Tag: Protein Model

PULCHRA 3.04 – All-atom Reconstruction & Refinement of Reduced Protein Models

PULCHRA 3.04

:: DESCRIPTION

PULCHRA (PowerfUL CHain Restoration Algorithm) is a simple command-line tool for all-atom reconstruction and refinement of reduced protein models. PUCLHRA can correct alpha carbon positions, add backbone and side chain atoms, improve hydrogen bonds patterns and check proper protein chirality.

::DEVELOPER

Center for the Study of Systems Biology

:: SCREENSHOTS

Command Line

:: REQUIREMENTS

  • C Complier

:: DOWNLOAD

PULCHRA

:: MORE INFORMATION

Citation

Rotkiewicz P., Skolnick, J.,
Fast procedure for reconstruction of full-atom protein models from reduced representations.
J. Comp. Chem., Jul 15, 29(9), 1460-5 (2008).

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

LatPack 1.9.1 – Folding Studies for Arbitrary Lattice Protein Models

LatPack 1.9.1

:: DESCRIPTION

LatPack is a collection of tools related to the folding simulations of lattice-protein models with arbitrary energy function.

::DEVELOPER

Bioinformatics Group
Albert-Ludwigs-University Freiburg

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 LatPack

:: MORE INFORMATION

Citation

HFSP J. 2008 Dec;2(6):396-404. Epub 2008 Nov 26.
Classifying proteinlike sequences in arbitrary lattice protein models using LatPack.
Mann M, Maticzka D, Saunders R, Backofen R.

FRST 1.2 – Protein Model Quality Estimation Method

FRST 1.2

:: DESCRIPTION

FRST serves to validate the energy of a protein structure. The server computes both an overall and a per-residue energy profile of a protein structure. The energy profile can be visualized in different ways, including a per-residue plot and a colored structure representation, accessible as a series of dynamic web pages.

::DEVELOPER

The BioComputing UP lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 FRST

:: MORE INFORMATION

Citation:

Silvio C.E. Tosatto.
The Victor/FRST Function for Model Quality Estimation.
Journal of Computational Biology 2005; 12(10):1316-1327

SELECTpro 1.0 – Protein Model Scoring/Selection and Side-Chain Prediction

SELECTpro 1.0

:: DESCRIPTION

SELECTpro is a novel structure-based model selection method derived from an energy function comprising physical, statistical, and predicted structural terms. Novel and unique energy terms include predicted secondary structure, predicted solvent accessibility, predicted contact map, beta-strand pairing, and side-chain hydrogen bonding.

::DEVELOPER

Institute for Genomics and Bioinformatics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 SELECTpro

:: MORE INFORMATION

Citation:

A. Randall, P. Baldi.
SELECTpro: effective protein model selection using a structure-based energy function resistant to BLUNDERs.
BMC Structural Biology, 8, 52, 2008

buccaneer 1.5 – Electron Density Interpretation/Protein Model Building software

buccaneer 1.5

:: DESCRIPTION

‘buccaneer‘ (BUild Connected C-Alphas, Nautical Excuse for Eponym Required) performs statistical chain tracing by identifying connected alpha-carbon positions using a likelihood-based density target.

::DEVELOPER

Kevin Cowtan

:: SCREENSHOTS

N/A

:: REQUIREMENTS

.:: DOWNLOAD

  buccaneer

:: MORE INFORMATION

Citation

Acta Crystallogr D Biol Crystallogr. 2006 Sep;62(Pt 9):1002-11. Epub 2006 Aug 19.
The Buccaneer software for automated model building. 1. Tracing protein chains.
Cowtan K.