Software Updates

AlphaPickle

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

R-pkgs-SBGrid

contains optional R pkgs

POKY

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

MODELLER

used for homology or comparative modeling of protein three-dimensional structures. From a sequence alignment with known related structures, MODELLER automatically calculates a model containing all non-hydrogen atoms using comparative protein structure modeling by satisfaction of spatial restraints. It can also perform de novo modeling of loops in protein structures and optimize various models of protein structure with respect to a flexibly defined objective function, multiple alignment of protein sequences and/or structures, clustering, searching of sequence databases, comparison of protein structures, etc.

ChimeraX

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.

NMRFx Structure

NMRFx Structure can be used to generate and analyze macromolecular structures and predict chemical shifts.

NMRFx Analyst

Software for NMR Processing, Visualization and Analysis Integrates code of NMRFx Processor, Structure and additional tools

CCP-EM

(Collaborative Computational Project for Electron cryo-Microscopy) a software framework and resulting software suite that includes tools for project and data management along with a focus on building and refinement of atomic models into cryo-EM reconstructions. The framework allows easy access to various programs and utilities from collaborators via Python task wrappers and a user-friendly graphical user interface or a command-line interface suitable for scripting.

xds_relaytx

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 v2.0 using a completely new model that was entered in CASP14.

CCP-EM

(Collaborative Computational Project for Electron cryo-Microscopy) a software framework and resulting software suite that includes tools for project and data management along with a focus on building and refinement of atomic models into cryo-EM reconstructions. The framework allows easy access to various programs and utilities from collaborators via Python task wrappers and a user-friendly graphical user interface or a command-line interface suitable for scripting.

PyEM

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

CcpNmr

a series of programs for macromolecular NMR spectroscopy integrated with the CCP data model, inspired partly by the program ANSIG (Per Kraulis) and partly by the program Sparky (T.D.Goddard and D.G.Kneller, UCSF).

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/

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.

R

a free software environment for statistical computing and graphics.

NMR TITAN

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

Amber (DFCI only)

a suite of biomolecular simulation programs. The term "Amber" refers to two things. First, it is a set of molecular mechanical force fields for the simulation of biomolecules (these force fields are in the public domain, and are used in a variety of simulation programs). Second, it is a package of molecular simulation programs which includes source code and demos.

ChimeraX

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

AutoDock for GPUs and other accelerators, Cuda accelerated version of AutoDock4.2.6. It leverages its parallelizable LGA by processing ligand-receptor poses in parallel over multiple compute units. The Cuda version was developed in collaboration with Nvidia to run AutoDock-GPU on the Oak Ridge National Laboratory's (ORNL) Summit, and it included a batched ligand pipeline developed by Aaron Scheinberg from Jubilee Development.

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.