Anthony (Ant) Nicholls is a physicist and entrepreneur from Plympton, Plymouth, England.
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Anthony (Ant) Nicholls is a physicist and entrepreneur from Plympton, Plymouth, England.
Nicholls was educated at Plympton Grammar School and then from 1979 studied Physics at Oxford before joining the Institute for Molecular Biophysics at Florida State University. There he studied quantum dispersion of excitations in biological systems with William Rhodes and in football with Bobby Bowden. He earned his Ph.D. in biophysics in 1988 and began a post-doc with Barry Honig at Columbia University, New York.
Nicholls has largely worked in molecular biophysics, designing software that is used in drug discovery applications.
While at Columbia University, he re-wrote the electrostatics program known as DelPhi. DelPhi took input from a coordinate file format of a molecule and calculated the electrostatic potential in and around the system, using a finite difference solution to the Poisson-Boltzmann equation.
Nicholls later wrote the graphics software GRASP. [1] GRASP was a graphics program written for Silicon Graphics computers that was used by the structural biology community to visualize macromolecules. It was the most widely used software for computing and displaying polyhedral molecular surfaces during the 1990s.
Work conducted on DelPhi and GRASP continues to be the intellectual property of Columbia University. As a result, Nicholls consulted with David Weininger, and decided in 1997 to found OpenEye in Santa Fe, New Mexico. [2] Nicholls has also been referred to as the "Steve Jobs of the Info Mesa" in regard to his work at OpenEye. [3] OpenEye has employed a number of notable people in cheminformatics, including Roger Sayle, developer of RasMol.
GROMACS is a molecular dynamics package mainly designed for simulations of proteins, lipids, and nucleic acids. It was originally developed in the Biophysical Chemistry department of University of Groningen, and is now maintained by contributors in universities and research centers worldwide. GROMACS is one of the fastest and most popular software packages available, and can run on central processing units (CPUs) and graphics processing units (GPUs). It is free, open-source software released under the GNU General Public License (GPL), and starting with version 4.6, the GNU Lesser General Public License (LGPL).
Chemistry at Harvard Macromolecular Mechanics (CHARMM) is the name of a widely used set of force fields for molecular dynamics, and the name for the molecular dynamics simulation and analysis computer software package associated with them. The CHARMM Development Project involves a worldwide network of developers working with Martin Karplus and his group at Harvard to develop and maintain the CHARMM program. Licenses for this software are available, for a fee, to people and groups working in academia.
Visual Molecular Dynamics (VMD) is a molecular modelling and visualization computer program. VMD is developed mainly as a tool to view and analyze the results of molecular dynamics simulations. It also includes tools for working with volumetric data, sequence data, and arbitrary graphics objects. Molecular scenes can be exported to external rendering tools such as POV-Ray, RenderMan, Tachyon, Virtual Reality Modeling Language (VRML), and many others. Users can run their own Tcl and Python scripts within VMD as it includes embedded Tcl and Python interpreters. VMD runs on Unix, Apple Mac macOS, and Microsoft Windows. VMD is available to non-commercial users under a distribution-specific license which permits both use of the program and modification of its source code, at no charge.
Molecular modelling encompasses all methods, theoretical and computational, used to model or mimic the behaviour of molecules. The methods are used in the fields of computational chemistry, drug design, computational biology and materials science to study molecular systems ranging from small chemical systems to large biological molecules and material assemblies. The simplest calculations can be performed by hand, but inevitably computers are required to perform molecular modelling of any reasonably sized system. The common feature of molecular modelling methods is the atomistic level description of the molecular systems. This may include treating atoms as the smallest individual unit, or explicitly modelling protons and neutrons with its quarks, anti-quarks and gluons and electrons with its photons.
Brian E. Paul is a computer programmer who originally wrote and maintained the source code for the open source Mesa graphics library until 2012, and is still active in the project. He began writing its source code in August 1993. Mesa is a free software/open source graphics library that provides a generic OpenGL implementation for rendering three-dimensional graphics on multiple platforms.
OpenEye Scientific Software is an American software company founded by Anthony Nicholls in 1997. It develops large-scale molecular modelling applications and toolkits. Following OpenEye's acquisition by Cadence Design Systems for $500 million in September 2022, the company was rebranded to OpenEye Cadence Molecular Sciences and operates as a business unit under Cadence.
Roger D. Jones is an American physicist and entrepreneur. He currently is a Research Fellow at the European Centre for Living Technology at the University of Venice, Italy.
PCPaint was the first IBM PC-based mouse-driven GUI paint program. It was developed by John Bridges and Doug Wolfgram. It was later developed into Pictor Paint.
John Bridges is the co-author of the computer program PCPaint and primary developer of the program GRASP for Microtex Industries with Doug Wolfgram. He is also the sole author of GLPro and AfterGRASP. His article entitled "Differential Image Compression" was published in the February 1991 issue of Dr. Dobb's Journal.
Arieh Warshel is an Israeli-American biochemist and biophysicist. He is a pioneer in computational studies on functional properties of biological molecules, Distinguished Professor of Chemistry and Biochemistry, and holds the Dana and David Dornsife Chair in Chemistry at the University of Southern California. He received the 2013 Nobel Prize in Chemistry, together with Michael Levitt and Martin Karplus for "the development of multiscale models for complex chemical systems".
SMILES arbitrary target specification (SMARTS) is a language for specifying substructural patterns in molecules. The SMARTS line notation is expressive and allows extremely precise and transparent substructural specification and atom typing.
George Frederick Oster NAS was an American mathematical biologist, and Professor of Cell and Developmental Biology at University of California, Berkeley. He made seminal contributions to several varied fields including chaos theory, population dynamics, membrane dynamics and molecular motors. He was a 1985 MacArthur Fellow.
Michael Peter Barnett was a British theoretical chemist and computer scientist. He developed mathematical and computer techniques for quantum chemical problems, and some of the earliest software for several other kinds of computer application. After his early days in London, Essex and Lancashire, he went to King's College, London, in 1945, the Royal Radar Establishment in Malvern in 1953, IBM UK in 1955, the University of Wisconsin Department of Chemistry in 1957, and the Massachusetts Institute of Technology Solid State and Molecular Theory Group in 1958.
DelPhi is a scientific application which calculates electrostatic potentials in and around macromolecules and the corresponding electrostatic energies. It incorporates the effects of ionic strength mediated screening by evaluating the Poisson-Boltzmann equation at a finite number of points within a three-dimensional grid box. DelPhi is commonly used in protein science to visualize variations in electrostatics along a protein or other macromolecular surface and to calculate the electrostatic components of various energies.
Klaus Schulten was a German-American computational biophysicist and the Swanlund Professor of Physics at the University of Illinois at Urbana-Champaign. Schulten used supercomputing techniques to apply theoretical physics to the fields of biomedicine and bioengineering and dynamically model living systems. His mathematical, theoretical, and technological innovations led to key discoveries about the motion of biological cells, sensory processes in vision, animal navigation, light energy harvesting in photosynthesis, and learning in neural networks.
James Michael Berger is an American academic working as a professor of biophysics and biophysical chemistry at Johns Hopkins University School of Medicine, where he is also the co-director of the Cancer Chemical and Structural Biology Program at the Sidney Kimmel Comprehensive Cancer Center and the director of the Johns Hopkins Institute for Basic Biomedical Sciences. His main area of research is the functions of molecular cellular machinery.
Barry H. Honig is an American biochemist, molecular biophysicist, and computational biophysicist, who develops theoretical methods and computer software for "analyzing the structure and function of biological macromolecules."
David Weininger was an American cheminformatician and entrepreneur. He was most notable for inventing the chemical line notations for structures (SMILES), substructures (SMARTS) and reactions (SMIRKS). He also founded Daylight Chemical Information Systems, Inc.