Tags : Browse Projects

Select a tag to browse associated projects and drill deeper into the tag cloud.

GNAT NER

Compare

  Analyzed about 2 months ago

GNAT is a library and web service capable of performing gene entity NER and normalization of biomedical articles. Mentions of genes and proteins in the articles are linked to to Entrez Gene identifiers. GNAT is available both for local download (suitable for large-scale processing) and as a web ... [More] service (suitable for more limited processing or testing). A combination of local and remote processing is also available, where CPU-heavy operations are performed locally and memory-intensive operations are performed remotely (this is suitable for large-scale processing where a large amount of memory is not available). GNAT uses LINNAEUS (Gerner et al., 2010) for species detection and BANNER (Leaman et al., 2008) in one part of its false positive filtering process. [Less]

29.8K lines of code

1 current contributors

12 months since last commit

2 users on Open Hub

Activity Not Available
0.0
 
I Use This
Licenses: No declared licenses

relax (molecular dynamics analysis)

Compare

  Analyzed about 1 year ago

relax is a program designed for the study of molecular dynamics of organic molecules, proteins, RNA, DNA, sugars, and other biomolecules through the analysis of experimental NMR data. It supports exponential curve fitting for the calculation of the R1 and R2 relaxation rates, calculation of the NOE ... [More] , reduced spectral density mapping, the Lipari and Szabo model-free analysis, study of domain motions via the N-state model or ensemble analysis and frame order dynamics theories using anisotropic NMR parameters such as RDCs and PCSs, and the investigation of stereochemistry. [Less]

1.72M lines of code

2 current contributors

about 1 year since last commit

1 users on Open Hub

Activity Not Available
5.0
 
I Use This

PPI Benchmark

Compare

  Analyzed almost 4 years ago

A comprehensive benchmark of kernel methods to extract protein-protein interactions from literature.

721K lines of code

2 current contributors

over 4 years since last commit

1 users on Open Hub

Activity Not Available
0.0
 
I Use This
Licenses: No declared licenses

ProDy

Compare

  Analyzed 7 months ago

ProDy is a free and open-source Python package for analysis and modeling of protein structural dynamics. It allows for efficient analysis of large datasets and is suitable for development or prototyping of structure-based analysis and modeling software.

41.5K lines of code

8 current contributors

7 months since last commit

1 users on Open Hub

Activity Not Available
5.0
 
I Use This

Force Field X

Compare

  Analyzed about 2 months ago

Force Field X (FFX) is a group of open source (GPL v. 3 with Linking Exception), platform independent modules for molecular biophysics. Key methods include: 1) Atomic Multipole Optimized Energetics for Biomolecular Applications (AMOEBA) force fields 2) Particle-mesh Ewald (PME) electrostatics with ... [More] support for space group symmetry 3) Generalized Kirkwood continuum electrostatics 4) Single and Dual-Topology Orthogonal Space Random Walk (OSRW) free energy methods 5) L-BFGS, Simulated Annealing and Dead-End Elimination optimization algorithms 6) Reciprocal space refinement for X-ray and Neutron Diffraction data sets 7) Real space refinement for X-ray Diffraction, Neutron Diffraction and CryoEM data sets 8) Shared memory, cluster parallel and coprocessor based parallelization strategies [Less]

416K lines of code

8 current contributors

5 months since last commit

1 users on Open Hub

Activity Not Available
5.0
 
I Use This

mmdb

Compare

  Analyzed 10 months ago

MMDB is a macromolecular coordinate library, written by Eugene Krissinel. It supports reading and writing two file formats, PDB and mmCIF, and provides high-level tools for working with coordinate files: orthogonal-fractional coordinate transforms, generation of symmetry mates, editing the ... [More] molecular structure and some others. Tarballs available at: ftp://ftp.ccp4.ac.uk/opensource/ [Less]

70.9K lines of code

0 current contributors

over 3 years since last commit

1 users on Open Hub

Activity Not Available
0.0
 
I Use This

Python Macromolecular Library (mmLib)

Compare

  Analyzed 4 months ago

The Python Macromolecular Library (mmLib) is a software toolkit and library of routines for the analysis and manipulation of macromolecular structural models, implemented in the Python programming language. It is accessed via a layered, object-oriented application programming interface, and provides ... [More] a range of useful software components for parsing mmCIF, and PDB files, a library of atomic elements and monomers, an object-oriented data structure describing biological macromolecules, and an OpenGL molecular viewer. The mmLib data model is designed to provide easy access to the various levels of detail needed to implement high-level application programs for macromolecular crystallography, NMR, modeling, and visualization. [Less]

54.7K lines of code

0 current contributors

almost 5 years since last commit

1 users on Open Hub

Activity Not Available
4.0
   
I Use This

sire

Compare

  Analyzed 11 months ago

Molecular modelling package in early developmental stage

5.95M lines of code

0 current contributors

over 2 years since last commit

1 users on Open Hub

Activity Not Available
0.0
 
I Use This

EMMA - Markov Model Algorithms

Compare

  Analyzed over 2 years ago

Markov models, often called Markov state models (MSMs) or kinetic transition networks, are concise and easy-to-analyze discrete models of continuous stochastic processes. They have been extensively used in the analysis of molecular dynamics (MD). The EMMA software provides a number of command line ... [More] tools that provide the basics of construction, validation and analysis of Markov models. EMMA is Java-based. [Less]

52.8K lines of code

4 current contributors

over 2 years since last commit

1 users on Open Hub

Activity Not Available
0.0
 
I Use This
Licenses: No declared licenses

Visualization of Protein-Ligand Graphs

Compare

  Analyzed about 2 months ago

The Visualization of Protein-Ligand Graphs (VPLG) software package computes and visualizes protein graphs. It works on the super-secondary structure level and uses the atom coordinates from PDB files and the SSE assignments of the DSSP algorithm.

999K lines of code

0 current contributors

almost 2 years since last commit

1 users on Open Hub

Activity Not Available
4.0
   
I Use This