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3 Biology and Molecular Biology
AABU_v1_0 POETA
Determination of proteinic structures: an experimentation program.
B. Coghlan, S. Fraga
Comput. Phys. Commun. 36(1985)391
AABU_v1_0 0001 AGAB
Association of proteins: adaptation and coupling of two available programs.
L. Seijo, B. Coghlan, S. Fraga
Comput. Phys. Commun. 41(1986)169
ABZD_v1_0 SIMLYS
SIMLYS: a software package for trajectory analysis of molecular dynamics simulations.
P. Kruger, M. Luke, A. Szameit
Comput. Phys. Commun. 62(1991)371
ABZD_v2_0 SIMLYS 2.0
SIMLYS version 2.0: A software package for trajectory analysis of molecular dynamics simulations.
P. Kruger, A. Szameit
Comput. Phys. Commun. 72(1992)265
ABZE_v1_0 PLEC
PLEC: a program for building, modelling and optimizing polypeptide structures.
M.L. Forcada
Comput. Phys. Commun. 64(1991)131
ACBG_v1_0 AMYRVF
Pair potential calculation of molecular associations: a vectorized version.
F. Torrens, E. Orti, J. Sanchez-Marin
Comput. Phys. Commun. 66(1991)341
ACEO_v1_0 AMYR
Molecular associations.
S. Fraga
Comput. Phys. Commun. 29(1983)351
ACEO_v1_0 0001 AGAB
Association of proteins: adaptation and coupling of two available programs.
L. Seijo, B. Coghlan, S. Fraga
Comput. Phys. Commun. 41(1986)169
ACFH_v1_0 DIAD
Determination of antigenic determinants.
S. Fraga
Comput. Phys. Commun. 30(1983)325
ADIT_v1_0 bics
Solutions of Poisson's equation in channel-like geometries.
M. Hoyles, S. Kuyucak, S.-H. Chung
Comput. Phys. Commun. 115(1998)45
ADIW_v1_0 AMYR 2
AMYR 2: a new version of a computer program for pair potential calculation of molecular associations.
F. Torrens, M. Rubio, J. Sanchez-Marin
Comput. Phys. Commun. 115(1998)87
ADNW_v1_0 CA3D
CA3D: a Monte Carlo code to simulate 3D buffered diffusion of ions in sub-membrane domains.
A. Gil, J. Segura
Comput. Phys. Commun. 136(2001)269
ADOJ_v1_0 SMMP
[SMMP] a modern package for simulation of proteins.
F. Eisenmenger, U.H.E. Hansmann, S. Hayryan, C.-K. Hu
Comput. Phys. Commun. 138(2001)192
ADOJ_v2_0 SMMP
An Enhanced Version of SMMP - Open-Source Software Package for Simulation of Proteins
Frank Eisenmenger, Ulrich H.E. Hansmann, Shura Hayryan, Chin-Kun Hu
Comput. Phys. Commun. 174(2006)422
ADOJ_v3_0 SMMP
SMMP v. 3.0 - Simulating proteins and protein interactions in Python and Fortran
Jan H. Meinke, Sandipan Mohanty, Frank Eisenmenger, Ulrich H.E. Hansmann
Comput. Phys. Commun. 178(2008)459
ADTU_v1_0 FRETsg
FRETsg: biomolecular structure model building from multiple FRET experiments.
G.F. Schroder, H. Grubmuller
Comput. Phys. Commun. 158(2004)150
ADTV_v1_0 tweezercalib
MatLab program for precision calibration of optical tweezers.
I.M. Tolic-Norrelykke, K. Berg-Sorensen, H. Flyvbjerg
Comput. Phys. Commun. 159(2004)225
ADTV_v2_0 tweezercalib
tweezercalib 2.0: Faster version of MatLab package for precise calibration of optical tweezers
Poul Martin Hansen, Iva Marija Tolic-Nørrelykke, Henrik Flyvbjerg, Kirstine Berg-Sørensen
Comput. Phys. Commun. 174(2006)518
ADTV_v2_1 tweezercalib
tweezercalib 2.1: Faster version of MatLab package for precise calibration of optical tweezers
Poul Martin Hansen, Iva Marija Tolic-Nørrelykke, Henrik Flyvbjerg, Kirstine Berg-Sørensen
Comput. Phys. Commun. 175(2006)572
ADUL_v1_0 ARVO
ARVO: A Fortran package for computing the solvent accessible surface area and the excluded volume of overlapping spheres via analytic equations
Ján Busa, Jozef Dzurina, Edik Hayryan, Shura Hayryan, Chin-Kun Hu, Ján Plavka, Imrich Pokorný, Jaroslav Skrivánek, Ming-Chya Wu
Comput. Phys. Commun. 165(2005)59
ADUL_v2_0 ARVO-CL
ARVO-CL: The OpenCL Version of the ARVO Package - An Efficient Tool for Computing the Accessible Surface Area and the Excluded Volume of Proteins via Analytical Equations
Ján Buša Jr., Shura Hayryan, Ming-Chya Wu, Ján Buša, Chin-Kun Hu
Comput. Phys. Commun. 183(2012)2494
ADXG_v1_0 HAWGC - histogram analysis with grayscale conversion
Quantitative histogram analysis of images
Oliver Holub, Sérgio T. Ferreira
Comput. Phys. Commun. 175(2006)620
ADZU_v1_0 MonteCarloMaplet
A Monte-Carlo Maplet for the Study of the Optical Properties of Biological Tissues
Man Ho Yip, M. J. Carvalho
Comput. Phys. Commun. 177(2007)965
AEBY_v1_0 MDVRY
MDVRY: a polarizable classical molecular dynamics package for biomolecules
M. Souaille, H. Loirat, D. Borgis, M.P. Gaigeot
Comput. Phys. Commun. 180(2009)276
AECJ_v1_0 g-permute
g-permute: Permutation-reduced Phase Space Density Compaction
F. Reinhard, O.F. Lange, J.S. Hub, J. Haas, H. Grubmüller
Comput. Phys. Commun. 180(2009)455
AEDA_v1_0 REACH
REACH: A Program for Coarse-Grained Biomolecular Simulation
Kei Moritsugua, Jeremy C. Smith
Comput. Phys. Commun. 180(2009)1188
AEEE_v2_0 PLUMED 2
PLUMED 2: New feathers for an old bird
Gareth A Tribello, Massimiliano Bonomi, Davide Branduardi, Carlo Camilloni, Giovanni Bussi
Comput. Phys. Commun. 185(2014)604
AEFD_v1_0 Chaste
Chaste: a test-driven approach to software development for biological modelling
Joe Pitt-Francis, Pras Pathmanathan, Miguel O. Bernabeu, Rafel Bordas, Jonathan Cooper, Alexander G. Fletcher, Gary R. Mirams, Philip Murray, James M. Osborne, Alex Walter, S. Jon Chapman, Alan Garny, Inge M. M. van Leeuwen, Philip K. Maini, Blanca Rodríguez, Sarah L. Waters, Jonathan P. Whiteley, Helen M. Byrne, David J. Gavaghan
Comput. Phys. Commun. 180(2009)2452
AEGB_v1_0 AFMPB: Adaptive Fast Multipole Poisson-Boltzmann Solver
AFMPB: An Adaptive Fast Multipole Poisson-Boltzmann Solver for Calculating Electrostatics in Biomolecular Systems
Benzhuo Lu, Xiaolin Cheng, Jingfang Huang, J. Andrew McCammon
Comput. Phys. Commun. 181(2010)1150
AEGB_v1_1 AFMPB
AFMPB: An Adaptive Fast Multipole Poisson-Boltzmann Solver for Calculating Electrostatics in Biomolecular Systems
Benzhuo Lu, Xiaolin Cheng, Jingfang Huang, J. Andrew McCammon
Comput. Phys. Commun. 184(2013)2618
AEGB_v2_0 Parallel AFMPB
Parallel AFMPB solver with automatic surface meshing for calculations of molecular solvation free energy
Bo Peng, Bo Zhang, Jingfang Huang, Nikos P. Pitsianis, Xiaobai Sun, Benzhuo Lu
Comput. Phys. Commun. 190(2015)173
AEGI_v1_0 NWChem
NWChem: a comprehensive and scalable open-source solution for large scale molecular simulations
M. Valiev, E.J. Bylaska, N. Govind, K. Kowalski, T.P. Straatsma, H.J.J. Van Dam, D. Wang, J. Nieplocha, E. Apra, T.L. Windus, W.A. de Jong
Comput. Phys. Commun. 181(2010)1477
AEGR_v1_0 TweezPal
TweezPal - Optical tweezers analysis and calibration software
Natan Osterman
Comput. Phys. Commun. 181(2010)1911
AEGT_v1_0 Browndye
Browndye: A Software Package for Brownian Dynamics
Gary A. Huber, J. Andrew McCammon
Comput. Phys. Commun. 181(2010)1896
AEHH_v1_0 TNAMD
TNAMD: Implementation of TIGER2 in NAMD
William J. Menz, Matthew J. Penna, Mark J. Biggs
Comput. Phys. Commun. 181(2010)2082
AEHT_v1_0 TimeSeriesStreaming.VI
TimeSeriesStreaming.VI: LabVIEW program for reliable data streaming of large analog time series
Fabian Czerwinski, Lene B. Oddershede
Comput. Phys. Commun. 182(2011)485
AEIC_v1_0 Eucb
Eucb: a C++ program for molecular dynamics trajectory analysis
Ioannis G. Tsoulos, Athanassios Stavrakoudis
Comput. Phys. Commun. 182(2011)834
AEJW_v1_0 AESS
AESS: Accelerated Exact Stochastic Simulation
David D. Jenkins, Gregory D. Peterson
Comput. Phys. Commun. 182(2011)2580
AEJY_v1_0 raft
C-library raft: reconstruction algorithms for tomography. Applications to X-ray Fluorescence Tomography
Eduardo X. Miqueles, Alvaro R. De Pierro
Comput. Phys. Commun. 182(2011)2661
AEKL_v1_0 SASSIE
SASSIE: A program to study intrinsically disordered biological molecules and macromolecular ensembles using experimental scattering restraints
Joseph E. Curtis, Sindhu Raghunandan, Hirsh Nanda, Susan Krueger
Comput. Phys. Commun. 183(2012)382
AEMP_v1_0 CASS
CASS - CFEL-ASG Software Suite
Lutz Foucar, Anton Barty, Nicola Coppola, Robert Hartmann, Peter Holl, Uwe Hoppe, Stephan Kassemeyer, Nils Kimmel, Jochen Küpper, Mirko Scholz, Simone Techert, Thomas A. White, Lothar Strüder, Joachim Ullrich
Comput. Phys. Commun. 183(2012)2207
AEPZ_v1_0 FindClosestAtom
An atomistic geometrical model of the B-DNA configuration for DNA-radiation interaction simulations
M.A. Bernal, D. Sikansi, F. Cavalcante, S. Incerti, C. Champion, V. Ivanchenko, Z. Francis
Comput. Phys. Commun. 184(2013)2842
AEQA_v1_0 g_contacts
g_contacts: Fast Contacts Search in Biomolecular Ensemble Data
Christian Blau, Helmut Grubmuller
Comput. Phys. Commun. 184(2013)2858
AEQD_v1_0 BACHSCORE
BACHSCORE. A tool for evaluating efficiently and reliably the quality of large sets of protein structures
E. Sarti, S. Zamuner, P. Cossio, A. Laio, F. Seno, A. Trovato
Comput. Phys. Commun. 184(2013)2862
AEQM_v1_0 Density Profile Tool
Computing 1-D atomic densities in macromolecular simulations: the Density Profile Tool for VMD
Toni Giorgino
Comput. Phys. Commun. 185(2014)317
AERI_v1_0 MDMC2
MDMC2: A molecular dynamics code for investigating the fragmentation dynamics of multiply charged clusters
David A. Bonhommeau, Marie-Pierre Gaigeot
Comput. Phys. Commun. 185(2014)684
AERU_v1_0 PLUMED-GUI (Collective variable analysis plugin)
PLUMED-GUI: an environment for the interactive development of molecular dynamics analysis and biasing scripts
Toni Giorgino
Comput. Phys. Commun. 185(2014)1109
AETQ_v1_0 GMXPBSA 2.0
GMXPBSA 2.0: a GROMACS tool to perform MM/PBSA and computational alanine scanning
C. Paissoni, D. Spiliotopoulos, G. Musco, A. Spitaleri
Comput. Phys. Commun. 185(2014)2920
AETQ_v1_1 GMXPBSA 2.1
GMXPBSA 2.1: a GROMACS tool to perform MM/PBSA and computational alanine scanning
C. Paissoni, D. Spiliotopoulos, G. Musco, A. Spitaleri
Comput. Phys. Commun. 186(2015)105
AETX_v1_0 SLDMOL
SLDMOL: A tool for the structural characterization of thermally disordered membrane proteins.
Joseph E. Curtis, Hailiang Zhang, Hirsh Nanda
Comput. Phys. Commun. 185(2014)3010
AEUO_v1_0 MonteGrappa
MonteGrappa: An iterative Monte Carlo program to optimize biomolecular potentials in simplified models
G. Tiana, F. Villa, Y. Zhan, R. Capelli, C. Paissoni, P. Sormanni, E. Heard, L. Giorgetti, R. Meloni
Comput. Phys. Commun. 186(2015)104
AEWB_v1_0 PDB4DNA
PDB4DNA: implementation of DNA geometry from the Protein Data Bank (PDB) description for Geant4-DNA Monte-Carlo simulations
E. Delage, Q.T. Pham, M. Karamitros, H. Payno, V. Stepan, S. Incerti, L. Maigne, Y. Perrot
Comput. Phys. Commun. 192(2015)282
AEWC_v1_0 TIGER2-NAMD
An Improved TIGER2 Implementation for NAMD Suitable for the BlueGene/Q Architecture
Aaron H. Brown, Tiffany R. Walsh
Comput. Phys. Commun. 192(2015)278
AEWS_v1_0 QMMMW
QMMMW: A wrapper for QM/MM simulations with Quantum ESPRESSO and LAMMPS
Changru Ma, Layla Martin-Samos, Stefano Fabris, Alessandro Laio, Simone Piccinin
Comput. Phys. Commun. 195(2015)191
AEXH_v1_0 PFMCal
Calibration of optical tweezers with non-spherical probes via high-resolution detection of Brownian motion
A. Butykai, F.M. Mor, R. Gaál, P. Domínguez-García, L. Forró, S. Jeney
Comput. Phys. Commun. 196(2015)599
AEXW_v1_0 MPBEC
MPBEC, a Matlab Program for Biomolecular Electrostatic Calculations
Sandra Vergara-Perez, Marcelo Marucho
Comput. Phys. Commun. 198(2016)179
AEXX_v1_0 REST2-NAMD
A Generic Implementation of Replica Exchange with Solute Tempering (REST2) Algorithm in NAMD for Complex Biophysical Simulations
Sunhwan Jo, Wei Jiang
Comput. Phys. Commun. 197(2015)304
AEYC_v1_0 Metadyn View
Metadyn View: Fast Web-Based Viewer of Free Energy Surfaces Calculated by Metadynamics
Petr Hosek, Vojtech Spiwok
Comput. Phys. Commun. 198(2016)222
AEZH_v1_0 BASDet
BASDet: Bayesian Approach(es) for Structure Determination from Single Molecule X-ray Diffraction Images
Michal Walczak, Helmut Grubmüller
Comput. Phys. Commun. 201(2016)159
AEZN_v1_0 ProtoMD
ProtoMD: A Prototyping Toolkit for Multiscale Molecular Dynamics
Endre Somogyi, Andrew Abi Mansour, Peter J. Ortoleva
Comput. Phys. Commun. 202(2016)337
AEZV_v1_0 DnaFabric
Geant4-DNA simulations using complex DNA geometries generated by the DnaFabric tool
S. Meylan, U. Vimont, S. Incerti, I. Clairand, C. Villagrasa
Comput. Phys. Commun. 204(2016)159
AFAO_v1_0 FabSim
FabSim: facilitating computational research through automation on large-scale and distributed e-infrastructures
Derek Groen, Agastya Bhati, James Suter, James Hetherington, Stefan Zasada, Peter V. Coveney
Comput. Phys. Commun. 207(2016)375