNA-binding proteins.

::DEVELOPER

Center for Informational Biology, Ochanomizu University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C++ COmpiler

:: DOWNLOAD

 KYG

:: MORE INFORMATION

Citation

Kim, O.T.P., Yura, K., Go, N. (2006)
Amino acid residue doublet propensity in the protein-RNA interface and its application to RNA interface prediction.
Nuc. Acids. Res. 34 (22), 6450-6460.

wLake 1.7 – Detecting Structural Water Molecules

wLake 1.7

:: DESCRIPTION

wLake is a tool which allows to identify clusters of a structural water molecules in given superimposed 3D structures.

::DEVELOPER

Aksianov E. (evaksianov@belozersky.msu.ru)

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Linux/ Windows

:: DOWNLOAD

 wLake

:: MORE INFORMATION

Citation

J Bioinform Comput Biol. 2008 Aug;6(4):775-88.
Conserved water molecules in X-ray structures highlight the role of water in intramolecular and intermolecular interactions.
Aksianov E1, Zanegina O, Grishin A, Spirin S, Karyagina A, Alexeevski A.

HAAD – Quick and Accurate Hydrogen Atom Addition

HAAD

:: DESCRIPTION

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.

::DEVELOPER

Yang Zhang’s Research Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
:: DOWNLOAD

 HAAD

:: MORE INFORMATION

Citation

Yunqi Li, Ambrish Roy and Yang Zhang,
HAAD: A Quick Algorithm for Accurate Prediction of Hydrogen Atoms in Protein Structures,
PLoS One, 2009 4: e6701

MVP/MVP-Fit 2.0 – Macromolecular Visualization and Processing

MVP/MVP-Fit 2.0

:: DESCRIPTION

MVP (Macromolecular Visualization and Processing) is mainly for the illustration and processing of structure-related information which is useful in structure prediction.

MVP-Fit can flexibly move only one domain of the whole model during the fitting process and still keep all the geometric restraints of bond lengths, bond angles and steric clashes for the model.

::DEVELOPER

Yang Zhang’s Research Group

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux/Windows
:: DOWNLOAD

 MVPMVP-Fit

:: MORE INFORMATION

Citation

D Xu, Y Zhang,
MVP-Fit: A Convenient Tool for Flexible Fitting of Protein Domain Structures with Cryo-Electron Microscopy Density Map ,
(2011, in preparation).

EDTSurf – Quick and Accurate Construction of Macromolecular Surfaces

EDTSurf

:: DESCRIPTION

EDTSurf is a open source program to construct triangulated surfaces for macromolecules. It generates three major macromolecular surfaces: van der Waals surface, solvent-accessible surface and molecular surface (solvent-excluded surface). EDTsurf also identifies cavities which are inside of macromolecules.

:DEVELOPER

Yang Zhang’s Research Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/Windows
:: DOWNLOAD

  EDTSurf

:: MORE INFORMATION

Citation

D. Xu, Y. Zhang (2009)
Generating Triangulated Macromolecular Surfaces by Euclidean Distance Transform.
PLoS ONE 4(12): e8140.

FG-MD – High-resolution Proteins Structure Refinement by Fragment-Guided MD simulation

FG-MD

:: DESCRIPTION

FG-MD is a molecular dynamics (MD) based algorithm for atomic-level protein structure refinement. Given an initial protein structure, 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 to re-shape the funnel of the MD energy landscape and guide the MD conformational sampling. FG-MD aims to refine the initial models closer to the native structure. It can also improve the local geometry of the structures by removing the steric clashes and improving the torsion angle and the hydrogen-binding networks.

::DEVELOPER

Yang Zhang’s Research Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Proteins. 2011;79 Suppl 10:147-60. doi: 10.1002/prot.23111. Epub 2011 Aug 23.
Automated protein structure modeling in CASP9 by I-TASSER pipeline combined with QUARK-based ab initio folding and FG-MD-based structure refinement.
Xu D1, Zhang J, Roy A, Zhang Y.

REMO 2.0 – Construct Full-atom Protein Models from C-alpha Traces

REMO 2.0

 

:: DESCRIPTION

REMO is a multifunctional program for constructing full-atom protein models from C-alpha traces by optimizing the backbone hydrogen-bonding networks. It gives options to choose models which are close to a given template or have more hydrogen-bonds. It has also options to build hydrogen atoms and side chain heavy atoms. The bond length and bond angle parameters are taken from CHARMM22.

::DEVELOPER

Yang Zhang’s Research Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / Mac OsX
  • Perl

:: DOWNLOAD

 REMO

:: MORE INFORMATION

Citation

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

BSP-SLIM – Low-Resolution Docking on Predicted Structures

BSP-SLIM

:: DESCRIPTION

BSP-SLIM is a new method for ligand-protein blind docking using low-resolution protein structures.

::DEVELOPER

Yang Zhang’s Research Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Borwser
:: DOWNLOAD

 NO 

:: MORE INFORMATION

Citation

Proteins. 2012 Jan;80(1):93-110. doi: 10.1002/prot.23165. Epub 2011 Oct 4.
BSP-SLIM: a blind low-resolution ligand-protein docking approach using predicted protein structures.
Lee HS1, Zhang Y.

SAXSTER – SAXS-assisted Protein Fold Recognition

SAXSTER

:: DESCRIPTION

SAXSTER is a new algorithm to combine small-angle x-ray scattering (SAXS) data and threading for high-resolution protein structure determination. Given a query sequence, SAXSTER first generates a list of template alignments using the MUSTER threading program from the PDB library. The SAXS data will then be used to prioritize the best template alignments based on the SAXS profile match, which are finally used for full-length atomic protein structure construction

::DEVELOPER

Yang Zhang’s Research Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Borwser
:: DOWNLOAD

 NO 

:: MORE INFORMATION

Citation

Biophys J. 2011 Dec 7;101(11):2770-81. doi: 10.1016/j.bpj.2011.10.046.
Improving protein template recognition by using small-angle x-ray scattering profiles.
dos Reis MA1, Aparicio R, Zhang Y.

ModRefiner 20111024 – High-resolution Protein Structure Refinement

ModRefiner 20111024

:: DESCRIPTION

ModRefiner is an algorithm for atomic-level, high-resolution protein structure refinement, which can start from either C-alpha trace, main-chain model or full-atomic model. Both side-chain and backbone atoms are completely flexible during structure refinement simulations, where conformational search is guided by a composite of physics- and knowledge-based force field. ModRefiner has an option to allow for the assignment of a second structure which will be used as a reference to which the refinement simulations are driven. One aim of ModRefiner is to draw the initial starting models closer to their native state, in terms of hydrogen bonds, backbone topology and side-chain positioning. It also generates significant improvement in physical quality of local structures. The standalone program also supports ab initio full-atomic relaxation, where the refined model is not restrainted by the initial model or the reference model.

::DEVELOPER

Yang Zhang’s Research Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/Windows
:: DOWNLOAD

  ModRefiner

:: MORE INFORMATION

Citation

Dong Xu and Yang Zhang.
Improving Physical Realism and Structural Accuracy of Protein Models by a Two-step Atomic-level Energy Minimization
(in preparation).