Tag: Refinement

IDEAFIX – Refinement of Variants in FFPE DNA Sequencing data

IDEAFIX

:: DESCRIPTION

IDEAFIX is a decision tree-based variant refinement tool that filters formaldehyde-induced cytosine deaminations from variant lists obtained from DNA sequencing data from FFPE specimens.

::DEVELOPER

Maitena Tellaetxe Abete

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • R

:: DOWNLOAD

IDEAFIX

:: MORE INFORMATION

Citation

Tellaetxe-Abete M, Calvo B, Lawrie C.
Ideafix: a decision tree-based method for the refinement of variants in FFPE DNA sequencing data.
NAR Genom Bioinform. 2021 Oct 27;3(4):lqab092. doi: 10.1093/nargab/lqab092. PMID: 34729472; PMCID: PMC8557387.

QRNAS – software tool for Refinement of Nucleic Acid structures

QRNAS

:: DESCRIPTION

QRNAS (Quick Refinement of Nucleic Acid Structures) is an extension of the AMBER simulation method with additional terms associated with explicit hydrogen bonds, co-planarity base pairs, backbone regularization, and custom restraints. QRNAS is capable of handling RNA, DNA, chimeras and hybrids thereof, and enables modeling of nucleic acids containing modified residues.

::DEVELOPER

Laboratory Of Bioinformatics And Protein Engineering

:: SCREENSHOTS

n/a

:: REQUIREMENTS

  • Linux / MacOsX

:: DOWNLOAD

QRNAS

:: MORE INFORMATION

Citation

Stasiewicz J, Mukherjee S, Nithin C, Bujnicki JM.
QRNAS: software tool for refinement of nucleic acid structures.
BMC Struct Biol. 2019 Mar 21;19(1):5. doi: 10.1186/s12900-019-0103-1. PMID: 30898165; PMCID: PMC6429776.

ARBitR – Assembly Refinement with Barcode-identity-tagged Reads

ARBitR

:: DESCRIPTION

ARBitR is an overlap aware genome assembly scaffolder for linked sequencing reads.

::DEVELOPER

ARBitR team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl

:: DOWNLOAD

ARBitR

:: MORE INFORMATION

Citation

Hiltunen M, Ryberg M, Johannesson H.
ARBitR: an overlap-aware genome assembly scaffolder for linked reads.
Bioinformatics. 2021 Aug 9;37(15):2203-2205. doi: 10.1093/bioinformatics/btaa975. PMID: 33216122; PMCID: PMC8352505.

Flex-EM – Fitting and Refinement of Atomic Structures

Flex-EM

:: DESCRIPTION

Flex-EM includes a rigid fitting stage followed by a refinement stage. Rigid fitting can be performed with Mod-EM or any other rigid fitting methods. The refinement stage starts with the components rigidly fitted in the approximate positions in the map. Two methods are available: conjugate gradients minimization (CG) and simulated annealing molecular dynamics (MD).

::DEVELOPER

Andrej Sali Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

  Flex-EM

:: MORE INFORMATION

Citation

M. Topf, K. Lasker, B. Webb, H. Wolfson, W. Chiu, A. Sali.
Protein Structure Fitting and Refinement Guided by Cryo-EM Density
Structure 16, 295-307, 2008

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).

MarViN 0.1.0 – Rapid Genotype Refinement for Whole-Genome Sequencing Data using Multi-Variate Normal Distribution

MarViN 0.1.0

:: DESCRIPTION

MarViN is an algorithm that models  linkage-disequilibrium (LD) using a simple multivariate Gaussian distribution.

::DEVELOPER

Illumina

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 MarViN

:: MORE INFORMATION

Citation:

Rapid genotype refinement for whole-genome sequencing data using multi-variate normal distributions.
Arthur R, O’Connell J, Schulz-Trieglaff O, Cox AJ.
Bioinformatics. 2016 Mar 9. pii: btw097

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.

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).

MONGOOSE 1.1 – Structural Analysis and Refinement of Constraint-based Metabolic Networks

MONGOOSE 1.1

:: DESCRIPTION

MONGOOSE (MetabOlic Network GrOwth Optimization Solved Exactly) is a package for structural analysis and refinement of constraint-based metabolic networks. Unlike other existing software, MONGOOSE uses exact rational arithmetic, which makes its results certifiably accurate.

::DEVELOPER

Berger Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • Python

:: DOWNLOAD

 MONGOOSE

:: MORE INFORMATION

Citation:

Genome Biol. 2012 Jan 31;13(1):r6. doi: 10.1186/gb-2012-13-1-r6.
MetaMerge: scaling up genome-scale metabolic reconstructions with application to Mycobacterium tuberculosis.
Chindelevitch L, Stanley S, Hung D, Regev A, Berger B.

i3Drefine / 3Drefine – Protein 3D Structure Refinement

i3Drefine / 3Drefine

:: DESCRIPTION

i3Drefine is a completely automated and computationally efficient protein 3D structure refinement method which based on an iterative and highly convergent energy minimization algorithm with a powerful all-atom composite physics and knowledge-based force fields and hydrogen bonding (HB) network optimization technique.

3Drefine: protein structure refinement server

::DEVELOPER

Dr. Jianlin Cheng’

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 i3Drefine

:: MORE INFORMATION

Citation

3Drefine: an interactive web server for efficient protein structure refinement.
Bhattacharya D, Nowotny J, Cao R, Cheng J.
Nucleic Acids Res. 2016 Apr 29. pii: gkw336

3Drefine: consistent protein structure refinement by optimizing hydrogen bonding network and atomic-level energy minimization.
Bhattacharya D, Cheng J.
Proteins. 2013 Jan;81(1):119-31. doi: 10.1002/prot.24167.

PLoS One. 2013 Jul 19;8(7):e69648. doi: 10.1371/journal.pone.0069648. Print 2013.
i3Drefine software for protein 3D structure refinement and its assessment in CASP10.
Bhattacharya D1, Cheng J.