Jan 31 2024
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IMP
(Integrative Modeling Platform) a program designed to allow mixing and matching of existing modeling components as well as the easy addition of new functionality.
Updated versions:
2.20.1 | Linux 64
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Jan 30 2024
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EMReady
a tool that improves the quality and interpretability of cryo-EM maps by local and non-local deep learning
Updated versions:
20230606 | Linux 64
1.1 | Linux 64
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Jan 29 2024
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SAMtools
(Sequence Alignment/Map) a generic format for storing large nucleotide sequence alignments that provides various utilities for manipulating alignments, including sorting, merging, indexing and generating alignments in a per-position format.
Updated versions:
1.19.2 | Linux 64
1.19.2 | OS X INTEL
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Jan 25 2024
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Chimera
a highly extensible, interactive molecular graphics program for interactive visualization and analysis of molecular structures and related data, including density maps, supramolecular assemblies, sequence alignments, docking results, trajectories, and conformational ensembles. It is often a tool of choice for rendering EM volumes.
Updated versions:
1.8.1 | Linux 64
1.15 | Linux 64
1.14 | Linux 64
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Jan 24 2024
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GROMACS
a versatile package that performs molecular dynamics of proteins, lipids and nucleic acids.
Updated versions:
2024-rc_arm | OS X INTEL
2024-rc | OS X INTEL
2024-rc_cu11.5.2 | Linux 64
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Jan 22 2024
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Dynamo-tools
a collection of tools for subtomogram averaging in dynamo.
Updated versions:
1.0.0 | OS X INTEL
1.0.0 | Linux 64
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Jan 22 2024
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Bowtie 2
an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences.
Updated versions:
2.5.3 | Linux 64
2.5.3 | OS X INTEL
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Jan 21 2024
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NAMD
a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems.
Updated versions:
3.0b5-netlrts-smp-CUDA | Linux 64
3.0b5-multicore-CUDA | Linux 64
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Jan 18 2024
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Protomo
a system that includes programs and shell scripts for electron tomography of thin specimens, providing an interactive graphical tool for fast initial alignment of a tilt series, shell scripts for the more time consuming refinement, and some other useful image manipulation utilities.
Updated versions:
3.1.0 | Linux 64
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Jan 18 2024
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CryoSieve
an advanced software solution designed for particle sorting/sieving in single particle analysis (SPA) for Cryogenic Electron Microscopy (cryo-EM).
Updated versions:
1.2.3 | Linux 64
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Jan 18 2024
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PHENIX
(Python-based Hierarchical Environment for INtegrated Xtallography) a software suite for the automated determination of molecular structures using X-ray crystallography and other methods.
Updated versions:
1.21-5207 | Linux 64
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Jan 18 2024
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MotionCor3
a multi-GPU program that corrects beam-induced sample motion on dose fractionated movie stacks. It implements a robust iterative alignment algorithm that delivers precise measurement and correction of both global and non-uniform local motions at single pixel level across the whole frame, suitable for both single-particle and tomographic images.
Updated versions:
1.0.1 | Linux 64
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Jan 18 2024
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AreTomo2
(Alignment and Reconstruction for Electron Tomography 2) is a GPU-accelerated software package that provides an integrated solution to both fiducial-free alignment and reconstruction for cryoEM tomography.
Updated versions:
1.0.0 | Linux 64
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Jan 17 2024
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aria2
a lightweight multi-protocol & multi-source command-line download utility. It supports HTTP/HTTPS, FTP, SFTP, BitTorrent and Metalink. aria2 can be manipulated via built-in JSON-RPC and XML-RPC interfaces.
Updated versions:
1.37.0 | Linux 64
1.37.0 | OS X INTEL
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Jan 16 2024
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TomoAND
a package for noise reduction in electron tomography with Anisotropic Nonlinear Diffusion.
Updated versions:
2.0 | Linux 64
2.0 | OS X INTEL
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Jan 16 2024
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IGV
(Integrative Genomics Viewer) a high-performance visualization tool for interactive exploration of large, integrated genomic datasets. It supports a wide variety of data types, including array-based and next-generation sequence data, and genomic annotations.
Updated versions:
2.17.0 | Linux 64
2.17.0 | OS X INTEL
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Jan 15 2024
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HKL2000
a data processing suite for X-ray crystallography that provides a sleek interface for devising a data collection strategy and processing data. HKL is based on the extended versions of Denzo, Xdisplayf and Scalepack. HKL was developed and is maintained by Wladek Minor (University of Virginia).
Updated versions:
722 | Linux 64
722 | OS X INTEL
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Jan 13 2024
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Focus
an interface for cryo-transmission electron microscopy (cryo-EM) data collection with computer image processing. Focus creates a user-friendly environment to import and manage data recorded by direct electron detectors and perform elemental image processing tasks in a high-throughput manner, while new data is being acquired at the microscope.
Updated versions:
1.1.0_nightly | OS X INTEL
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Jan 10 2024
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XDS
(X-ray Detector Software) a software tool for processing single-crystal monochromatic diffraction data recorded by the rotation method.
Updated versions:
20230630 | Linux 64
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Jan 10 2024
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TomoTwin-cryoet
a deep metric learning based particle picking procedure for cryo-ET
Updated versions:
0.8.0 | Linux 64
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Jan 09 2024
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DIALS
(Diffraction Integration for Advanced Light Sources) a software project for the analysis of crystallographic diffraction images for many new methods from shutterless, fine-sliced rotation scans to randomly-oriented snapshots of serial crystallography. It uses multiple CPU and GPU machines to increase speed and accuracy based on a comprehensive physical model.
Updated versions:
3.17.0 | OS X INTEL
3.17.0 | Linux 64
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Jan 04 2024
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Chroma
a generative model for designing proteins programmatically.
Updated versions:
20231201 | Linux 64
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Jan 04 2024
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ChimeraX
a tool of the next-generation molecular visualization program from the Resource for Biocomputing, Visualization, and Informatics (RBVI), following UCSF Chimera. Compared to Chimera, ChimeraX has improved graphics (e.g. interactive ambient shadows); faster handling of large structures (millions of atoms); and a more modern, single-window user interface.
Updated versions:
1.6.1_c9 | Linux 64
1.6.1 | Linux 64
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Jan 04 2024
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BLAST+
a suite of BLAST (Basic Local Alignment Search Tool) tools that utilizes the NCBI C++ Toolkit with a number of performance and feature improvements over the legacy BLAST applications.
Updated versions:
2.15.0 | OS X INTEL
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Jan 04 2024
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Coot
(Crystallographic Object-Oriented Toolkit) an application that supports model building and real space refinement. This application interfaces with refmac, Phenix, and several other applications. Coot was recognized as the best structural biology application in 2008 by SBGrid.
Updated versions:
0.9.8.92 | Linux 64
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