Associative memory, Water mediated, Structure and Energy Model (AWSEM) protein simulation code
Clone or download
adavtyan
Latest commit 6394a4c Aug 23, 2018
Permalink
Failed to load latest commit information.
DNA_Ion_tools adding tools May 4, 2016
Makefiles README file for Makefiles Feb 11, 2017
create_project_tools Tools update based on amylometer brunch May 7, 2018
debugging Corrected version generated by new script that does the rounding like… May 11, 2011
dimer_interface_protocol clustering and folders Aug 11, 2017
examples edit for AWSEM-IDP feature Aug 20, 2018
examples_for_9Oct12_version Updating examples May 3, 2016
frag_mem_tools bug fix Jul 29, 2018
old_lammps_3Jun11 All the code is tranfered to the current LAMMPS version of Oct 3rd 2012. Oct 3, 2012
old_lammps_9Oct12 The code is brought to the latest verson of LAMMPS (May 2nd, 2016) May 3, 2016
parameters
results_analysis_tools Very important update of BuildAllAtomsFromLammps.py. PSF file works w… Aug 23, 2018
LAMMPS_INSTRUCTION.txt No commit message Mar 11, 2011
LICENSE Create LICENSE May 7, 2018
README.md Update README.md Jan 11, 2018
atom_vec_awsemmd.cpp Bug fix May 3, 2016
atom_vec_awsemmd.h adding virtual keywords to atom_vec_awsemmd.h May 4, 2016
compute_contactmap.cpp The code is brought to the latest verson of LAMMPS (May 2nd, 2016) May 3, 2016
compute_contactmap.h The code is brought to the latest verson of LAMMPS (May 2nd, 2016) May 3, 2016
compute_pairdistmat.cpp
compute_pairdistmat.h The code is brought to the latest verson of LAMMPS (May 2nd, 2016) May 3, 2016
compute_q_onuchic.cpp The code is brought to the latest verson of LAMMPS (May 2nd, 2016) May 3, 2016
compute_q_onuchic.h The code is brought to the latest verson of LAMMPS (May 2nd, 2016) May 3, 2016
compute_q_wolynes.cpp The code is brought to the latest verson of LAMMPS (May 2nd, 2016) May 3, 2016
compute_q_wolynes.h
compute_totalcontacts.cpp The code is brought to the latest verson of LAMMPS (May 2nd, 2016) May 3, 2016
compute_totalcontacts.h The code is brought to the latest verson of LAMMPS (May 2nd, 2016) May 3, 2016
fix_backbone.cpp Removing some of the redundant parameters and blocks, including memb_… Jun 18, 2018
fix_backbone.h Removing some of the redundant parameters and blocks, including memb_… Jun 18, 2018
fix_go-model.cpp bug fix May 3, 2016
fix_go-model.h The code is brought to the latest verson of LAMMPS (May 2nd, 2016) May 3, 2016
fix_qbias.cpp The code is brought to the latest verson of LAMMPS (May 2nd, 2016) May 3, 2016
fix_qbias.h The code is brought to the latest verson of LAMMPS (May 2nd, 2016) May 3, 2016
fix_spring_rg_papoian.cpp edit for AWSEM-IDP feature Aug 20, 2018
fix_spring_rg_papoian.h edit for AWSEM-IDP feature Aug 20, 2018
fragment_memory.cpp multichain AMH-Go bugfix Jan 12, 2018
fragment_memory.h Update Aug 8, 2012
pair_ex_gauss_coul_cut.cpp The code is brought to the latest verson of LAMMPS (Feb 9th, 2017) Feb 9, 2017
pair_ex_gauss_coul_cut.h All the code is tranfered to the current LAMMPS version of Oct 3rd 2012. Oct 3, 2012
pair_excluded_volume.cpp The code is brought to the latest verson of LAMMPS (Feb 9th, 2017) Feb 9, 2017
pair_excluded_volume.h The code is brought to the latest verson of LAMMPS (May 2nd, 2016) May 3, 2016
pair_go-contacts.cpp Resolving compatibility issues with the latest version of LAMMPS May 3, 2018
pair_go-contacts.h The code is brought to the latest verson of LAMMPS (May 2nd, 2016) May 3, 2016
smart_matrix_lib.h Removing some of the redundant parameters and blocks, including memb_… Jun 18, 2018

README.md

Proteins and other biomolecules can be simulated on a computer primarily in two ways: relying either on atomistic or coarse-grained force fields. The latter approaches, which enable treating large systems at long timescales, come in with rather broad variety of choices, compared with the atomistic models. In particular, many useful coarse-grained protein force fields require prior knowledge of the native structure for the specific protein target, often with the stated goal of simulating protein folding kinetics and dynamics. These methods, however, cannot be used when the target protein structure is unknown or non-native interactions play a significant role. To address such problems, several coarse-grained protein force fields have been developed in the last 30 years or so that allow de novo structure prediction even in the absence of sequence homology. The AWSEM potential is a prominent member of this latter group, where various research groups have successfully demonstrated its broad applications in monomeric protein structure prediction, binding predictions of dimers and multimeric assemblies, folding of membrane proteins, and structural and kinetic studies of protein-DNA complexes. AWSEM naturally covers the whole spectrum between native-structure-based and de novo methods, and can be used both with the knowledge of native structures, and without such explicit knowledge. In the latter case it relies solely on sequence information. Because AWSEM's potential is analytical and differentiable, it is currently implemented as a molecular dynamics algorithm (AWSEM-MD).

The AWSEM force field grew out of the Associative Memory Hamiltonian (AMH) family of protein modeling potentials, developed over many years by Professor Peter Wolynes and his group at the University of Illinois at Urbana-Champaign, the University of California in San Diego and Rice University. The contact and water-mediated interactions were developed by Papoian, Ulander, and Wolynes in 2004 ("Water in Protein Structure Prediction" ; Proc. Natl. Acad. Sci. USA; 2004, 101 , 3352), when the revised AMH was renamed AMW (where W stands for water). The original AMH/AMW programs were written in FORTRAN by many people over 20 years, including Mark Friedrichs, Richard Goldstein, Zaida Luthey-Schulten, Kristin Koretke, Corey Hardin, Michael Eastwood, Michael Prentiss, Garegin Papoian, Johan Ulander, Chenghang Zong, Cecillia Clementi and Vanessa Oklejas, among others.

The AWSEM potential is based on a three-bead per amino-acid residue representation of protein chains, having many terms representing the backbone stereochemistry, independent and cooperative hydrogen bonding, water-mediated tertiary interactions, and biasing local structural preferences based on short fragment memories. Dr. Aram Davtyan, while being a graduate student in Prof. Garegin Papoian's group at the University of Maryland, designed the architecture of AWSEM's code, and implemented its main features in C++, as an add-on package compatible with the LAMMPS simulation platform. Dr. Nicholas Schafer and Dr. Weihua Zheng from Prof. Peter Wolynes' group at Rice University also made significant early contributions to AWSEM's development, applications and documentation. Currently, AWSEM software is being actively developed by many members and alumni of the Papoian and Wolynes laboratories, as well as other scientists. Dr. Aram Davtyan continues to serve as software's lead developer.

To cite AWSEM and for a complete description of the forcefield please refer to the following paper and its supporting information.

Aram Davtyan, Nicholas P. Schafer, Weihua Zheng, Cecilia Clementi, Peter G. Wolynes, and Garegin A. Papoian, "AWSEM-MD: Protein Structure Prediction Using Coarse-Grained Physical Potentials and Bioinformatically Based Local Structure Biasing", The Journal of Physical Chemistry B 2012 116 (29), 8494-8503
http://http://pubs.acs.org/doi/abs/10.1021/jp212541y

Please refer to the follwoing link for AWSEM-MD instalation and project setup: https://github.com/adavtyan/awsemmd/wiki