Software Updates

AlphaPickle

a multipurpose Python script for producing plots and user-legible files from the output of AlphaFold2 (notebook) and Colabfold (notebook).

POKY

a software suite for multidimensional NMR and 3D structure calculation of biomolecules.

MODELLER

a tool used for homology or comparative modeling of protein three-dimensional structures.

NMRFx Structure

a tool that can be used to generate and analyze macromolecular structures and predict chemical shifts.

NMRFx Analyst

a tool for NMR processing, visualization and analysis that integrates code of NMRFx Processor, Structure and additional tools.

PDBstat

a C/C++ application developed as a coordinate and protein NMR restraint converter. This user-friendly tool provides an integrated set of computational methods for protein NMR restraint analysis and structure quality assessment, relabeling of prochiral atoms with correct IUPAC names, and analysis of atomic position consistency based on their convergence across a protein NMR ensemble.

DENSS

(DENsity from Solution Scattering) an algorithm used for calculating ab initio electron density maps directly from solution scattering data.

MDAnalysis

an object-oriented Python library to analyze trajectories from molecular dynamics (MD) simulations in many popular formats. It can write most of these formats, too, together with atom selections suitable for visualization or native analysis tools.

AlphaFold

an implementation of the inference pipeline of AlphaFold using a completely new model that was entered in CASP14.

PyEM

a set of Python modules and command-line utilities for electron microscopy of biological samples.

CcpNmr Analysis

a series of programs for macromolecular NMR including AnalysisAssign, AnalysisScreen, AnalysisMetabolomics and AnalysisStructure, and with version 3, the addition CcpNmr ChemBuild.

DeepEMhancer

(Deep cryo-EM Map Enhancer) a python package designed to perform non-linear post-processing of cryo-EM maps for local sharpening, automatic masking and denoising. Systems using cuda 11+ should use the 20210511 version of deepEMhancer, and the modified models distributed in /programs/share/deepemhancer/20210511/deepEMhancerModels/production_checkpoints/

NMR TITAN

an easy-to-use software package for the two-dimensional lineshape analysis of titration experiments.

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.

AutoDock-GPU

a Cuda accelerated version of AutoDock4.2.6, AutoDock for GPUs and other accelerators.

RNA Framework

a modular toolkit developed to deal with RNA structure probing and post-transcriptional modifications mapping high-throughput data. Toolkit will help with automatic reference transcriptome creation, automatic reads preprocessing (adapter clipping and trimming) and mapping, scoring and data normalization, and accurate RNA folding prediction by incorporating structural probing data.

AmberTools

a suite of programs that allows users to carry out molecular dynamics simulations, particularly on biomolecules. The suite can be used to carry out complete (non-periodic) molecular dynamics simulations (using NAB) with either explicit water or generalized Born solvent models. The independently developed packages work well by themselves, and with Amber itself.