Voroprot 0.7.6.7 – Explore Geomeric Features of Protein Structure

Voroprot 0.7.6.7

:: DESCRIPTION

Voroprot is an interactive cross-platform software tool that provides a unique set of capabilities for exploring geomeric features of protein structure. Voroprot allows the construction and visualization of the Apollonius diagram (also known as additively weighted Voronoi diagram), the Apollonius graph, protein alpha shapes, interatomic contact surfaces, solvent accessible surfaces, pockets and cavities inside protein structure.

::DEVELOPER

VU Institute of Biotechnology

:: SCREENSHOTS

Voroprot

::REQUIREMENTS

  • Linux / Windows / MacOsX

:: DOWNLOAD

 Voroprot

:: MORE INFORMATION

Citation

Kliment Olechnovič, Mindaugas Margelevičius and Česlovas Venclovas (2010)
Voroprot: an interactive tool for the analysis and visualization of complex geometric features of protein structure.
Bioinformatics (2011) 27 (5): 723-724.

ProSAT+ – Protein Structure Annotation Tool

ProSAT+

:: DESCRIPTION

ProSAT+ (PRO: tein S: tructure A: nnotation T: ool-plus) is a tool to explore the relation between sequence and structural properties.

::DEVELOPER

Heidelberg Institute for Theoretical Studies

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

ProSAT+: visualizing sequence annotations on 3D structure.
Stank A, Richter S, Wade RC.
Protein Eng Des Sel. 2016 Jun 9. pii: gzw021

ReUPRed 20160310 – Identification of Repetitive Units in Protein Structures

ReUPRed 20160310

:: DESCRIPTION

ReUPRed (Repetitive Units Predictor) is a novel method for the fast automatic prediction of repeat units and repeat classification using an extensive Structure Repeat Unit Library (SRUL) derived from RepeatsDB.

::DEVELOPER

The BioComputing UP lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

 ReUPRed

:: MORE INFORMATION

Citation

Identification of repetitive units in protein structures with ReUPred.
Hirsh L, Piovesan D, Paladin L, Tosatto SC.
Amino Acids. 2016 Jun;48(6):1391-400. doi: 10.1007/s00726-016-2187-2

PDBest 1.39 – Manipulating and Enhancing Protein Structures

PDBest 1.39

:: DESCRIPTION

PDBest (PDB Enhanced Structures Toolkit)  is a freely available platform for manipulating, filtering and normalizing biomolecules in Protein Data Bank (PDB) and mmCIF structure files.

::DEVELOPER

PDBest team , the Bioinformatics and System Laboratory (LBS) at Universidade Federal de Minas Gerais, Brazil.

:: SCREENSHOTS

PDBest

:: REQUIREMENTS

  • Windows/ Linux/ MacOsX

:: DOWNLOAD

 PDBest

:: MORE INFORMATION

Citation

PDBest: a user-friendly platform for manipulating and enhancing protein structures.
Gonҫalves WR, Gonҫalves-Almeida VM, Arruda AL, Meira W Jr, da Silveira CH, Pires DE, de Melo-Minardi RC.
Bioinformatics. 2015 Apr 24. pii: btv223

PRaptorX Property – Protein Structure Property Prediction

PRaptorX Property

:: DESCRIPTION

RaptorX Property is a web server predicting structure property of a protein sequence without using any template information.

::DEVELOPER

Xu group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

  NO

:: MORE INFORMATION

Citation:

RaptorX-Property: a web server for protein structure property prediction.
Wang S, Li W, Liu S, Xu J.
Nucleic Acids Res. 2016 Apr 25. pii: gkw306.

MODELLER 9.16 – Comparative Protein Structure Modeling

MODELLER 9.16

:: DESCRIPTION

MODELLER is used for homology or comparative modeling of protein three-dimensional structures. The user provides an alignment of a sequence to be modeled with known related structures and MODELLER automatically calculates a model containing all non-hydrogen atoms. MODELLER implements comparative protein structure modeling by satisfaction of spatial restraints, and can perform many additional tasks, including de novo modeling of loops in protein structures, optimization of various models of protein structure with respect to a flexibly defined objective function, multiple alignment of protein sequences and/or structures, clustering, searching of sequence databases, comparison of protein structures, etc

::DEVELOPER

Andrej Sali Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/Windows/MacOsX

:: DOWNLOAD

  MODELLER

:: MORE INFORMATION

Citation

Methods Mol Biol. 2014;1137:1-15. doi: 10.1007/978-1-4939-0366-5_1.
Protein structure modeling with MODELLER.
Webb B1, Sali A.

N. Eswar, M. A. Marti-Renom, B. Webb, M. S. Madhusudhan, D. Eramian, M. Shen, U. Pieper, A. Sali.
Comparative Protein Structure Modeling With MODELLER.
Current Protocols in Bioinformatics, John Wiley & Sons, Inc., Supplement 15, 5.6.1-5.6.30, 2006.

Fitmunk – Improving Protein Structures by accurate, automatic Modeling of Side-chain Conformations

Fitmunk

:: DESCRIPTION

Fitmunk provides a framework for fitting conformations on a fixed backbone into electron density.

::DEVELOPER

Fitmunk team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Fitmunk: improving protein structures by accurate, automatic modeling of side-chain conformations.
Porebski PJ, Cymborowski M, Pasenkiewicz-Gierula M, Minor W.
Acta Crystallogr D Struct Biol. 2016 Feb;72(Pt 2):266-80. doi: 10.1107/S2059798315024730.

FUSION – de novo Protein Structure Prediction

FUSION

:: DESCRIPTION

FUSION is a fragment-free probabilistic graphical model for conformational sampling in continuous space and assess its accuracy using ‘blind’ protein targets with a length up to 250 residues from the CASP11 structure prediction exercise.

::DEVELOPER

Jianlin Jack Cheng , Debswapna Bhattacharya

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Improving Protein Fold Recognition by Deep Learning Networks.
Jo T, Hou J, Eickholt J, Cheng J.
Sci Rep. 2015 Dec 4;5:17573. doi: 10.1038/srep17573.

GR-Align 1.5 – Aligning Protein Structures

GR-Align 1.5

:: DESCRIPTION

GR-Align (GRaphlet-based Aligner) is a fast heuristic procedure for aligning/comparing protein structures according to the Contact Map Opverlap maximization (CMO) paradigm. The algorithm is based on a Needleman-Wunch algorithm where the cost for matching two residues is their graphlet degree similarity.

GR-Align packages contains three software: CMap, DCount, and GR-Align:
CMap converts protein structures (.pdb) files into contact map graphs (leda graphs .gw)
DCount computes the graphlet degree signatures (.ndump files) from Contact Maps
GR-Align aligns protein structures (requieres both contact maps and signatures files)

::DEVELOPER

Nataša Pržulj

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 GR-Align

:: MORE INFORMATION

Citation:

Bioinformatics. 2014 May 1;30(9):1259-65. doi: 10.1093/bioinformatics/btu020. Epub 2014 Jan 17.
GR-Align: fast and flexible alignment of protein 3D structures using graphlet degree similarity.
Malod-Dognin N1, Pržulj N.

C2S 2.0 – Contact Map-based Protein Structure Reconstruction Pipeline

C2S 2.0

:: DESCRIPTION

C2S (Contacts-to-Structure) is an automated procedure for building full atom protein structures based on contact maps.

::DEVELOPER

COMPREC

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

C2S

:: MORE INFORMATION

Citation

J Membr Biol. 2014 May;247(5):409-20. doi: 10.1007/s00232-014-9648-x. Epub 2014 Mar 29.
Automated procedure for contact-map-based protein structure reconstruction.
Konopka BM1, Ciombor M, Kurczynska M, Kotulska M.