Nov 27 2024
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Amber
a suite of biomolecular simulation programs. It began in the late 1970's, and is maintained by an active development community.
Updated versions:
24 | Linux 64
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Nov 26 2024
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TomoDRGN
a tool that extends the cryoDRGN framework to cryo-ET by learning heterogeneity from datasets in which each particle is sampled by multiple projection images at different stage tilt angles.
Updated versions:
1.0.0 | Linux 64
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Nov 22 2024
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AlphaFold
an implementation of the inference pipeline of AlphaFold v2.0 using a completely new model that was entered in CASP14.
Updated versions:
2.3.2_20241024 | Linux 64
3.0.0 | Linux 64
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Nov 20 2024
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spIsoNet
a tool designed to correct for the preferred orientation problem in cryoEM by self-supervised deep learning, by recovering missing information from well-sampled orientations in Fourier space.
Updated versions:
1.0_cu11.8 | Linux 64
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Nov 19 2024
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GisSPA
a GPU accelerated program, can translationally and rotationally localize the target protein complex in cellular lamellae, as prepared with a focused ion beam, using single cryo-electron microscopy images without tilt-series, and reconstruct the protein complex at near-atomic resolution.
Updated versions:
1.1.2 | Linux 64
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Nov 18 2024
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SBGrid Installer
an application for managing an SBGrid software installation. Users can choose a subset of applications for installation on their laptops or desktops or configure site installations for clusters, servers or cloud resources. This version is the command-line interface. A graphical version is available for download on the SBGrid wiki : https://sbgrid.org/wiki/client_downloads .
Updated versions:
2.11.11 | Linux 64
2.11.11 | OS X INTEL
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Nov 18 2024
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Boltz-1
an open-source model which predicts the 3D structure of proteins, rna, dna and small molecules; it handles modified residues, covalent ligands and glycans, as well as condition the generation on pocket residues.
Updated versions:
0.1.0 | Linux 64
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Nov 16 2024
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RELION
(REgularised LIkelihood OptimisatioN) a stand-alone computer program for Maximum A Posteriori (MAP) refinement of (multiple) 3D reconstructions or 2D class averages in cryo-electron microscopy.
Updated versions:
4.0.1_m1 | OS X INTEL
4.0.1 | OS X INTEL
4.0.0_m1 | OS X INTEL
4.0.0 | OS X INTEL
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Nov 15 2024
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cryoDRGN
a neural network based algorithm for heterogeneous cryo-EM reconstruction. In particular, the method models a continuous distribution over 3D structures by using a neural network based representation for the volume.
Updated versions:
3.4.2 | Linux 64
3.4.1 | Linux 64
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Nov 14 2024
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CryoSegNet
a tool for accurate cryo-EM protein particle picking by integrating the foundational AI image segmentation model and specialized U-Net
Updated versions:
1.0.0 | Linux 64
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Nov 13 2024
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POKY
a software suite for multidimensional NMR and 3D structure calculation of biomolecules.
Updated versions:
20240829 | OS X INTEL
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Nov 13 2024
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CcpNmr Analysis
a series of programs for macromolecular NMR including AnalysisAssign, AnalysisScreen, AnalysisMetabolomics and AnalysisStructure, and with version 3, the addition CcpNmr ChemBuild.
Updated versions:
3.2.2.1 | Linux 64
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Nov 12 2024
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ModelAngelo
an automatic atomic model building program for cryo-EM maps.
Updated versions:
1.0.13 | Linux 64
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Nov 12 2024
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CCP4
(Collaborative Computational Project, Number 4) a collection of programs and associated data and software libraries used for macromolecular structure determination by X-ray crystallography.
Updated versions:
8.0.017 | OS X INTEL
8.0 | OS X INTEL
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Nov 12 2024
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POKY
a software suite for multidimensional NMR and 3D structure calculation of biomolecules.
Updated versions:
20240829 | Linux 64
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Nov 11 2024
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MiLoPYP
a self-supervised molecular pattern mining and particle localization in situ.
Updated versions:
0.5.0 | Linux 64
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Nov 08 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:
0.9.8.8 | OS X INTEL
0.9.6 | OS X INTEL
0.8.9.2 | OS X INTEL
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