PINTS – Patterns In Non-homologous Tertiary Structures

PINTS

:: DESCRIPTION

PINTS finds reoccuring three-dimensional patterns of amino acids. These amino-acids are close in space but not necessarily close or co-linear in sequence, for example the serine-protease catalytic triad. Unlike other tools, PINTS does not aim to find proteins adopting a similar fold.

::DEVELOPER

the Cell Networks Protein Evolution group based at the University of Heidelberg.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 PINTS

:: MORE INFORMATION

Citation

A. Stark, S. Sunyaev, R.B. Russell,
A model for statistical significance of local similarities in structure‘,
J. Mol. Biol, 326, 1307-1316, 2003.

SLITHER – Prediction of free Energy Profile along the Access Channel within a Protein

SLITHER

:: DESCRIPTION

SLITHER is a web server that can generate contiguous conformations of a molecule along a curved tunnel inside a protein, and the binding free energy profile along the predicted channel pathway.

::DEVELOPER

SLITHER team

:: SCREENSHOTS

n/a

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2009 Jul;37(Web Server issue):W559-64. doi: 10.1093/nar/gkp359. Epub 2009 May 11.
SLITHER: a web server for generating contiguous conformations of substrate molecules entering into deep active sites of proteins or migrating through channels in membrane transporters.
Lee PH1, Kuo KL, Chu PY, Liu EM, Lin JH.

XmMol 3.1 – Macromolecular Visualization and Modeling tool

XmMol 3.1

:: DESCRIPTION

XmMol is a desktop macromolecular visualization and modeling tool designed to be easy to use, configure and enhance. Its graphics are based on X11, and part of its user interface is based on Motif. Thus it provides a way of displaying structures on any X11 server.

::DEVELOPER

XmMol team

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / SUN Solaris/ Dec Alpha

:: DOWNLOAD

 XmMol

:: MORE INFORMATION

Citation

J Mol Graph. 1995 Feb;13(1):67-72, 62.
XmMol: an X11 and motif program for macromolecular visualization and modeling.
Tufféry P.

GRE4Zn – Geometric REstriction for Zinc-binding

GRE4Zn

:: DESCRIPTION

GRE4Zn is a novel computational program to characterize the zinc-binding sites in protein structures, by restricting the distances between zinc and its coordinating atoms.

::DEVELOPER

Haiyan Liu Group

:: SCREENSHOTS

n/a

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Biochim Biophys Acta. 2014 Jan;1844(1 Pt B):171-80. doi: 10.1016/j.bbapap.2013.03.001. Epub 2013 Mar 14.
Computationally characterizing and comprehensive analysis of zinc-binding sites in proteins.
Liu Z1, Wang Y, Zhou C, Xue Y, Zhao W, Liu H.

BALBES 1.1.5 – Molecular Replacement

BALBES 1.1.5

:: DESCRIPTION

BALBES is a system for solving protein structures using x-ray crystallographic data. Molecular Replacement(MR) is its core scientific method. BALBES aims to integrate all components, necessary for finding a solution structure by MR, into one system. It consists of a database, scientific programs and a python pipeline. The system is automated so that it needs no user’s intervention when running complicated combination of jobs such as model searching, molecular replacement and refinement.

:: DEVELOPER

Computational Crystallography Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 BALBES

:: MORE INFORMATION

Citation:

F.Long, A.Vagin, P.Young and G.N.Murshudov
BALBES: a Molecular Replacement Pipeline
Acta Cryst. D64 125-132(2008)

Rclick – Comparison of RNA 3D Structures

Rclick

:: DESCRIPTION

Rclick is capable of superimposing the RNA 3D structures by using the algorithm of clique matching and 3D least squares fitting.

::DEVELOPER

Rclick team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Rclick: A web server for comparison of RNA 3D structures.
Nguyen MN, Verma C.
Bioinformatics. 2014 Nov 12. pii: btu752.

NAFlex – Analysis of Nucleic Acids Flexibility

NAFlex

:: DESCRIPTION

NAFlex is a web interface for the study of Nucleic Acids Flexibility.NAFlex allows the user to incorporate structures from the Protein Data Bank, filling gaps and removing structural inconsistencies if any. It also allows to build canonical (average or sequence-adapted) nucleic acid structures using a variety of predefined internal libraries and to create specific nucleic acids conformations.

::DEVELOPER

The Molecular Modeling and Bioinformatics (MMB) research group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2013 Jul;41(Web Server issue):W47-55. doi: 10.1093/nar/gkt378. Epub 2013 May 17.
NAFlex: a web server for the study of nucleic acid flexibility.
Hospital A1, Faustino I, Collepardo-Guevara R, González C, Gelpí JL, Orozco M.

MDWeb / MDMoby – Web-based Platform for Molecular Dynamics Simulations

MDWeb / MDMoby

:: DESCRIPTION

MDWeb is a personal workspace providing standard protocols to prepare structures, run standard molecular dynamics simulations and to analyze trajectories. MDWeb and MDMoby constitute a web-based platform to help access to molecular dynamics (MD) in the standard and high-throughput regime. The platform provides tools to prepare systems from PDB structures mimicking the procedures followed by human experts. It provides inputs and can send simulations for three of the most popular MD packages (Amber, NAMD and Gromacs). Tools for analysis of trajectories, either provided by the user or retrieved from our MoDEL database are also incorporated.

::DEVELOPER

the Molecular Recognition & Bioinformatics Group.

:: SCREENSHOTS

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 No

:: MORE INFORMATION

Citation

MDWeb and MDMoby: an integrated web-based platform for molecular dynamics simulations.
Hospital A, Andrio P, Fenollosa C, Cicin-Sain D, Orozco M, Gelpí JL.
Bioinformatics. 2012 May 1;28(9):1278-9. Epub 2012 Mar 21.

SHIFTX2 1.13 – Improved Protein Chemical Shift Prediction

SHIFTX2 1.13

:: DESCRIPTION

SHIFTX2 is a web server that predicts 1H, 13C, and 15N protein chemical shifts using the 3D structure (PDB coordinates) of the protein of interest for both backbone and sidechain atoms.SHIFTX2 combines ensemble machine learning methods with sequence alignment-based methods to calculate protein chemical shifts for backbone and side chain atoms. SHIFTX2 has been trained on a carefully selected set of 197 proteins and tested on a separate set of 61 proteins. Both the training and testing sets consisted of high resolution X-ray structures (<2.1 Angs) with carefully verified chemical shifts assignments. SHIFTX2 is able to attain correlation coefficients between experimentally observed and predicted backbone chemical shifts of 0.9800 (15N), 0.9959 (13CA), 0.9992 (13CB), 0.9676 (13CO), 0.9714 (1HN), 0.9744 (1HA) and RMS errors of 1.1169, 0.4412, 0.5163, 0.5330, 0.1711, and 0.1231 ppm, respectively. Comparisons to other chemical shift predictors using the same testing data set indicates that SHIFTX2 is substantially more accurate (up to 26% better by correlation coefficient with an RMS error that is up to 3.3X smaller) than any other program.

::DEVELOPER

Wishart Pharmaceutical Research Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 SHIFTX2

:: MORE INFORMATION

Citation

Beomsoo Han, Yifeng Liu, Simon Ginzinger, and David Wishart. (2011)
SHIFTX2: significantly improved protein chemical shift prediction.
Journal of Biomolecular NMR, Volume 50, Number 1, 43-57. doi: 10.1007/s10858-011-9478-4