San Diego Supercomputer Center

A Rapid Bootstrap Algorithm for the RAxML Web Servers

Despite recent advances achieved by application of high-performance computing methods and novel algorithmic techniques to maximum likelihood (ML)-based inference programs, the m...

The Protein Data Bank

The Protein Data Bank [PDB; Berman, Westbrook et al. (2000), Nucleic Acids Res. 28 , 235–242; http://www.pdb.org/] is the single worldwide archive of primary structural data of ...

The RCSB Protein Data Bank: redesigned web site and web services

The RCSB Protein Data Bank (RCSB PDB) web site (http://www.pdb.org) has been redesigned to increase usability and to cater to a larger and more diverse user base. This article d...

The structure of the chromophore within DsRed, a red fluorescent protein from coral

DsRed, a brilliantly red fluorescent protein, was recently cloned from Discosoma coral by homology to the green fluorescent protein (GFP) from the jellyfish Aequorea . A core qu...

First principles implementation of solvent effects without outlying charge error

In this work, we present a sound modified implementation of the noniterative approach for the inclusion of solvent effects for molecular-shaped cavities in conventional ab initi...

Outcome of the First wwPDB Hybrid/Integrative Methods Task Force Workshop

Are Current Semiempirical Methods Better Than Force Fields? A Study from the Thermodynamics Perspective

The semiempirical Hamiltonians MNDO, AM1, PM3, RM1, PDDG/MNDO, PDDG/PM3, and SCC-DFTB, when used as part of a hybrid QM/MM scheme for the simulation of biological molecules, wer...