Software Updates

Vina-GPU

a heterogeneous OpenCL implementation of AutoDock Vina.

AlphaFold

an implementation of the inference pipeline of AlphaFold v2.0 using a completely new model that was entered in CASP14.

BUSTER

a software system containing crystallographic structure refinement using Bayesian statistical methods (BUSTER), ligand fitting (rhofit) and a fully automated pipeline (Pipedream) to drive a structure based fragment/ligand screening pathway.

VMD

a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting.

TM-align

an algorithm for sequence independent protein structure comparisons.

OmegaFold

a high-resolution de novo Structure Prediction from Primary Sequence

Xplor-NIH

a package for biomolecular structure determination from experimental NMR data combined with known geometric data. Xplor–NIH was derived from XPLOR version 3.851 and contains all of the functionality therein in addition to numerous new features designed to render a highly flexible architecture and foster the rapid and easy development of new functionality.

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.

PDBFixer

an easy to use application that fixes problems in Protein Data Bank files in preparation for simulating. Fixes include: adding missing heavy or hydrogen atoms, building missing loops, convert non-standard residues to their standard equivalents, deleting unwanted heterogens or chains from the model, and building a water box for explicit solvent simulations.

ModeRNA

a program for comparative modeling of RNA 3D structures.