GP4Rate 1.0.0 – Inference of Functionally Important Regions in Protein Tertiary Structures

GP4Rate 1.0.0

:: DESCRIPTION

GP4Rate is a C++ program which combines Gaussian processes and phylogenetics to infer conserved sites in protein tertiary structures.

::DEVELOPER

Yifei (Yi-Fei) Huang 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • PErl

:: DOWNLOAD

GP4Rate

:: MORE INFORMATION

Citation

PLoS Comput Biol. 2014 Jan;10(1):e1003429. doi: 10.1371/journal.pcbi.1003429. Epub 2014 Jan 16.
Phylogenetic Gaussian process model for the inference of functionally important regions in protein tertiary structures.
Huang YF, Golding GB.

FuncPatch – Inferring Conserved Functional Regions in Protein Tertiary Structures

FuncPatch

:: DESCRIPTION

FuncPatch is developed for inferring conserved functional regions in protein tertiary structures.

::DEVELOPER

Yifei (Yi-Fei) Huang 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Bioinformatics. 2014 Oct 15. pii: btu673.
FuncPatch: A web server for the fast Bayesian inference of conserved functional patches in protein 3D structures.
Huang YF1, Golding GB

IntFOLD 5.0 – Integrated Protein Structure and Function Prediction Server

IntFOLD 5.0

:: DESCRIPTION

The IntFOLD server is a novel independent server that integrates several cutting edge methods for the prediction of structure and function from sequence.

::DEVELOPER

McGuffin Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

IntFOLD: an integrated server for modelling protein structures and functions from amino acid sequences.
McGuffin LJ, Atkins JD, Salehe BR, Shuid AN, Roche DB.
Nucleic Acids Res. 2015 Mar 27. pii: gkv236.

Nucleic Acids Res. 2011 Jul;39(Web Server issue):W171-6. doi: 10.1093/nar/gkr184. Epub 2011 Mar 31.
The IntFOLD server: an integrated web resource for protein fold recognition, 3D model quality assessment, intrinsic disorder prediction, domain prediction and ligand binding site prediction.
Roche DB1, Buenavista MT, Tetchner SJ, McGuffin LJ.

Buenavista, M. T., Roche, D. B., & McGuffin, L. J. (2012)
Improvement of 3D protein models using multiple templates guided by single-template model quality assessment.
Bioinformatics, 28, 1851-1857

TimeScapes 1.5 – Molecular Dynamics Analysis tool

TimeScapes 1.5

:: DESCRIPTION

TimeScapes is an analysis package that can be used to efficiently detect and characterize significant conformational changes in simulated biomolecular systems. The program makes use of a particular type of “coarse-grained” model to reduce the level of detail in the spatial representations of long MD trajectories. TimeScapes decomposes structural changes into a set of key side-chain motions, providing greater sensitivity to a wide range of significant conformational changes than is typically obtained from traditional RMSD-based metrics.

::DEVELOPER

D. E. Shaw Research

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Window / Linux / Mac OsX
  • Python

:: DOWNLOAD

TimeScapes

:: MORE INFORMATION

Citation

J Chem Theory Comput. 2009 Oct 13;5(10):2595-605. doi: 10.1021/ct900229u.
Automated Event Detection and Activity Monitoring in Long Molecular Dynamics Simulations.
Wriggers W, Stafford KA, Shan Y, Piana S, Maragakis P, Lindorff-Larsen K, Miller PJ1, Gullingsrud J, Rendleman CA, Eastwood MP, Dror RO, Shaw DE.

FlexS 2.1.3 – Predict Ligand Superpositions

FlexS 2.1.3

:: DESCRIPTION

FlexS is a computer program for predicting ligand superpositions. For a given pair of ligands, FlexS predicts the conformation and orientation of one of the ligands relative to the other one. In FlexS the reference-ligand is assumed to be rigid, thus, it should be given in a conformation which is similar to the bound state. The superposition algorithm in FlexS requires only little manual intervention. Nevertheless, in some cases additional information about the ligands or even the superposition is known. You can integrate this knowledge into the computations with FlexS by carrying out single steps manually. Thus, FlexS is designed for interactive work on ligand pairs as well as for ligand-based virtual screening.

::DEVELOPER

BioSolveIT GmbH 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/Windows/SGI Irix

:: DOWNLOAD

 FlexS

:: MORE INFORMATION

Citation

C. Lemmen, T. Lengauer, and G. Klebe.
FLEXS: A method for fast flexible ligand superposition.
Journal of Medicinal Chemistry, 41:4502–4520, 1998.

PPDbench – Benchmarking of Docking software on Protein-peptide Complexes

PPDbench

:: DESCRIPTION

PPDbench server is made in order to provide an easy webserver to calculate FNAT, L-RMSD and I-RMSD values of docked and original poses of protein-peptide complexe’s.

::DEVELOPER

PPDbench team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

  NO

:: MORE INFORMATION

Citation

Benchmarking of different molecular docking methods for protein-peptide docking.
Agrawal P, Singh H, Srivastava HK, Singh S, Kishore G, Raghava GPS.
BMC Bioinformatics. 2019 Feb 4;19(Suppl 13):426. doi: 10.1186/s12859-018-2449-y.

ccPDB 2.0 – Compilation and Creation of datasets from PDB

ccPDB 2.0

:: DESCRIPTION

ccPDB is designed to provide service to scientific community working in the field of function or structure annoation of proteins. This database of datasets is based on Protein Data Bank (PDB), where all datasets were derived from PDB. ccPDB have four modules; i) compilation of datasets, ii) creation of datasets, iii) web services and iv) Important links.

::DEVELOPER

ccPDB team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

  NO

:: MORE INFORMATION

Citation

ccPDB 2.0: an updated version of datasets created and compiled from Protein Data Bank.
Agrawal P, Patiyal S, Kumar R, Kumar V, Singh H, Raghav PK, Raghava GPS.
Database (Oxford). 2019 Jan 1;2019. doi: 10.1093/database/bay142.

ccPDB: compilation and creation of data sets from Protein Data Bank.
Singh H, Chauhan JS, Gromiha MM; Open Source Drug Discovery Consortium, Raghava GP.
Nucleic Acids Res. 2012 Jan;40(Database issue):D486-9. doi: 10.1093/nar/gkr1150.

GRIFFIN 1.0 – Construction of Simulation Models of Membrane Proteins in Lipid Environments

GRIFFIN 1.0

:: DESCRIPTION

GRIFFIN (Grid-based Force-Field Input) is a versatile methodology for optimizing protein-lipid interfaces during the set-up of membrane-protein molecular dynamics simulations. It is a stand-alone suite of tools designed to work alongside any existing molecular dynamics software, such as NAMD or GROMACS.

::DEVELOPER

Forrest Lab , Faraldo Lab

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Linux
  • C++ Compiler

:: DOWNLOAD

 GRIFFIN

:: MORE INFORMATION

Citation

Staritzbichler R, Anselmi C, Forrest LR, Faraldo-Gómez JD (2011)
GRIFFIN: A versatile methodology for optimization of protein-lipid interfaces for membrane protein simulations.
J Chem Theor Comput 7:1167-1176.

PDBFlex – Exploring Flexibility in Protein Structures

PDBFlex

:: DESCRIPTION

The PDBFlex database explores the intrinsic flexibility of protein structures by analyzing structural variations between different depositions and chains in asymmetric units of the same protein in PDB. It allows to easily identify regions and types of structural flexibility present in a protein of interest.

::DEVELOPER

Godzik Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser
:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

Nucleic Acids Res. 2016 Jan 4;44(D1):D423-8. doi: 10.1093/nar/gkv1316. Epub 2015 Nov 28.
PDBFlex: exploring flexibility in protein structures.
Hrabe T, Li Z, Sedova M, Rotkiewicz P, Jaroszewski L, Godzik A.

ConSole – Contact Map based Solenoid Detection

ConSole

:: DESCRIPTION

The ConSole algorithm provides a fast and accurate tool to recognize solenoid protein structures as a whole and to identify individual solenoid repeat units from a structure.

::DEVELOPER

Godzik Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • Python
  • BioPython
:: DOWNLOAD

 ConSole

:: MORE INFORMATION

Citation:

BMC Bioinformatics. 2014 Apr 27;15:119. doi: 10.1186/1471-2105-15-119.
ConSole: using modularity of contact maps to locate solenoid domains in protein structures.
Hrabe T, Godzik A